Cloning Extinct Species, Part II

Questions by Anonymous, answers by Theresa Mecklenborg

Hello,
How would you clone a passenger pigeon?
Would you need the passenger pigeons bones?
Mourning Doves look almost like the Passenger Pigeon.
Would maybe be necessary to use some of the Mourning Dove DNA to help clone the Passsenger Pigeon?
What does the word genome mean?
If you do not find a completely preserved genome how would you go about cloning the passenger pigeon?
Do you have to try to make a complete genome for the extinct species that you are trying to clone?
An appropriate sort of host egg and host mother to put the completely preserved genome in the passenger pigeon.
What does host egg mean?
What does host mother mean?
Thanks for your help!!!

What does the word genome mean?

The genome is all the genetic information in an organism. For animals and plants, this usually refers to the DNA found inside the nucleus of each cell, but can also include DNA found in mitochondria (energy-producing parts of a cell) and chloroplasts (the part of the cell that lets plants photosynthesize). Mitochondrial DNA has changed very little over time, so the mitochondria of one species are very similar to the mitochondria of related species. This is handy for inter-species cloning, because it means the mitochondria of the host egg are similar enough to the mitochondria of the animal being cloned that they will probably work just fine for the clone.

What does host egg mean?

To clone an animal, you remove the nucleus from the donor cell (a cell from the animal you are cloning) and place it in an egg cell whose nucleus has been removed. This egg cell is called a host egg. It provides the nutrients and energy for the cell to divide and develop into a new organism. To develop, the egg cell must be "tricked" into thinking it has been fertilized, usually by giving it an electric shock. Then it will divide and develop as a normal fertilized egg would.

What does host mother mean?

Once the donor nucleus has been inserted into the host egg, the egg needs somewhere to develop. The best place for an egg to develop is inside an animal that can provide the developing fetus with nutrients, proper temperatures, and appropriate hormones and other developmental signals. The animal the egg is implanted into is called the host mother. The host mother could be the animal you are cloning (if it is female), the animal the host egg came from, or an unrelated individual. In experiments, scientists usually use a host mother that is unrelated to the animal being cloned or to the animal that provided the host egg, so that it is easier to tell whether the animal is actually a clone. (If the nucleus wasn't properly removed from the host egg, the new animal could just be the offspring of the animal that provided the host egg. If the host mother could have been pregnant, the new animal might be its own offspring instead of a clone. Choosing host egg providers and host mothers that are obviously different from the animal you're trying to clone is a good way to make sure everything worked properly.)

How would you clone a passenger pigeon?

Cloning in general works like this:

1. Remove the nucleus from a donor cell (a cell from the organism you are cloning).
2. Remove the nucleus of a host egg and replace it with the donor nucleus.
3. Stimulate the egg cell so it begins dividing as if it were fertilized.
4. Implant egg cell into appropriate host mother.
5. Wait for clone to be born.

Since we're dealing with birds, which have very large and delicate egg cells, the implanting part becomes very difficult. No one has successfully cloned any birds yet, just mammals. Assuming techniques to work around this difficulty are developed eventually, Passenger Pigeons present another problem -- they're extinct, so we don't have any living Passenger Pigeon cells to extract a nucleus from. Instead, we have preserved skins and skeletons, which might contain enough DNA to reconstruct the contents of the nucleus. To get this DNA and use it to produce a clone, you would need to:

1. Extract DNA from your sample.
2. Purify it, being extremely careful to avoid contamination with bacteria, human DNA, or other samples in the lab.
3. Amplify it via a polymerase chain reaction (PCR).
4. Remove mitochondrial DNA.
5. Assemble the fragments of nuclear DNA into chromosomes.
6. Package the chromosomes into a nucleus. (Hypothetically -- we're not sure how to do this yet.)
7. Proceed with the cloning procedure outlined above.

This is all quite difficult, especially steps 5 and 6. It also relies on there being sufficient nuclear DNA present in the sample to extract, amplify, and assemble.

If you do not find a completely preserved genome how would you go about cloning the passenger pigeon?

If you didn't have enough DNA to reassemble the whole genome, but you did have a lot of it, you could try adding parts of related species' genomes to try to fill in the missing parts. Related species' genomes would also be useful as a guide in figuring out how to assemble the fragments of DNA extracted from a Passenger Pigeon specimen.

Do you have to try to make a complete genome for the extinct species that you are trying to clone?

Short answer: Yes. Long answer: Probably. Much of the DNA found in eukaryotes (plants, animals, and other organisms whose cells have nuclei) is so-called "junk DNA". We don't know what this DNA does -- some of it may code for proteins, some of it appears to play a role in regulating the amount of protein produced by other genes, and some of it may really be junk. If you had a nearly-complete genome that only left out the real junk, you would most likely be able to clone the organism. However, we don't know what's junk and what's not, so it's safest to say we do need the entire genome.

Would you need the passenger pigeons bones?

You would need some kind of tissue sample. The ideal sample would be some skin, muscle, or bone marrow kept frozen or mummified, but I don't think there are any specimens like that. Since we're looking for nuclear DNA, we need cells, not just structures like feathers. There could be useable DNA in the skin of particularly well-preserved stuffed birds. There could be useable DNA in cells trapped inside bones. As of 1962, there were at least 16 Passenger Pigeon skeletons and 1,532 skins and mounts in various museums and private collections [1]. I'm not sure where the skeletons are these days, but material is certainly available.

The last known Passenger Pigeon, Martha, died in 1914 at the Cincinnati Zoo. Nuclear DNA has been recovered from human bone fragments from 1918 (see http://users.rcn.com/web-czar/dna.htm), so it would probably be possible to recover at least some nuclear DNA from a passenger pigeon. However, it would still be difficult to assemble the extracted fragments of DNA into a complete genome. Remember, nuclear DNA is much harder to extract and amplify than mitochondrial DNA is, so although mitochondrial DNA has been recovered from human specimens up to a few thousand years old, that's not necessarily all that promising for cloning purposes.

Mourning Doves look almost like the Passenger Pigeon.

Yes, they do. Mourning Doves (Zenaidura macroura) are the closest living relatives of Passenger Pigeons (Ectopistes migratorius). Mourning Doves are smaller and less brightly colored than Passenger Pigeons. Left: This stuffed Passenger Pigeon belongs to Garrie Landry. Right: This photograph of a Mourning Dove is copyrighted by Brad Sillasen

Would maybe be necessary to use some of the Mourning Dove DNA to help clone the Passenger Pigeon?

Since the two species are closely related, their DNA should be similar, so if DNA was needed to "patch up" an incomplete Passenger Pigeon genome, Mourning Doves would be a good source for this DNA. Mourning Doves would probably also be a good choice for host eggs and host mothers.

An appropriate sort of host egg and host mother to put the completely preserved genome in the passenger pigeon.

I'm not entirely sure what you're asking here. As you suggested earlier, Mourning Doves are closely related to Passenger Pigeons, so they might be good choices to provide host mothers and host eggs. Other pigeons, particularly larger ones like Rock Doves (common city pigeons), could also be good choices.

Thanks for your help!!!