What does this mean? Total number of chromosomes/genes, mitochondrial DNA, sheer amount of similar dna, statistical DNA analysis, or what?
i see this often, for example that i am nearly identical to a tree, a pig, a horse, a fruit fly or a blade of grass as far as the geneticist is concerned.
Could somebody point me to some references?
Excellent question. I’ve heard 95% up to 99% but lately the 98% figure seems to be the final figure. scientists don’t bother to challenge these various numbers, so it appears to me that these numbers are rather subjective. After all, it has been less than a year ago that the estimate for the number of genes in the human genome has been reduced to 30,000 from 100,000 at a great cost, so I don’t believe we’ll have a conclusion for the bonobo genome for a long long time.
What figure you come up with is partly determined by what part of the genetic code you are talking about. An organism’s DNA is made up not only of sequences that code for genes, but also long stretches of “junk” DNA that do not. Because it is not subject to selection (as far as we know) this junk DNA is free to accumulate mutations and so differs more between organisms than functional DNA. The 98% figure, in general, refers to comparing sequences nucleotide-by-nucleotide, including junk DNA. If nucleotide differences between just active genes is compared, human-chimp similarity nears 99.4%. See this site for more information. The figure also can vary somewhat due to the exact section of the genetic code being compared.
Obviously you have no idea how science works - scientists are very active in challenging one another’s results. Differences between published figures are mostly due to how you calculate it, not subjectivity.
In paractice it means nothing. A relatively small number of different genes can be the difference between two totally different species. So what? This fact is an interesting curiousity, but the two species are still as different as they are.
I suppose it’s a meaningful fact about how genetics works, although it tells us nothing about how different species are.
Well, perhaps. But the statistics on genetic similarity may help drive home the point that, as different as two species are, those real differences (evaluated objectively) would also show that they are in fact more alike than we’d sometimes care to admit.
Well so far so good. But i want to know about the underlying math and/or statistical analysis that drives these estimates. What is being compared, how does junk DNA fit into the picture and whatnot like that.
Where can i find out about the number of genes possessed by a living organism, say a fruit fly, common vegetation, the human genome or even a worm?
Well so far so good. But i want to know about the underlying math and/or statistical analysis that drives these estimates. What is being compared, how does junk DNA fit into the picture and whatnot like that.
Where can i find out about the number of genes possessed by a living organism, say a fruit fly, common vegetation, the human genome or even a worm?
Sorry, don’t have a cite but I think these numbers are often arrived at via DNA hybridization studies. This is by far the easiest way to compare large amounts of DNA without sequencing it all. Given that the Human Genome is only now being decoded, but these numbers have been thrown around at least since I was an undergrad (mid eighties) I think this type of experiment is often what is being referred to. This would include all chromosomal DNA, coding and non-coding, but exclude mitochondrial DNA.
The people I rate at knowing the most about simians in the world are at the Yerkes Primate Research Centers across the US of A.(*) They use the figure of 98.4%. See this link (scroll down to Section 4, Genomics). They do the DNA studies themselves. The 3 digits of accuracy are regularly used.
(*) An opinion possibly influenced by “knowing closely” someone that works there.
As I said, there are different things being compared here and different ways of doing it. One of the seminal papers on the subject was by Mary-Claire King & Allan C. Wilson (1975. Evolution at Two Levels in Humans and Chimpanzees, Science: 188:107). They looked at data on chimp and human proteins as well as hybridization studies of nuclear DNA. Proteins give info on the genetic code because each amino acid in a sequence is generated by a codon composed of three nucleotides in the DNA. This method of course can’t give any info on “junk” DNA. On the other hand, because some amino acids are coded for by more than one codon, it doesn’t find all possible variations between gene sequences. In DNA hybridization studies, sections of DNA from one species is mixed with DNA from another, forming “hybrid” strands. Hydrogen bonds will only form between complementary base pairs, so that the strength of association, and hence the thermal stability, depends on the degree of similarity of the strands. The degree of nucleotide homology can then be estimated by measuring the temperature at which the strands separate (melt).
These methods are relatively crude, but King and Wilson found they gave similar esimates converging on about 98% similarity between human and chimp genomes (98% of amino acid sequences in the same proteins identical; or 98% of nucleotide sequences in the nuclear DNA identical).
More recently, more precise methods such as nucleotide sequencing have become available. This can be done for both nuclear and mitochondrial DNA, and genes and junk DNA can be distinguished. Here, once again one is comparing the percent of nucleotide sequences that are identical between two genomes.
All these methods yield similar results: human and chimp genomes are at least 98% identical, and more so if just the nucleotide sequences of genes themselves are compared.
Here’s the Database on Genome Sizes (DOGS). It gives mostly information on the total amount of DNA found in different organisms’ genomes (which includes junk DNA). The number of genes is much more difficult to get at and requires detailed functional analyses - witness the wildly varying estimates on number of human genes, even now that the genome has been sequenced.
Obviously you have no idea how subjectivity…
The selection of genetic parameters used to measure the differences between two entities is subjective by its very nature. With regard to scientific challenges, my point was that I am not hearing a debate,“98 is wrong, it should be 99.4”.
If I use the 99.4% figure for example and a genome of 30,000 genes(although I know this is not scientific) forgive me for thinking that but for the matter of .006x30,000= 180 genes, Einsteins major achievement might be breaking off a twig to insert into a termite mound for the purpose of licking off a meal.
I mean how significant is 99.4% really?
You said
Which leads me to ask, “If a sphere of 1 inch is compared to a sphere of 2 inches, is the former 50% of the latter?”
Of course not, its barely more than 10%, okay, say 12.5%.
Now when it comes to genetics, are we even limited to three dimensions of variability? Who knows how many permutations of expression a few genes can generate? My point is, even the use of genetics as a numerical basis for comparison is highly subjective.
greinspace, these numbers are objective, derived mathematically from hard data. The reason they differ is because they are measuring somewhat different things. The main reason you are not hearing a debate over whether “98% is wrong, it should be 99.4%” is that both figures are correct, they are just referring to different parts of the genome. And you are pretty unlikely to hear any kind of real debate about such genetic analyses unless you are a habitual reader of the primary literature in Science, Nature, and other technical journals.
I think I understand the point you are trying to make, greinspace, but you are just not expressing yourself very clearly.
It is in fact true that the percentage of congruence in nucleotide sequences (which is objective numerical data) is
not directly related to the degree of morphological divergence between species. In fact, speciation can take place with almost no divergence in nuceotide sequences, due to translocations or inversions within chromosomes that prevent hybridization. On the other hand, small changes in the genes that regulate development can have a major impact on morphology - and this seems to account for much of the difference between chimps and humans. Some species with an equivalent degree of nucleotide divergence to chimps and humans are virtually identical morphologically. So it’s the kind of genetic changes, rather than the amount per se, that is important. Part of the reason this “98%” figure has received so much publicity is that scientists were startled to find that humans and chimps were genetically so similar, given the large morphological and behavioral differences.
What it is related to, however, is the time of divergence of lineages. For such analyses it’s preferred to use “junk” DNA. Since mutations there are not subject to selection, their accumulation is related mainly to the mutation rate alone. This allows us to use them as a “molecular clock,” since the degree of divergence in nucleotide sequence is (approximately, and with some exceptions) correlated with the time since the lineages split. For chimps and humans, the figure is 4.6-6.2 million years - which is far less than had previously been thought.