Genome Advance of the Month

The X and Y of human origins: Using Y chromosome sequencing data to explore human evolution

Human evolution fascinates the public. The National Museum of Natural History (NMNH), part of the Smithsonian Institution, devotes an entire exhibit to the topic in the Hall of Human Origins. One floor above the human origins exhibit is Genome: Unlocking Life's Code, an exhibit developed by NMNH and the National Human Genome Research Institute (NHGRI) that highlights the use of genomics to explore human evolution.  

Rapid advances in genomic sequencing are beginning to provide insight into the complex narrative of human ancestry embedded in human DNA, particularly through genetic variation. Genetic variants are sequences of DNA base pairs that differ from more common ancestral sequences and can be traced to specific human populations, both past and present. A researcher can search for variants in an individual's genetic code and determine how related that person is to certain ethnic and geographic populations. For males, researchers sequence the Y chromosome, since this allele is always passed down from father to son; for females, mitochondrial DNA is sequenced, since a daughter inherits this material from her mother. Genetic variants found in these sequencing data can be used to construct a paternal or maternal evolutionary tree, showing how certain human populations connect to each other.

The ability to sequence the Y chromosome, a relatively recent development in the field of genomics research, is discussed in two papers published in Science this past August, the topic of the August Genome Advance of the Month. The male-specific portion of the Y chromosome, a region of the DNA strand that does not normally exchange base pairs with the nearby X chromosome, is "a powerful tool with which to study human history" and determine when the most common male ancestors existed, according to a research team primarily from the Stanford University School of Medicine Department of Genetics. This research team led by Dr. Carlos Bustamante and others involved in the study of human evolution, uses this region of the chromosome to find variants specific to certain male evolutionary shifts.

In the past, sequencing the whole Y chromosome posed challenges for researchers attempting to unlock evolutionary information hidden in this strand of DNA. This difficulty was due, in part, to the highly repetitive sequences of the Y chromosome, as explained in a Nature article, "Genome Biology: Tales of the Y Chromosome," by Dr. Huntington F. Willard of Duke University's Institute for Genome Sciences and Policy.  

Now, the Y chromosome's stretch of well-preserved DNA sequences can be used to more accurately estimate when specific ancestral male populations emerged. It can also provide clues for when these male populations diverged into various subgroups with their own set of genetic variants, referred to as haplogroups.

The Stanford research team sequenced a group of 69 males from nine diverse populations. To analyze the sequencing data for common genetic variants, they used a "haploid model expectation maximization algorithm," a computational method that finds any common changes in the samples' DNA sequences. The group located 11,640 single-nucleotide variants, or SNVs, (which are a change in one nucleotide of the sequenced DNA strand), and were able to identify 2,293 SNVs from previously conducted research. This data was used to construct a Y chromosome-based evolutionary tree to illustrate the relatedness between the sequenced populations. Their work further confirmed previous data on the ancestral origins of Y chromosome haplogroups, and addressed long-standing gaps in the evolutionary tree, particularly among African populations. 

In another Science paper that explored sequencing of the Y chromosome, Dr. Paolo Francalacci and Dr. Laura Morelli from the University of Sassari, Department of Zoology and Genetic Evolution, and their colleagues, studied the main haplogroups in Europe. They focused specifically on male samples from the small, isolated island of Sardinia. Based upon genetic variants in the male-specific portion of the Y chromosome, this team of researchers estimated when the Sardinian male population genetically merged with European mainland groups.  Their goal was to locate a single common ancestor based on sequencing data from 1,204 Sardinian males. They discovered 11,763 single-nucleotide changes, of which, 6,751 had not previously been reported in other research papers.

The Italian research team used these genetic variants to construct a paternal evolutionary tree that looked at relatedness between Sardinian haplogroups and their European ancestors. What the researchers found is that many of the Sardinian samples were closely related to common European haplogroups. In order to pinpoint historically when the Sardinian population began to deviate in their genetic code, the team sequenced samples from the Basque Country, Northern Italy, Tuscany and Corsica along with others to compare genetic variations. Sardinian-specific SNVs indicate moments when the genetic makeup of the Sardinian male population began to differ from its European roots. They verified this variant data using archeological records that marked a European expansion into Sardinia beginning roughly 7,700 years ago.

The group was also able to estimate the origination of the Y chromosome -- the existence of the most common human male ancestor. They provided a range of time from about 180,000 to 200,000 years ago, consistent with mitochondrial DNA analysis. The Stanford team provided a similar estimate from their sequencing results (120,000 to 156,000 years ago) and hypothesized that, contrary to previous conclusions that a male common ancestor ("Adam") did not originate until after a female common ancestor ("Eve"), the origin of the male Y chromosome is very similar to the origin of mitochondria. In other words, the most common male and female ancestor related to current human beings may have existed at the same time.

Both papers compared their evolutionary data with archeological evidence, demonstrating the usefulness of using sequencing data to establish the evolution of ancestral populations. They present an interesting link between sequencing technologies and archeology. From combining sequencing data with archeological findings, scientists are better able to "root" human evolutionary relationships with concrete historical data.

Read the Studies:

Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, Atzeni R, Pilu R, Busonero F, Maschio A, Zara I, Sanna D, Useli A, Urru MF, Marcelli M, Cusano R, Oppo M, Zoledziewska M, Pitzalis M, Deidda F, Porcu E, Poddie F, Kang HM, Lyons R, Tarrier B, Gresham JB, Bingshan L, Tofanelli S, Alonso S, Dei M, Lai S, Mulas A, Whalen MB, Uzzau S, Jones C, Schlessinger D, Abecasis G, Sanna S, Sidore C, Cucca F. Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny. Science, 341(6145): 565-569. 2013. [PubMed]

Poznik GD, Henn BM, Yee M, Sliwerska E, Euskirchen G, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD. Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females. Science, 341(6145): 562-565. 2013. [PubMed]

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Posted: September 30, 2013