Conceptual evolutionary homology question.

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Lacipart

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Not quite sure where to post this, as it isn't an MCAT question but deals with the topics covered by it. I am a Gen Bio TA and got this email from am eager student. It's has a kind of complex wording but seems pretty strait forward. Just wondering of any of you guys can confirm my guess as to the answer 😳
Hey there. I have a biology question for you which you might be interested in helping me with.

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No doubt you're familar with an RNA codon table such as this. Due to the redundany of the genetic code, obviously multiple codons can code for the same amino acid.

The question is a matter of an evolutionary homology in the broadest sense; would it be fair of me to say that the overall sequence similarity between us and chimps (upwards of 95% identical, but lets focus here on protein encoding genes of course) is a homology in itself? In other words, by my rough logic, there is no need for the two genomes to be so similar as a sequence similarity of even 66% would have no phenotypic effect, correct? (changing one nucleotide out of a codon of three will not necessarily change the amino acid in the majority of cases).

Do you think my logic here is good?

Is he just asking if the Universal genetic code is further proof for evolution... or something like that?
 
Sounds like he is trying to apply a relatively narrow definition to broader meaning which is has no business defining. Homology is a term used to define structures which are made from the same morphogenic precursors in separate species. For instance, a bat wing is homologous to a human arm, in that the same structures are used, morphologically speaking, to create them, while a birds wing is only analogous to a butterfly wing, since they preform the same function, but are derived from different precursors. Homology does not define the relatedness of species. The human is not homologous to the chimp. I don't think, strictly speaking, that a human hand could be considered homologous to a chimp hand, they are both derived from the same precursors, but they are also both hands, they are the same structure. This is on the species level. On the genetic level, yes, individual genes can be considered homologs if they code for a similar protein that has the same general functionality. There are two types of genetic homologs, paralogs and orthologs. In paralogs, the last common ancestor underwent gene duplication before speciation split the lineages of the two genes or proteins, e.g. human beta-globin is the paralog of both human alpha-globin and horse alpha-globin, while all three are paralogs of human myoglobin. In Orthologs, the last common ancestor split into two lineages without gene duplication. Horse alpha-globin is the ortholog of human alpha-globin and human myoglobin is an ortholog of horse myoglobin.

As to the second part, obviously, even though humans and chimps are more than 95% similar in their genomes, there are some very apparent phenotypic differences. So while individual genes may need only be 66% similar to maintain phenotype (I didn't look this up, just taking the kid's word for it), on the Genomic level, even 95% similarity is enough to cause drastic phenotypic changes. So I think the main problem with the student's logic is that he is taking some rather narrow terms and broadly applying them in inappropriate ways without really knowing what they mean.
 
Didn't pay attention to OP
 
I would consider other topics like codon bias. Sure the 3rd position allows for wobble, but we prefer to use certain codons over others. Using different codons shows that we retain the same protein homology, but it obviously makes us more distantly related than an organism that shares our codon bias.

What she's saying makes sense; we can be 100% the same in protein sequence even if we're only 67% similar in DNA sequence.

Though I'm not really understand where she's going with the question.. I'd ask her to clarify.
 
yeah, the question makes little sense. Ask him/her to rephrase, using twice the words and half the vocabulary 🙂
 
Sounds like he is trying to apply a relatively narrow definition to broader meaning which is has no business defining. Homology is a term used to define structures which are made from the same morphogenic precursors in separate species. For instance, a bat wing is homologous to a human arm, in that the same structures are used, morphologically speaking, to create them, while a birds wing is only analogous to a butterfly wing, since they preform the same function, but are derived from different precursors. Homology does not define the relatedness of species. The human is not homologous to the chimp. I don't think, strictly speaking, that a human hand could be considered homologous to a chimp hand, they are both derived from the same precursors, but they are also both hands, they are the same structure. This is on the species level. On the genetic level, yes, individual genes can be considered homologs if they code for a similar protein that has the same general functionality. There are two types of genetic homologs, paralogs and orthologs. In paralogs, the last common ancestor underwent gene duplication before speciation split the lineages of the two genes or proteins, e.g. human beta-globin is the paralog of both human alpha-globin and horse alpha-globin, while all three are paralogs of human myoglobin. In Orthologs, the last common ancestor split into two lineages without gene duplication. Horse alpha-globin is the ortholog of human alpha-globin and human myoglobin is an ortholog of horse myoglobin.

As to the second part, obviously, even though humans and chimps are more than 95% similar in their genomes, there are some very apparent phenotypic differences. So while individual genes may need only be 66% similar to maintain phenotype (I didn't look this up, just taking the kid's word for it), on the Genomic level, even 95% similarity is enough to cause drastic phenotypic changes. So I think the main problem with the student's logic is that he is taking some rather narrow terms and broadly applying them in inappropriate ways without really knowing what they mean.

the similiarity of human hands and chimp hands is most definately a homology. a bat wing and human arm, while homologous in that they derived from the same precusor, but are not strictly homologies because they have different functions. I don't really know anything about evolutionary genetics, so I won't comment on that.

