I understand that we have 46 DNA molecules in the nucleus of our cells, arranged in 23 pairs: 22 autosomal and 1 sex chromosome pairs.

I have read in different sources that the pairs contain nearly identical members, excluding any mutations. I have also read that the pairs contain 1 member we inherited from our mothers and 1 we inherited from our fathers, which are different due to inheritance.

This seems contradictory, given that genealogical companies match up on the differences on these chromosomes.

My understanding was that meiosis creates sperm and egg cells that each carry 23 chromosomes - they are haploids. During the first steps of meiosis that creates the reproductive cells we have a combining of the parent's chromosome pair from their parents to create 4 daughter cells, each independently viable, where the recombination of the chromosome pair has occurred at somewhat predictable spots (for you perhaps :-) ) and that these spots can be related to genes. It is this step that give us our genetic variation between siblings for example. A new person's DNA is partially formed from any one of these highly varied daughter cell possibilities.

Fertilization combines the reproductive cells to produce the 46 chromosome zygote with is again diploid.

I think this understanding supports the second interpretation that our chromosome pairs are not 2 nearly identical DNA molecules but are distinct.

Have I got this right? Is there a missing process or a misunderstanding in my interpretation?

  • 2
    $\begingroup$ I think there is a bit of confusion about what is meant by identical/distinct. Two genes could appear identical, or nearly so, yet have different functions, say by just swapping a couple of nucleotides. $\endgroup$
    – jamesqf
    Jan 29, 2021 at 18:30
  • $\begingroup$ I am referring to the sequencing of SNPs, not to the function or expression of those sequences. Do both chromosomes in a chromosome pair have nearly identical sequences of ACTG excluding differences due to sequencing techniques and/or trivial transpositions of the sequence number up or down. $\endgroup$
    – Stephen
    Jan 29, 2021 at 19:05
  • 1
    $\begingroup$ Could you elaborate on why you think the two sentences are contradictory? Nearly identical does not mean completly identical. SNPs are real single letter diferences between individual chromosomes - and not just differences due to sequencing technique. Genes are just small functional sections of the long chromosome sequence. What has been explained to you about sequences of genes does directly apply to sequence of chromosomes. The diferences are small and yet very important. $\endgroup$
    – BagiM
    Jan 30, 2021 at 6:38
  • $\begingroup$ @BagiM One source stated that the two chromosomes in a pair will be identical except for the possibility of a very small number of snp differences could be due to mutation only. I believe this to be contradictory to the statement that within a pair one chromosome comes from the maternal source and one from the paternal source as there is no reason to think the donors would contribute identical dna. I suppose what I am trying to ascertain is if there is a process somewhere in the fertilization steps where the donor chromosomes recombine, e.g. mix, before they form the new individual's dna. $\endgroup$
    – Stephen
    Jan 30, 2021 at 20:34

3 Answers 3


Homologous chromosomes (those that are paired up), excluding the sex pair are almost identical in size, shape and genes (members as you called them) present in them.

Genes determine traits and each homologous chromosome controls the same traits. The level of identity of a gene inside a population varies between genes. There are very conserved ones that do not change even between humans and yeast and others that vary alot event inside a species. This changes can be small in sequence length, a simple base (letter) swap or one deletion, and have a huge effect on the traits. This is how chimps and humans are very different but share 98.6% of their genome and humans are very similar and share 99.9% of their genome.

In summary, on the bigger scale homologous chromosomes are very similar (size, shape, traits inside), on the smaller scale homologous chromosomes have small changes that affect greatly.

EDIT: elaborating on when recombination occurs.

The zygote do not recombine the chromosomes it gets from it's parents. Each parent chromosomes recombine in the first step of meiosis. We do not expect them to be identifcal on the gene level (or the SNPs level). Each chromosome represent each paren't genetic material.

Lets look at parents A chromosomes
parent a Paternal: a-b-c-d-e                     parent b Paternal: a-B-c-D-e
parent a Maternal: a-B-C-D-e                   parent b Maternal: a-b-C-D-e
possible recombination (a)                       possible recombination (b)
(a-I) a-B-C-d-e                                         (b-I) a-B-C-D-e
(a-II) a-b-c-D-e                                         (b-II) a-b-c-D-e

Now the child can be any of the 4 possible combinations (and obviously all other not shown). Let's say (a-I) and (b-II). This chromosomes do not recombine until they get to the meiosis stage.

