Chapter D, Problem 1P

Why might mitochondrial, Y chromosome, and autosomal DNA provide different perspectives on our evolutionary past $-$ for example, with respect to our relationship with Neandertals?

Summary Introduction

To analyze:

The reason for the relationship of mitochondria, Y chromosome, and autosomal DNA with different aspects of our evolutionary past, for example regarding our relationship with Neandertals.

Introduction:

The evolutionary relationships of closely related organisms show different evolutionary processes in a relatively short time that has been of interest to a biologist since a long time. The comparative study of phylogenies concluded from the DNA sequences with different inheritance patterns i.e. mitochondrial, autosomal, and X & Y chromosomal loci delivers best widespread conclusions of the evolutionary history.

Explanation of Solution

Mitochondria DNA: The first genetic evidence for an African origin of modern humans was analyzed from the study of mitochondrial DNA (mtDNA) polymorphism. The mtDNA specifically gives the genealogical history and evolutionary relationship of mammalian species.

The mtDNA are inherited maternally; they do not show any recombination of alleles; unlike the nuclear genome, some non-coding mtDNA can evolve quickly which leads to a variation in the mtDNA within closely related species. In mammals, the rate of mutation in mtDNA is higher than nuclear genomes i.e. $\text{10}$ times higher. This reflects lower levels of DNA repair mechanisms in mtDNA than nuclear genome. A construction of phylogenetic tree allows the identification of a common ancestor of the species.

The regions around the Great Rift Valley of East Africa have been home to humans and hominin ancestors for at least 4 million years. The model of Human evolution called as RAO model (for recent African origin) proposes humans are evolved from a small African population. The RAO model suggests that modern humans arose approximately $\text{120000 to 200000}$ years ago, while the MRE model- Multiregional suggests a much older age for our species i.e. 2 million years ago. RAO model suggests that the genetic diversity should be greatest in Africa, and outside Africa, it would be a subset of that found in Africa (suggest the migration from Africa).

Y chromosome: The Y chromosome sequence variation provides complementary mtDNA analysis. Y chromosome is strictly paternally inherited, and outside the pseudo-autosomal region, it does not show any recombination with other chromosomes. Y chromosome sequence is poor and provides very less sequence diversity. It has short tandem repeats (Y-STR) that can mutate rapidly about $0.1\%$ per Y-STR per generation.

According to the RAO model, more diversity is observed within African Y chromosome sequence than non-African sequences. As the mtDNA and Y chromosomes are strictly maternal and paternal, their haplotypes can be used to trace the migration patterns.

Autosomal DNA: The analysis of thousands of human genome sequences demonstrated that autosomal genetic diversity in African population is greater compared to the non-African population. Likewise, the study of Single nucleotide polymorphic DNA of worldwide sample population revealed the highest frequency of unique alleles in Africans compared to Non- Africans.

From all of these aspects, the mtDNA of Neandertals is different from the modern human, and it also does not show any inbreeding. The comparative nuclear genome sequences revealed that $4\%$ of modern human genome is of Neandertal origin.

The hybridization of Neandertals genome with modern human genome revealed that inbreeding took place after the migration of modern humans out of Africa. The other analysis also revealed that Neandertal DNA is unevenly distributed in the human genome; for example, no Neandertal DNA on the X chromosome, rather on autosomes, carries Neandertal DNA with precise distribution.

Conclusion

The comparative study of phylogenies concluded from the DNA sequences with different inheritance patterns i.e. mitochondrial, autosomal, and X & Y chromosomal loci, delivers best widespread conclusions of the evolutionary history.