Image: Ton Koene/Corbis
Dramatic news this week showing how, when humans diverged out of Africa they encountered many new environments and quickly diversified into them. The record of this has been found in the Y chromosome, which males uniquely inherit from their fathers. Females inherit two X chromosomes, one from each parent so it is impossible to say from which unless you have the parents' genome too. Males inherit their Y chromosome from their father and an X chromosome from their mother. For this reason the Y chromosome represents the history of the male line.
Researchers David Poznik and Carlos Bustamante and their colleagues of Stanford University found that within the space of about 150 years, some 50,000 years ago, a single site on the Y chromosome mutated to form two distinct male lines, followed very quickly by a second mutation at the same site creating a third line. These three lines can still be traced in the modern Euro-Asian populations.
It is believe the mutation occurred probably in the Arabian peninsula:
That area of the Y tree describes the crucial period when modern humans began going global, sometime after they left Africa between 70,000 and 50,000 years ago. The earlier family tree showed that the three major Eurasian genetic groups that survive today emerged from those pioneering migrants, who were probably living in the Arabian peninsula. But exactly how the ancestors of those three groups relate to one another, and how quickly they diverged after leaving Arabia was not resolved.We know that at least one branch of this evolving human tree came into contact with, and interbred with, Neanderthals but so far Y chromosome analysis has failed to find any individual who inherited his Y chromosome from a Neanderthal father. This of course could mean that these are very rare and so have not been found yet. The possibility of them being found still exists however especially since evidence emerged recently that some humans may well be carrying Y chromosomes from an extinct species of human.
Michael Hammer at the University of Arizona in Tucson and his colleagues identified a Y chromosome unlike any other in a small group of people who can trace their roots back to Cameroon.Technical detail is given in Michael Hammer's team's publication in the Cell Press journal, American Journal of Human Genetics:
It is so different from any other Y chromosome so far found that it may actually have entered the modern gene pool via an ancient human that lived in western Africa, says Bustamante. "It might be our first glimpse of archaic interbreeding within Africa."
We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.If confirmed this will be the second example of diverging and evolving humans forming a ring species, or a species in transition between an ancestor and several descendant species, much to the consternation of creationist pseudo-scientists who continue to insist, in the face if contrary evidence, that there is no evidence for human evolution nor of transition between an ancestral and a descendant species. Once again we find that creationism is not supported by real-world evidence and is refuted by science.
Main Text
Characterizing the root of the phylogenetic tree of individual genetic loci has influenced many researchers in their attempts to infer the time and place of the origin of anatomically modern humans (AMHs).1, 2, 3, 4 Analyses of the nonrecombining portion of the Y chromosome and mtDNA have suggested that recent common ancestors lived in sub-Saharan Africa within the last 200,000 years.5 However, estimates of the time to the most recent common ancestor (TMRCA) have been consistently lower for the Y chromosome (∼60–140 thousand years ago [kya])6, 7, 8 than for mtDNA (∼140–240 kya).9, 10 A variety of evolutionary processes (e.g., natural selection, differential migration of males and females, and/or a skew in the breeding sex ratio) have been invoked to explain this difference.11, 12, 13
Genotyping of a DNA sample that was submitted to a commercial genetic-testing facility demonstrated that the Y chromosome of this African American individual carried the ancestral state of all known Y chromosome SNPs. To further characterize this lineage, which we dubbed A00 (see Figure S1, available online, for proposed nomenclature), we sequenced multiple regions (totaling ∼240 kb) of the X-degenerate portion of this chromosome, as well as a subset of these regions (∼180 kb) on a chromosome belonging to the previously known basal lineage A1b (which we rename here as A0). We note that all sampling procedures described herein were approved by and performed according to the ethical standards of the University of Arizona Human Subjects Committee. The ancestral state of each polymorphic site was inferred with pairwise alignments between the human (UCSC Genome Browser hg18) and chimpanzee (panTro3) reference sequences, and mutations were assigned to the branches (i.e., A00 and A0) shown as thick lines in Figure 1 on the basis of an infinite-sites model (Table S1). To estimate the TMRCA of the Y chromosome tree that incorporates the newly discovered root defined by A00, we developed a likelihood-based method that uses mutation rates recently estimated by Kong et al.,14 who performed high-coverage whole-genome sequencing on 78 human pedigrees.
