DNA sequences from Humans, Chimps and birds

[kitkat]

I recently read where the DNA sequences between Humans and Chimps are nearly identical 100% but in bird species they are not identical across the board. It is now believed that the differences between us and chimps is how these sequences are turned on and off and to what degree in protein produced in each group. My question is why are there differences in different species of bird sequences? Shouldn't they be all identical in sequences but different in how they are expressed?

[Psycho]

I recently read where the DNA sequences between Humans and Chimps are nearly identical 100% but in bird species they are not identical across the board. It is now believed that the differences between us and chimps is how these sequences are turned on and off and to what degree in protein produced in each group. My question is why are there differences in different species of bird sequences? Shouldn't they be all identical in sequences but different in how they are expressed?

Well considering your original premise that "DNA sequences between Humans and Chimps are nearly identical 100%" isn't correct, that means it isn't true that it is just due to epigenetic.

 

The reason there are larger differences in bird species is because they have been evolving from their common ancestor longer so more mutation has had a chance to occur.

Edited October 28, 2011 by Psycho

[kitkat]

Well considering your original premise that "DNA sequences between Humans and Chimps are nearly identical 100%" isn't correct, that means it isn't true that it is just due to epigenetic.

 

The reason there are larger differences in bird species is because they have been evolving from their common ancestor longer so more mutation has had a chance to occur.

 

 

There are many articles that state they are almost 100% identical and epigenetics is the differences between the two. Compared to birds though, there should be many more DNA sequences that mutated since the split between humans and chimps, there were several species of bipelalism pre-humans after the split until homo sapiens emerged. In birds, their body shape has very few variations in structure across the entire species so I do not think they had more time since their common ancestor split.

 

The variation of birds of Darwin's finches happened rapidly in speciation so one would assume that their DNA sequences are almost identical too.

[Psycho]

There are many articles that state they are almost 100% identical and epigenetics is the differences between the two.

Can you provide a scientific source that states they are almost 100% identical then, using that phrasing. As it isn't true.

[Arete]

1. Mutation rates are subject to differences based on organism, gene and time, so direct comparison between birds and homonids is not appropriate e.g. http://mbe.oxfordjournals.org/content/22/7/1561.short

 

2. Most mutations are silent: http://en.wikipedia.org/wiki/Silent_mutation and thus don't result in phenotypic changes.

 

3. Phenotypically divergent species can share most of the same genes (e.g. "genomic islands of speciation" model) http://www.ncbi.nlm.nih.gov/pubmed/16076241

 

4. Morphologically indistinguishable species can be genetically divergent. (e.g. cryptic species http://en.wikipedia.org/wiki/Cryptic_species_complex)

 

5. Genetic drift means reproductively isolated species accumulate more genetic divergence the longer they have been isolated: http://en.wikipedia.org/wiki/Genetic_drift

 

6. Selective sweeps will cause rapid phenotypic differentiation whilst leaving most of the genome identical http://en.wikipedia.org/wiki/Selective_sweep

 

Thus an expectation of a linear, direct correlation with phenotypic divergence and genetic divergence is no founded

[kitkat]

Can you provide a scientific source that states they are almost 100% identical then, using that phrasing. As it isn't true.

 

If you look up, "What It Relly Means to be 99% Chimpanzee and "The Differences Between Human and Chimpanzee is in the Junk DNA is just two of many articles.

 

1. Mutation rates are subject to differences based on organism, gene and time, so direct comparison between birds and homonids is not appropriate e.g. http://mbe.oxfordjournals.org/content/22/7/1561.short

 

2. Most mutations are silent: http://en.wikipedia.org/wiki/Silent_mutation and thus don't result in phenotypic changes.

 

3. Phenotypically divergent species can share most of the same genes (e.g. "genomic islands of speciation" model) http://www.ncbi.nlm.nih.gov/pubmed/16076241

 

4. Morphologically indistinguishable species can be genetically divergent. (e.g. cryptic species http://en.wikipedia.org/wiki/Cryptic_species_complex)

 

5. Genetic drift means reproductively isolated species accumulate more genetic divergence the longer they have been isolated: http://en.wikipedia.org/wiki/Genetic_drift

 

6. Selective sweeps will cause rapid phenotypic differentiation whilst leaving most of the genome identical http://en.wikipedia.org/wiki/Selective_sweep

 

Thus an expectation of a linear, direct correlation with phenotypic divergence and genetic divergence is no founded

 

Doesn't HGT have a part in this also with respect to retroviruses?

