I have performed a phylogenetic analysis using CLUSTALW and obtained a phylogenetic tree. I know how to read a phylogenetic tree and how to relate the sequence similarity between two sequences by looking at the tree, but what I am concerned about is how one can decipher the father-daughter relationship by looking at the tree? Also, if I want to isolate the sequence of the father corresponding to a daughter sequence how can I do that? I have attached the corresponding image. In the image, I know that sequences "QXN18196" and "QXN18436" are closely related. But will it be safe to say that sequence "QXN18520" is the father sequence for both the sequences? Or if I want to establish a father-daughter relationship for the whole tree, what will be the relation between the sequences?enter image description here

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    $\begingroup$ Better terminology in this context is to use Parent-Children/child relationships, rather than Father-Daughter $\endgroup$
    – JRodrigoF
    Oct 21 '21 at 18:10
  • $\begingroup$ Thank you so much for your answer. I am still not sure how can one establish that relation from phylogeny. Or to put it another way, what is the right approach to determine a parent-child relationship between a set of sequences, say 6 sequences. $\endgroup$ Oct 22 '21 at 5:46

Unless you have wildly differing mutation rates on different branches, you can't say that QXN18520 has the same sequence as the most recent common ancestor of QXN18196 and QXN18436, because QXN18520 was collected today, not back whenever QXN18196 and QXN18436 shared a common ancestor. All that you can say from this phylogeny is that there probably existed a common ancestor of QXN18196 and QXN18436, marked here by 5e-9[86.8], and that this common ancestor and QXN18520 shared a common ancestor even further back, marked here by 5e-9[0].

(General observation: Note also that for a number of reasons, phylogenies often don't reflect reality -- they are simply a maximum likelihood estimate of the actual ancestral pedigree, often under some very unrealistic assumptions, and/or according to an incomplete or incorrect view of reality -- e.g. the samples that you have collected may have a lot of allele matches due to identity by state (IBS) rather than identity by descent (IBD). In other words, let phylogenies inform you, but don't assume they are the absolute truth.)

  • $\begingroup$ Thank you so much for your answer. I was wondering then how can one establish a father-daughter relation from the phylogenetic tree? If phylogeny is an estimate of ancestral pedigree, then how can one find out if a set of sequences really do have a father-daughter relationship? $\endgroup$ Oct 21 '21 at 16:46
  • $\begingroup$ @satyamsangeet if you suspect there is a literal father and a literal daughter in the data somewhere, and you want to detect this, then you first need to know which chromosome the alleles came from. For the autosomal diploid chromosomes (1-22), inheritance is via random assortment, and you would expect very close to 50% of the alleles will match between father and daughter, but only if all markers are widely spaced apart (so that you have low linkage disequilibrium). If all or even some alleles are in high linkage disequilibrium, then allele sharing can deviate from 50%. (ctd...) $\endgroup$ Oct 22 '21 at 18:50
  • $\begingroup$ However what I just said about 50% sharing between father and daughter is only really true if you have diploid data for both individuals (meaning you have the alleles for a given locus from both chromosomes). If you have alleles from only one chromosome for the father and the daughter, then you would expect only 25% sequence identity (sequence match), because you're missing half the data. Also, note that you can't tell who the father is and who the daughter is simply by looking at the percentage of sequence identity. $\endgroup$ Oct 22 '21 at 18:54
  • $\begingroup$ @satyamsangeet Chromosome X is inherited differently to chromosomes 1-22 between father and child. You would expect a 100% match between the father's alleles and one of the daughter's alleles, if you have diploid data for the daughter. The father has only one copy of the X chromosome, so you would only ever have haploid data for the father, and you would be able to tell he's the male based on this, if in general your data is diploid. If you have only haploid data for all samples (if you have alleles from only one of the daughter's X chromosomes), then you would expect sequence identity of 50%. $\endgroup$ Oct 22 '21 at 18:57
  • $\begingroup$ Then the Y chromosome is of course not even possessed by the daughter, but will be present for the father if it has been sampled (this is another way to tell the father and daughter apart). And the mitochondrial chromosome will be present for all individuals, if it has been sampled, but it will not match between a father and a daughter in general -- it should only match between a daughter and her mother (or a son and his mother). $\endgroup$ Oct 22 '21 at 18:58

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