But lay off the kid, he' prolly just like us a few years ago, a neurotic pre-med trying to make a good impression so he can get a lor. I say he's right-sharing codons is a homology.
 
[quote="In other words, by my rough logic, there is no need for the two genomes to be so similar as a sequence similarity of even 66% would have no phenotypic effect, correct? (changing one nucleotide out of a codon of three will not necessarily change the amino acid in the majority of cases)."[/quote]

If he's talking about differences on a codon-to-codon basis, then yes, changing one nucleotide out of three will not necessarily change the amino acid product. In this case, 66% (2/3) of the codon is not changed. However, I don't think he can apply this 66% to the entire genome and say that if two organisms share this percentage in sequence similarity, then there would be "no phenotypic effect," as it was with an individual codon. On the contrary, there could be huge phenotypic differences, especially in terms of functionality! I think I understand what your student is trying to say, but his reasoning is flawed in that he is not considering other forms of mutations that account for differences in genomic sequences (in this case, the 33%). He is only considering "substitutions," which are generally less harmful because they often lead to silent mutations. Try insertion or deletion mutations and you will see that a 33% difference in (coding) genomic sequence can account for alot!
 
Only 1.5% of the genome actually codes for protein. The rest is non-coding or only codes for RNA involved in gene regulation. So, a small difference in genotype can result in huge difference in phenotype. 5% is more than three times the percentage of coding genome.
 
the similiarity of human hands and chimp hands is most definately a homology. a bat wing and human arm, while homologous in that they derived from the same precusor, but are not strictly homologies because they have different functions. I don't really know anything about evolutionary genetics, so I won't comment on that.

Well, every genetics book I've ever seen shows bat wings and human arms and whale vestigial legs and bird wings with the homologous bones highlighted as the classical example of homology. And if codons make homology, then every species on the planet is a homologue, since just about every species uses the same genetic alphabet to code for proteins, aside from a few bacterial differences (such as mitochondria among others.) The genetic alphabet is highly conserved.
 
Sounds like he is trying to apply a relatively narrow definition to broader meaning which is has no business defining. Homology is a term used to define structures which are made from the same morphogenic precursors in separate species. For instance, a bat wing is homologous to a human arm, in that the same structures are used, morphologically speaking, to create them, while a birds wing is only analogous to a butterfly wing, since they preform the same function, but are derived from different precursors. Homology does not define the relatedness of species. The human is not homologous to the chimp. I don't think, strictly speaking, that a human hand could be considered homologous to a chimp hand, they are both derived from the same precursors, but they are also both hands, they are the same structure.
Yikes -- wrong info! I came across this thread by a google search and felt the need to comment on this in case anyone else stumbles upon this thread. This explanation is so wrong. Homologous by its very definition is any structure that shares common ancestry (but do not necessarily share the same function). In the event that homologous structures DO share the same function, they are known as orthologous structures. On the other side of the spectrum, if two structures function similarly (as in the example of bird vs. insect wings) but are NOT ancestrally related, they are analagous structures. The similarity between analagous structures come about because of similar environmental extremes select for certain features that are shared amongst a wide variety of species than enhances their ability to survive and reproduce and thereby, increase their fitness. (Analgous structures occur as a result of convergent evolution, while homologous structures occur due to divergent evolution). This is the essence of evolution by natural selection.

Note, homology has absolutely nothing to do with morphology as this person pointed out. A bat wing and the human are (same function, but different ancestral origin) are analgous structures, as are the bird and butterfly wing example. Homology DOES define the relatedness of species (consider what a phylogenic tree tells you).

On a genetic level, gene duplications during recombination and transpositions (protein "domain shuffling") give rise to protein families (an evolving ancestral protein that gives rises to similar functioning protein or protein subunits, example: different classes of hemoglobin), as well as Homologous Proteins (structures that have similar function but as a result in slight changes in structure and levels of gene expression -- are categorized under a unique species, example: Horse vs. Human Cytochrome C). This is accurate:

On the genetic level, yes, individual genes can be considered homologs if they code for a similar protein that has the same general functionality. There are two types of genetic homologs, paralogs and orthologs. In paralogs, the last common ancestor underwent gene duplication before speciation split the lineages of the two genes or proteins, e.g. human beta-globin is the paralog of both human alpha-globin and horse alpha-globin, while all three are paralogs of human myoglobin. In Orthologs, the last common ancestor split into two lineages without gene duplication. Horse alpha-globin is the ortholog of human alpha-globin and human myoglobin is an ortholog of horse myoglobin.

The wording quoted by the OP is a little confusing. The fact that most of our DNA is nearly identical is due to the fact that we share common ancestry but the differences are a result of mutation and chemical changes that occur naturally. Therefore, both chimps and humans are homologs of one another, both as a whole and on a molecular level (proteins, genes, etc). As far as our phenotypic differences, although we are genetically similar, the reason why human and chimps are phenotypically different is because in addition to slight variations in protein structure (though function is the same), on a genetic level, mutations in DNA can impart changes in gene expression, thus altering, when, where, and how much of the relevant protein would be transcribed. This results in differing behavioral and adaptive differences between both species.
 
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