  • $\begingroup$ I am asking about an individual, not a population. I do not use members to refer to genes, I use members to refer to the individual chromosomes within a pair. I am also not asking about the impact of a mutation of a gene's base pairs. $\endgroup$
    – Stephen
    Jan 29, 2021 at 14:48
  • $\begingroup$ @Stephen Is your question "In each pair of chromosomes, are the parental and maternal chromosomes nearly identical or very distinct?". If you want an answer about an individual we need background about him, otherwise he is merely a random sample from population with every possible pairs of parents. I think my answer shows that chromosomes are almost identical on the macro scale and slightly distinct (but not much) on the micro scale. If you elaborate more I could expand my answer $\endgroup$
    – Hachiloni
    Jan 30, 2021 at 17:29
  • $\begingroup$ I think that if you need to know specifics about an individual to answer this question then the question is not clear as I am asking about the typical results of the general reproductive cycle. $\endgroup$
    – Stephen
    Jan 30, 2021 at 20:39
  • $\begingroup$ This is an attempt to understand at very high level what the strands of DNA in each chromosome of a pair are expected to be. To reword it, looking at the sequences of SNPs of an individual's DNA do we expect the sequences of the 2 chromosomes of a pair to be (nearly) identical, e.g. because the maternal and paternal donor DNA was combined and then duplicated, or do they remain distinctly identifiable as maternal and paternal complete, undivided chromosomes? $\endgroup$
    – Stephen
    Jan 30, 2021 at 20:41
  • $\begingroup$ I think you may have been trying to answer "in a chromosome pair is the location and function of genes identical on each of the 2 chromosomes", which I understand to be "yes". $\endgroup$
    – Stephen
    Jan 30, 2021 at 20:46

I have read in different sources that the pairs contain nearly identical members, excluding any mutations

"Nearly" is doing a lot of work there.

You have a copy of Chr 1 from your father and a copy from your mother. Your copies might have mutations as compared to your parents that happened either in you as you were developing, or in the gametes as compared to the stem cells they originated from, but most of the differences between your maternal copy and your parental copy were caused by long ago mutations that have been in your parents' families for generations, (we'd be more likely to call those polymorphisms, rather than mutations) not mutations that just happened.

Even with those differences, your two copies of Chr 1 are at least 99% identical.

  • 1
    $\begingroup$ I think now that you've hit on what I needed to understand. Although there likely are differences caused by who we inherited the chromosome from, which are useful to understand from a genealogical point of view, these sequence differences are derived from, to use your number, about 1% of the matches, thus, "nearly" could be considered accurate, "from a certain point of view". $\endgroup$
    – Stephen
    Jan 31, 2021 at 22:03

Two major resources of genetic variation between siblings:

1- Random segregation of chromosomes during meiosis I. consider only mother: the mother has 46 chromosomes, 23 from grandmother and 23 from grandfather. during meiosis anaphase I, pairs of similar (homologous) chromosomes are segregated randomly. finally you have egg cells with 23 chromosomes, some from grandfather and some from grandmother. this can make 2^23 (8 millions) different combination of chromosomes for egg, and 2^23 for sperm and 2^46 (7000 billions) different combinations totally.

2- Recombination of homologous chromosomes during meiosis I. which is exchange of chromosome pieces during meiosis I metaphase, and I see you know enough about it.

Also, there are other resources of variation which are out of the level of this question.

  • $\begingroup$ Hello and thanks for answering. I do understand the points you've made in point 1. I am curious about the other sources of variation if you care to leave a reference. I think my confusion arises in the fertilization step - whether or not the donor chromosomes "pair up" but remain intact as one source indicated, or if the donor chromosomes undergo random segregation and combination akin to point 1, and then replicate before forming the chromosome pair of the new individual. My original understanding had been the former. $\endgroup$
    – Stephen
    Jan 30, 2021 at 20:45

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