[Psycho]

If you look up, "What It Relly Means to be 99% Chimpanzee and "The Differences Between Human and Chimpanzee is in the Junk DNA is just two of many articles.

 

 

 

 

I asked where you got a source that says and I quote "state they are almost 100% identical". The first clearly states that the number is 99% which in genetic terms is no where near close to 100%.

 

The second states (if you revert back to the original source rather than using a third hand version) and I quote "their genomes are more than 98.5% identical at protein coding loci.", which once again is no where near 100%, not to mention that it is only referring to the exonic sequences.

 

So your original premise is incorrect, especially when you consider the fact that only 1-2% of human DNA codes for proteins.

Edited October 28, 2011 by Psycho

[Arete]

Doesn't HGT have a part in this also with respect to retroviruses?

 

Generally, the assumption of reproductive isolation between chimps and humans (and bird species) is reasonably sound.

HGT through a retrovirus is likely to minute/undetectable on the genomic scale: http://www.biomedcentral.com/1471-2148/11/276

Edited October 28, 2011 by Arete

[kitkat]

excellent study!

 

I asked where you got a source that says and I quote "state they are almost 100% identical". The first clearly states that the number is 99% which in genetic terms is no where near close to 100%.

 

The second states (if you revert back to the original source rather than using a third hand version) and I quote "their genomes are more than 98.5% identical at protein coding loci.", which once again is no where near 100%, not to mention that it is only referring to the exonic sequences.

 

So your original premise is incorrect, especially when you consider the fact that only 1-2% of human DNA codes for proteins.

 

To me there is not much difference when you state 99% or 100% but if it was 50% then to me it means a hugh gap.

 

I asked where you got a source that says and I quote "state they are almost 100% identical". The first clearly states that the number is 99% which in genetic terms is no where near close to 100%.

 

The second states (if you revert back to the original source rather than using a third hand version) and I quote "their genomes are more than 98.5% identical at protein coding loci.", which once again is no where near 100%, not to mention that it is only referring to the exonic sequences.

 

So your original premise is incorrect, especially when you consider the fact that only 1-2% of human DNA codes for proteins.

 

 

I probably do not understand what percentages means to genetics as opposed to common language that defines percentages.

Edited October 29, 2011 by kitkat

[Ringer]

What they mean when they say that humans and chimps have ~99% is that many genes can attach to halves of genomes from those animals.

 

You can separate DNA by heating it and causing the bonds between the bases to be broken. If you have a racemate mixture of human and chimp DNA some of the halves of the separate species will attach to each other to the matching bases. Since pure DNA will separate at a certain temperature, like 90 C IIRC, if two halves of separate animals attach they will separate earlier since there are less attachment points the overall bond strength is weaker. By calculating how much less heat is needed, you can find out how many matches there were. There are other ways I believe, but that is a good example and the only one I could explain somewhat adequately.

[Psycho]

What they mean when they say that humans and chimps have ~99% is that many genes can attach to halves of genomes from those animals.

 

You can separate DNA by heating it and causing the bonds between the bases to be broken. If you have a racemate mixture of human and chimp DNA some of the halves of the separate species will attach to each other to the matching bases. Since pure DNA will separate at a certain temperature, like 90 C IIRC, if two halves of separate animals attach they will separate earlier since there are less attachment points the overall bond strength is weaker. By calculating how much less heat is needed, you can find out how many matches there were. There are other ways I believe, but that is a good example and the only one I could explain somewhat adequately.

Really, does that actually work, it seems unlikely due to the amount of contact points been far more varied between the percentages of CG and AT pairing due to them having different bond numbers, this would have far greater effect on the strength of bonding of DNA strands, hence promoter regions of a large percentage of eukaryotic genes having TATTA boxes, as this affect allows easier DNA melting in the ribosomal complex.

 

If you already had the sequence then you might as well compare the DNA sequences using bioinformatics, which is how they actually get the percentage figures.

 

To me there is not much difference when you state 99% or 100% but if it was 50% then to me it means a hugh gap

What has been missed in this whole concept is what DNA is, human DNA consists of 3 billion base pairs so a 1% differences is 30 million individual differences.

 

Now taking into account that only 1.5% of those 3 billion bases code for proteins that is 45 million exonic bases, then they are only 98.5% similar so that means there is 675000 differences in only around 23,000 genes.

