In those graphs, its pretty clear that most African populations between themselves as well as most European, East Asian and Native American populations are relatively genetically very close to each other (in term of genetic distance). They "cluster" with one another in term of genetic distance. This is produced by a series of migration, isolation, bottleneck effect and back migration and admixture.
But some people find it strange, because we also know that African populations, usually, have a very high level of genetic diversity too (for example, nucleotide diversity). So how can certain populations be both genetically diverse while being genetically close at the same time?
To answer that question, I decided to make a little simple/toy example, which I think is easy to understand without the need to do any calculation.
EXAMPLE:
quote: Population 1: individual 1:AAGGT individual 2:CCTAG individual 3:TGCCA
Population 2: individual 1:AAGGT individual 2:CTTAG individual 3:TGCCA
Population 3: individual 1:GTATC individual 2:GTATC individual 3:GTATC
Here we have 3 populations. Each with 3 individuals. For each individual, we have a string of DNA nucleotides (for simplicity, we can view it as a continuous string of DNA. I also show only 1 allele per locus as if non-autosomal). Let's consider them as SNP. Each position in the string correspond to a locus. So in population 1, individual 1, at locus 1, you got nucleotide A (Adenine). In population 3, individual 2, locus 4, you got T. And so on.
Genetic distance: If we take a little time to look at it. It's easy to see that population 1 and 2 are almost genetically similar. So they are genetically very close to one another.
Population 3 is very different from population 1 and 2. Population 3 have different nucleotides than population 1 and 2, at almost every locus.
So, population 1 and 2 are much closer to each other in term of genetic distance than with population 3.
Diversity: Here we can see that population 3 is not very diversified. In fact, their diversity is zero. At locus 1, they all got G. At locus 2, they all got T, and so on.
Not the same thing could be said about population 1 and 2. Population 1 has at locus 1 got A, C and T for the 3 individuals. Clearly, 3 different nucleotides. Same for locus 2, with A, C and G. And so on. Same could be said about population 2.
So Population 1 and 2, are much more genetically diverse than population 3.
Conclusion : Here we have a simple example of 2 populations being relatively genetically close to each other, compared to with population 3, while at the same time exhibiting a high level of genetic diversity. The studies (graphs/trees) I posted are practical examples of it.
I hope this post will help people who are mixing up the concept of genetic distance with genetic diversity.
the lioness, Member # 17353
posted
a well thought out explanation
Ponsford Member # 20191
posted
The greater the genetic distance of any group from Africa[Africans] the lesser their genetic diversity e.g. Native Americans.The lesser the genetic diversity of any group the greater their Linkage Disequilibrium.
Trollkillah # Ish Gebor Member # 18264
posted
quote:Originally posted by the lioness,: a well thought out explanation
I hope the part of alleles and locus got trough.
In the meanwhile, we can conclude that when these mutations occurred, these populations were very small (population density), with only a few members to the family. After the Holocene Epoch, members of populations started to increase, due to climatic fluctuations and changes
posted