Genetic Differences amoung species

[ecoli]

This is based off of something that someone in my lab said the other day... so if what he says is true, I would very much like to talk about it.

 

Humans and chimps are only lile 98.% genetically similar. (some people say 85%, but whatever, my point is the same). But, there are different strains of E.coli (same species, though) that are as much as 60% different. Why are these difference less important in unicellular organisms then they are in primates?

 

Why is 2% enough to be very different species of primate, but a much larger percent difference is considered the same species of bacteria?

[insane_alien]

probably because our DNA is HUMUNGOUS compared with E.Coli DNA. Also since its more complex smaller changes result in bigger differences. probably got something to do with nongenetic development as well

[ecoli]

...probably got something to do with nongenetic development as well

 

 

could you expand on that, perchance?

[Skye]

One thing to consider is that animals are combining their genes with one another through sex every generation. This only happens through horizontal gene transfer with bacteria, which is not as frequent and only applies to a gene here or there.

[ecoli]

Given all this, why are they still considered one species?

[treva]

Speciation in prokaryotes is based more off then just DNA sequences. Even though yeah you have lots of DNA polymorphism within bacterial species, that one species will exhibit all the same physiology, for example they will all prefer to grow in the same microenviroment, produce a majority of the same enymes, have almost identical morphology, etc etc. Besides even if you get a point mutation in an enzyme (that would ultimatly lead to a decrease in DNA homology) that enzyme is still going to be conserved in function among the species, if it wasn't theres a good chance that bacteria might die.

 

I believe bacterial DNA polyermase also has a lower fidelity then Eukaryotic DNA polymerase, so more mistakes = more mutations = less homology.

[jeskill]

Given all this, why are they still considered one species?

 

I think it's because our concept of species is entirely subjective.

 

We don't have one species definition that can be used for every organism. Chimps and humans seem to fit into the biological species concept well (they don't inter-mate in nature) but bacteria and fungi tend to hybridize or mate with individuals that have larger relative genotypic differences. This is most likely (partially) due to the differences in mutation rates.

 

In my opinion, there needs to be a definition of species that can be used across phylums. I heard that someone (I forget who) suggested using divergence times to denote species, genus, family, etc. It might be a more useful definition for taxonomy, but then the problem becomes, how do we accurately measure divergence times of organisms that aren't in the fossil record (like fungi, for example)?

[Nashyboyo]

A quote from an article published by nature.

 

"Human−chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level."

 

Nature 429, 382-388 (27 May 2004) | doi: 10.1038/nature02564

 

Reading this may help better understand the complexities of comparitive genomics.

 

http://www.answersingenesis.org/docs2005/0905chimp.asp

 

[jeskill]

The chimp article is indeed very cool. But I'm confused as to how your link helps us better understand the complexities of comparative genomics. It seems to be more a diatribe against evolution using a few statements that are taken out of context. I'm also confused as to how exactly you would relate this article to species concepts of chimps/humans vs. bacteria.

[ecoli]

The chimp article is indeed very cool. But I'm confused as to how your link helps us better understand the complexities of comparative genomics. It seems to be more a diatribe against evolution using a few statements that are taken out of context. I'm also confused as to how exactly you would relate this article to species concepts of chimps/humans vs. bacteria.

 

indeed, I have heard the argument before, but it doesn't really change my question.

[jeskill]

So, just out of curiosity, e.coli, have you read much about this species concept debate? I'm assuming you use a phylogenetic species concept in your work?

 

It's kind of a big issue with the stuff I work on (fungi). When I do phylogenetic comparisons, I use operational taxonomic units (OTUs) that are (sort of) arbitrarily decided on before analysis.

[Mokele]

Well, one thing comes to mind, namely why bother with "species" for things which either don't have a gene pool (a hypothetical asexual organism which never exchanges DNA) or have such a broad one as to make attempts to define 'species' futile? Wouldn't it make more sense to recongize how different they are from the usual animal/plant model by calling them something distinct, rather than trying to force them into a term for which there is no analagous concept in their evolution?

 

Mokele

[ecoli]

So, just out of curiosity, e.coli, have you read much about this species concept debate? I'm assuming you use a phylogenetic species concept in your work?

 

no, not really. The remark wasn't really related to my lab work.

 

Wouldn't it make more sense to recongize how different they are from the usual animal/plant model by calling them something distinct, rather than trying to force them into a term for which there is no analagous concept in their evolution?

 

What did you have in mind?

[Mokele]

Not a clue; all of my work and almost all of my education has focused on animals, so I'm nowhere near familiar enough with fungi or microorganisms to even venture a guess.

 

A very weird part of me says: "Make it standard practice to name all microbial taxa in 133t. The highest level of classification will be the H/-\><0r."

 

Mokele

[Nashyboyo]

The chimp article is indeed very cool. But I'm confused as to how your link helps us better understand the complexities of comparative genomics. It seems to be more a diatribe against evolution using a few statements that are taken out of context. I'm also confused as to how exactly you would relate this article to species concepts of chimps/humans vs. bacteria.

 

The link

Sorry I got tired and just read the title at the top of the page and assumed the text would be sufficient.

 

Chimps/humans vs bacteria

Whether there is a 40% difference or 2% difference between genomes there is still a sufficient difference to give rise to the phenotype in question.

 

This is an attempt to answer the first post in this thread.