 

That is equivalent to an average of 29.35 different base pairs per gene. Then you have to take into account that a single mutation within a gene can completely inactive it, so you see how different humans and chimps really are. In reality most of those mutations won't have much affect at all, however you only need 1/300 to and 10% of the genes in humans suddenly have radically altered function to there homologue in chimps.

 

But you can also use this mutation rate to see how long species diverged from each other as it tends to happen at a fairly constant rate so that is how you can find common ancestors to species.

Edited October 29, 2011 by Psycho

[Greg Boyles]

There are many articles that state they are almost 100% identical and epigenetics is the differences between the two. Compared to birds though, there should be many more DNA sequences that mutated since the split between humans and chimps, there were several species of bipelalism pre-humans after the split until homo sapiens emerged. In birds, their body shape has very few variations in structure across the entire species so I do not think they had more time since their common ancestor split.

 

The variation of birds of Darwin's finches happened rapidly in speciation so one would assume that their DNA sequences are almost identical too.

 

Almost 100% identical but there are never the less differences. And even the small number of different genes amounts to quite a few given that we have tens of thousnads of them.

 

 

 

http://www.answersingenesis.org/articles/tj/v17/n1/dna

 

A new report in the Proceedings of the National Academy of Sciences suggests that the common value of >98% similarity of DNA between chimp and humans is incorrect.¹ Roy Britten, author of the study, puts the figure at about 95% when insertions and deletions are included. Importantly, there is much more to these studies than people realize.

 

The >98.5% similarity has been misleading because it depends on what is being compared. There are a number of significant differences that are difficult to quantify. A review by Gagneux and Varki² described a list of genetic differences between humans and the great apes. The differences include ‘cytogenetic differences, differences in the type and number of repetitive genomic DNA and transposable elements, abundance and distribution of endogenous retroviruses, the presence and extent of allelic polymorphisms, specific gene inactivation events, gene sequence differences, gene duplications, single nucleotide polymorphisms, gene expression differences, and messenger RNA splicing variations.’²

 

Specific examples of these differences include:

 

1. Humans have 23 pairs of chromosomes while chimpanzees have 24. Evolutionary scientists believe that one of the human chromosomes has been formed through the fusion of two small chromosomes in the chimp instead of an intrinsic difference resulting from a separate creation.
2. At the end of each chromosome is a string of repeating DNA sequences called a telomere. Chimpanzees and other apes have about 23 kilobases (a kilobase is 1,000 base pairs of DNA) of repeats. Humans are unique among primates with much shorter telomeres only 10 kilobases long.³
3. While 18 pairs of chromosomes are ‘virtually identical’, chromosomes 4, 9 and 12 show evidence of being ‘remodeled.’⁴ In other words, the genes and markers on these chromosomes are not in the same order in the human and chimpanzee. Instead of ‘being remodeled’ as the evolutionists suggest, these could, logically, also be intrinsic differences because of a separate creation.
4. The Y chromosome in particular is of a different size and has many markers that do not line up between the human and chimpanzee.⁵
5. Scientists have prepared a human-chimpanzee comparative clone map of chromosome 21 in particular. They observed ‘large, non-random regions of difference between the two genomes.’ They found a number of regions that ‘might correspond to insertions that are specific to the human lineage.’⁶

These types of differences are not generally included in calculations of percent DNA similarity.

 

In one of the most extensive studies comparing human and chimp DNA,⁶ the researchers compared >19.8 million bases. While this sounds like a lot, it still represents slightly less than 1% of the genome. They calculated a mean identity of 98.77% or 1.23% differences. However, this, like other studies only considered substitutions and did not take insertions or deletions into account as the new study by Britten did. A nucleotide substitution is a mutation where one base (A, G, C, or T) is replaced with another. An insertion or deletion (indel) is found where there are nucleotides missing when two sequences are compared.

 

 

 

[Ringer]

Really, does that actually work, it seems unlikely due to the amount of contact points been far more varied between the percentages of CG and AT pairing due to them having different bond numbers, this would have far greater effect on the strength of bonding of DNA strands, hence promoter regions of a large percentage of eukaryotic genes having TATTA boxes, as this affect allows easier DNA melting in the ribosomal complex.

 

I'm fairly certain they do this, I could just be crazy though. I can't seem to find a source and I can't remember where I read/heard it now. I don't know why or how I would just make all that up though. . .

 

It is easier just to compare SNPs, but I was pretty tired when I wrote that and didn't want to explain SNPs and PCRs.

