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what is the Definition of Homologous Chromosomes?

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Homologous chromosomes are chromosome pairs (one from each parent) that are similar in length, gene position, and centromere location.

and then

The position of the genes on each homologous chromosome is the same.

are length, gene position of a pair of chromosomes the same or similar?

if exactly the same (I guess not), job well done.

if just similar, What is the Definition of similar? 99% same?

in the case of a pair of human Chromosome 1, what is the exact number of base pairs that are the same?

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    $\begingroup$ Before posting to this site you should research your question. Although you have cited one source, there are better places to look. You need to understand the (molecular) biological concepts rather than make the mistake of physical scientists in thinking things are defined by numerical cutoffs. Wikipedia can be a good source, and here gives a good basic explanation, which is fleshed out in the section on meiosis in Alberts et al. on NCBI bookshelf — an excellent resource. $\endgroup$
    – David
    Commented Aug 1, 2019 at 10:02

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Unfortunately despite the impression given by the many poor explanations available (including the one you quoted), homologous is not a synonym for similar.

Homology is defined as the existence of shared ancestry1,2. Thus, structures being homologous simply means they had a common ancestor — i.e. homology is a relationship not a property of an individual structure.

The "definition" you quote is actually a description of what you typically see when comparing two homologous chromosomes within a species. High levels of sequence similarity suggest homology, but are not sufficient to prove it. (To test that requires building phylogenetic trees.)

(One classic example of this is the superficial similarity between dolphins and sharks, which is an example of convergence not homology. Another is the homology between bird and bat wings — they are not homologous as wings, though they are homologous as tetrapod forelimbs.)

Consequently, for two chromosomes to be homologous they must have descended from a (potentially much earlier) chromosome that has been duplicated possibly for many generations (the ancestral chromosome might even have existed in a now extinct ancestral species).

So, if an inversion happens within a chromosome (and changes the ordering of the genetic loci) that chromosome is still homologous to the parental type chromosome that didn't undergo inversion.

ETA: Note that chromosomes don't need to be in the same cell (or even the same species) to be homologous and chromosomes can be homologous even if the cell they are in is not diploid. For example, the human chromosome 1 is homologous to the chimpanzee chromosome 1.

Similarity is a measurement of "distance" between sequences, but while very similar sequences are likely to be homologous there is no magical value of similarity that proves (or disproves) homology.

Individual humans are about 99.9% identical (depends on how you measure this) at the nucleotide level, so that will also be true for chromosome 1.

Finally, the UC Berkeley Museum of Paleontology also has useful resources for understanding evolution including some material on homology — e.g.: https://evolution.berkeley.edu/evolibrary/article/lines_04

References:

1: Brigandt, Ingo, "Essay: Homology". Embryo Project Encyclopedia (2011-11-23). ISSN: 1940-5030 http://embryo.asu.edu/handle/10776/1754.

2: Mindell, D. P., & Meyer, A. (2001). Homology evolving. Trends in Ecology & Evolution, 16(8), 434-440.

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  • $\begingroup$ Sorry to be a wet blanket after all your work, but it seems to me this is not answering the (very naive) question which is about diploidy — at least the first quotation — the poster perhaps confusing it with the use of homology in relation to similar genes or gene regions (but seldom chromosomes) between species $\endgroup$
    – David
    Commented Aug 1, 2019 at 7:22
  • $\begingroup$ The first link the poster gives has a classic picture of a pair of human chromosomes and refers to one being maternal and one paternal. It doesn’t say anything about diploidy, but that is what that reflects (isn’t it) and was a choice of words to try to explain what I thought was your misinterpretation. The term “homologous chromosomes” was (I imagine) used years before the term “homologous” was used in comparing the sequences of genes from different organisms. PS Criticize my arguments, say if you think I am violating the code of conduct, but please do not make general personal observations. $\endgroup$
    – David
    Commented Aug 1, 2019 at 20:02
  • $\begingroup$ @David: My apologies, that was not intended as a personal attack. I will delete the offending comment and be more careful in the future to keep my focus on content. ——— I still don't see why you think the OP is asking about diploidy. The concept of homologous chromosomes are most commonly introduced during discussions of meiosis (which in my experience will always be presented in a diploid context for lower level students). Consequently it seems natural to discuss the concept of homologous chromosomes in a diploid. However, I will edit my answer to emphasize this distinction. $\endgroup$
    – tyersome
    Commented Aug 3, 2019 at 2:15

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