Tracing the dispersal of human populations By analysis of polymorphisms in the Non-recombining region of the Human Y Chromosome

Underhill et al 2000 Nature Genetics 26: 358-361Underhill et al 2001 Annals of Human Genetics 65: 43-62

Homo erectus The first example of Homo erectus, known as "Java Man," was discovered in Indonesia in 1893. Fossil remains of Homo erectus have since been found throughout Africa and Asia, making it the first wide-ranging hominid. Despite the primitive appearance of its skull, the erectus skeleton is very similar to that of modern humans, although more robust (thicker and heavier). Homo erectus was probably the first hominid to use fire. 1.8 mya - 300,000 years ago first fossil found in 1893

Homo sapiens (archaic) Also known as Homo heidelbergensis, this species has a brain that was larger than H. erectus' and smaller than that of a modern human. The brain was enclosed in a skull that was more rounded than H. erectus'. Fossil remains of archaic Homo sapiens have been found in Africa and Europe. 500,000 - 200,000 years ago first fossil found in 1921

Homo sapiens neanderthalensis Averaging five and a half feet in height and possessing short limbs, Neanderthals were well-adapted to living in a cold climate. Attached to their robust (thick andheavy) bones were powerful muscles. The Neanderthal's brain was larger than the brain of living humans, although its shape was longer from front to back and not as rounded in the front. 230,000 - 30,000 years ago first fossil found in 1856

Homo sapiens (modern) Modern Homo sapiens, also known as Homo sapiens sapiens, have been around for the past 120,000 years. Homo sapiens living about 40,000 years ago made elaborate tools out of bone, antler, ivory, stone, and wood, and produced fine artwork in the form of carvings and cave paintings. 120,000 years ago - present

Traditional paleoanthropological studies look at where things that look and act like us first appeared and when.

Underhill, Cavalli-Sforza and colleagues have used various DNA polymorphisms to follow human evolution.

Phylogeography analyzes genetic diversity to predict time to a most recent common ancestor.

In addition, the location of populations with diverse alleles is used to predict the location of first appearance of common ancestral genes.

Phylogeography assumes a correspondence between overall distribution of polymorphisms and past human movements.

Underhill et al 2001

Sampled polymorphic loci on the Y chromosome to followhuman evolution.

Sampled DNA from 1062 men.

Represent 52 indigenous populations distributed around the world.

In preliminary studies, they identified 218 Y-linked polymorphic loci. Most loci were biallelic –

either an ancestral or derived allele.

After scoring each man’s DNA for all 218 loci, they found 131 different haplotypes.

A haplotype represents a group of genes that do not separate by recombination.

Each haplotype is the collection of alleles for

that non-recombining group of genes in an individual.

Examples include the human MHC locus, The non-recombining region of the mammalian

Y chromosome.

One approximately every 200-500 kb in the human genome.

NRY haplotypes from Jefferson family members

The differences between haplotypes is used to estimatethe time to the most recent common ancestor to be 60,000 years.

Using maximum parsimony analysis, they grouped the haplotypes into 10 haplogroupsGreat ape DNA used to make a root in the tree.

The geographic distribution of the haplogroups indicates how people migrated to colonize the whole world.

Maximum Parsimony Analysis: Fewest changes to establish relationshipsbetween all individuals.

Sample population with 4 biallelic loci:

ABCDAB’CDA’BCDAB’C’DAB’CD’A’B’C’DA’B’CD

ABCD_____________________

AB’CD A’BCD _________ __________ AB’C’D AB’CD’ A’BC’D A’B’CD

Each step is one mutation from progenitor – estimate time based on uniform mutation rate.

Maximum parsimony analysis of polymorphisms in human Y chromosomes

Distribution model assumes that genotypes of modern indigenous people reflects earlymigration routes

Caveots

Continuous gene flow

Selection effects

Effects of recent events such as migrations

Estimated time to most recent common ancestor is based on the number of differences that distinguish the haplotypes, an assumed mutation rateand an assumed model of population evolution

Caveots

Stable mutation rate

Selection

Unpredicted population bottlenecks

Predicted time to common ancestor is 59,000 years. 95% confidence interval is 40,000 – 140,000 years.

Paleological evidence indicates modern humans spread throughout Africa 90,0000-130,000 years ago.

Estimates based on mitochondrial DNA also indicate common ancestor 100,000-200,000 years ago.

91, 42; 140,000-40,000 years ago 59,000

Yap, RPSY, 89; 50,000-45,000

201, 09; 45,000-30,000

172; 30,000-20,0000

30,000

35, 02; <18,000

60,00045,000

18,000 30,00030,000

60,00045,000

18,000 30,00030,000

60,00045,000

18,000 30,00030,000

60,00045,000

18,000 30,00030,000

Earlier studies with Mitochondrial DNA monitor the female lineage of modern humans

Human genome sequence allowed identification of stable haplotypes of autosomal genes.

These have recently also been used to trace the lineage of modern humans

The time line is harder to determine and generally the Estimated time to common ancestor is longer

Distribution patterns are harder to follow but are Generally consistent with data from the NRY analysis.

Y chromosome analysis fits with roughly with paleological and mitochondrial DNA evidence.

Reveals more migration events than paleological record.

Estimates a fairly recent date to our most recent common ancestor.

Did our family replace other humans that existed earlier?Y vs. Mitochondrial time to most recent common ancestor.

Reasons for the expansion of our single hominid family are still being examined.

100,000 years ago Homo sapiens filled Africa according to the fossil record

300,000 years ago Homo erectus had migrated all over Europe and AsiaNeanderthal man and Java man

Why did modern humans spread out and take over all available niches?

One suggestion is FOXP2 mutation

FOXP2 is a transcription factor that affects speech

Family with a known dominant mutation –Problems with motor aspects of speech but also Cognitive aspects

Molecular studies of variation at FOXP2 locusShows FOXP2 has significantly high rate of evolution in hominid lineage – rapid substitutions comparing Humans to chimps and other mammals

This analysis concludes that the Human FOXP2 allele may have evolved less than 100,000 years ago.