[kitkat]

Almost 100% identical but there are never the less differences. And even the small number of different genes amounts to quite a few given that we have tens of thousnads of them.

 

 

 

http://www.answersingenesis.org/articles/tj/v17/n1/dna

 

 

I noticed that you said humans are unigue in that we have shorter telemeres compared to chimps. I thought telemere length was associated with aging and death. Chimps do not live longer that we do so what gives and why is this information so confusing?

 

I certainly do not want to insult anyone here but I read everything I can find on this subject and it is difficult to grasp the meaning of statistics of DNA differences when they are talking about differences aspects of the sequencing depending on who the author wants to focus on in their research. How many models are there on different methods of obtaining the specific goal post of the DNA terminology that defines what particular aspect of the DNA sequences that you are trying to compare? I have heard that percentages are based on the mitochondria lineage and the DNA lineage but now we have the retroviruses input, other mechanisms involved, etc.

[Psycho]

I noticed that you said humans are unigue in that we have shorter telemeres compared to chimps. I thought telemere length was associated with aging and death. Chimps do not live longer that we do so what gives and why is this information so confusing?

 

I certainly do not want to insult anyone here but I read everything I can find on this subject and it is difficult to grasp the meaning of statistics of DNA differences when they are talking about differences aspects of the sequencing depending on who the author wants to focus on in their research. How many models are there on different methods of obtaining the specific goal post of the DNA terminology that defines what particular aspect of the DNA sequences that you are trying to compare? I have heard that percentages are based on the mitochondria lineage and the DNA lineage but now we have the retroviruses input, other mechanisms involved, etc.

When telomeres run out the cell can no longer divide however different animal species loose telomere length at different rates with some even been able to increase their telomere length, this is what most of the research is into how to increase telomere length, stop reduction or in the case of cancer stop immortality.

 

Mitochondrial DNA is completely different for the rest of human DNA and doesn't divide with cell division and isn't stored in the nucleus, the main source of information that can be gain from it is genetic divergence due to a constant rate of mutation occurring and no mixing of genes.

DNA linage is just the same thing but via the nuclear DNA, if you want to follow male linage in organisms this is one of the only way, it is also useful for tracking a certain gene through a population.

Retrovirus input just happens, I don't really see what your issue is, it doesn't really relate to the other topics unless you were trying to follow retrovirus history.

 

I fail to see the complexity they are different things and that is how it is, would you think it odd that artists paint in red, yellow and blue, painting would be far easier if you just didn't use blue, it would also rather defeat the point as your picture wouldn't represent what you were painting.

Edited October 29, 2011 by Psycho

[jeskill]

Almost 100% identical but there are never the less differences. And even the small number of different genes amounts to quite a few given that we have tens of thousnads of them.

 

 

 

http://www.answersin...s/tj/v17/n1/dna

 

 

 

 

 

 

Uh, you just quoted "Answers in Genesis".

 

lol.

[Psycho]

Uh, you just quoted "Answers in Genesis".

 

lol.

I fail to see the problem, it is well referenced. If you are looking to answer the specific question "What are the genetic differences between Chimps and Humans?" it's a useful source, the actual problem with it is that it is 8 years old and therefore misses out on all the new data.

 

Of course if you wanted to answer the question "How similar are the Genetics of Chimps and Humans?" then it is useless as a stand alone source, but you should never use one source of information anyway.

Edited October 29, 2011 by Psycho

[CharonY]

The website is lousy in terms of information, as it mixes up different aspects and levels of genomic organization quite a bit. In any case, a flat value such as 95 or 99% is not very helpful to draw direct conclusions, especially without a proper context. What has been shown, for instance is that coding regions differ by around 1-1.8% IIRC between chimpanzees and humans. However non-coding regions under much less selective pressure and thus the average over the whole genome (the sequence) amounts to the 95% shown by Britten. Note that despite the mentioned differences in genomic organization, the DNA-sequence is roughly 95%-98% identical (depending whether you analyze only coding regions or not).

 

That being said, I am not quite sure what the OP meant. Genetic differences between bird species can be quite large, depending on how related they are. The same with apes, and other mammals for that matter.

[kitkat]

It is because birds look more like each other then humans compared to chimps.

[Ophiolite]

It is because birds look more like each other then humans compared to chimps.

You are only saying that because you are a human. If you were a bird you would consider us and chimps pretty well identical. Actually, when you consider penguins, birds of paradise, eagles, woodpeckers, seagulls, emus, etc I don't see how you can say they lool more like each other than humans and chimps.