Assuming that mutations in the X-degenerate portion of the Y chromosome follow the linear model presented by Kong et al.,14 we adjusted for male-specific mutation processes. If μY is the mutation rate per year per base for the Y chromosome, L is the length of sequence analyzed for the autosomes, T is the average number of new mutations per genome in the autosomes, g is the generation time, b is the increment in mutation rate per base per year increment in the paternal age, F is the number of mutations originating in the mother, and g0 is the average age of fathers in the study,14 then . We obtained median values and generated 90% confidence intervals (CIs) for μY as a function of g (ranging from 20 to 40 years) by sampling 100,000 times from normal distributions for each of the parameters T ∼ N (63.2 [SD = 0.9]), b ∼ N (2.01 [SD = 0.17]), and F ∼ N (14.2 [SD = 3.12]), which result from the number of observed mutations (4,933 in 78 pedigrees), the linear coefficient in the linear fit of mutations as a function of paternal age (2.01 per year [SEM = 0.17 per year]), and the 71 mutations that can be confirmed as de novo and of maternal origin in five pedigrees,14 respectively. We then divided those values by 2.68 × 109 (the length of autosomal sequence covered in each of the 78 trios) to obtain estimates and CIs for μY (Figure S2). This resulted in a range for μY (across values of g) of 4.39 × 10−10 ≤ μY ≤ 7.07 × 10−10. To obtain point estimates of the ages of nodes in Figure 1, we used the median value of μY at age 30 years (6.17 × 10−10). To obtain upper and lower bounds of the CIs, we used the lower and upper bounds of μY, respectively. Estimates of mutation rate in Kong et al.14 are consistent with those from a variety of large-scale sequencing studies,15, 16, 17, 18, 19 making it unlikely that our TMRCA estimates are strongly biased by an excess of false negatives in genome sequence data from human pedigrees.
Figure 1 Genealogy of A00, A0, and the Reference Sequence
Lineages on which mutations were identified and lineages that were used for placing those mutations on the genealogy are indicated with thick and thin lines, respectively. The numbers of identified mutations on a branch are indicated in italics (four mutations in A00 were not genotyped but are indicated as shared by Mbo in this tree). The time estimates (and confidence intervals) are indicated kya for three nodes: the most recent common ancestor, the common ancestor between A0 and the reference (ref), and the common ancestor of A00 chromosomes from an African American individual and the Mbo. Two sets of ages are shown: on the left are estimates (numbers in black) obtained with the mutation rate based on recent whole-genome-sequencing results as described in the main text, and on the right are estimates (numbers in gray) based on the higher mutation rate used by Cruciani et al.6
We estimated the TMRCA of human Y chromosomes as 338 kya (95% CI = 237–581 kya). Using a joint likelihood20 and the same mutation rate, we also estimated a divergence time between A0 chromosomes and the human reference as 202 kya (95% CI = 125–382 kya), a time that is older than that previously obtained by Cruciani et al. (142 kya).6 This discrepancy in the age of A0 is due to the fact that the earlier study did not utilize mutation rates based on recently obtained whole-genome sequence data.14, 15, 16, 17, 18 If we were to use the higher mutation rate (1.0 × 10−9 per base per year6) rather than a realistic range derived from whole-genome sequencing (4.39 × 10−10 − 7.07 × 10−10), the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ∼39 kya6 (i.e., versus ∼63 kya for the mutation rate used here). It is difficult to reconcile the younger estimate with the timing of the out-of-Africa dispersal on the basis of the analyses of autosomal DNA21 and the fossil record outside of Africa.22, 23, 24, 25 Regardless of which mutation rate is applied, the analysis of relative ages of nodes26 shows that the TMRCA of the A00-rooted tree is 67% older (95% CI = 35%–126%) than that of the A0-rooted tree.
We then genotyped a set of six Y chromosome short tandem repeats (Y-STRs) (DYS19, DYS388, DYS390, DYS391, DYS392, and DYS39327) and found that the A00 chromosome carried the following alleles: 16-11-19-10-12-13. Upon searching a large pan-African database consisting of 5,648 samples from ten countries (Cameroon, Nigeria, Ghana, Senegal, Uganda, Tanzania, Malawi, Zimbabwe, Mozambique, and South Sudan), we identified 11 Y chromosomes that were invariant and identical to the A00 chromosome at five of the six Y-STRs (2 of the 11 chromosomes carried DYS19-16, whereas the others carried DYS19-15). These 11 chromosomes were all found in a sample of 174 (∼6.3%) Mbo individuals from western Cameroon (Figure 2). Seven of these Mbo chromosomes were available for further testing, and the genotypes were found to be identical at 37 of 39 SNPs known to be derived on the A00 chromosome (i.e., two of these genotyped SNPs were ancestral in the Mbo samples) (Table S1). Using the joint likelihood for the split of two lineages and a sublineage internal to one of them,20 we estimated that the most recent common ancestor of the African American and Mbo A00 chromosomes lived between 2.6 and 73 kya (95% CI, maximum likelihood estimate = 17 kya).
We also estimated the level of variation among nine A00 lineages (i.e., including one additional Mbo individual) by using a battery of 95 Y-STRs for which all individuals had no missing data; (Table S2). A median-joining network28 shows that the African American A00 lineage is 11 mutational steps from the nearest Mbo and that the maximum difference between any pair of Mbo is nine steps (Figure 3 and Table S2). On the basis of these levels of within- and between-group variation, we calculated a second divergence time estimate of 564–2,697 years (Table 1) by assuming a mean Y-STR mutation rate of 1.32 × 10−4 and 2.76 × 10−5 per year, respectively.29, 30.
Figure 2Map Showing Cameroon and the Approximate Location where Mbo Speakers Live
Figure 3Median-Joining Network of A00 Haplotypes
The network is based on haplotypes (constructed with 95 Y-STRs) of eight Mbo and an African American (AA) individual. All mutations are assumed to be single step and were given equal weight during the construction of the network. Marker names are indicated without “DYS” at the beginning.
Mendez, Fernando L.; Krahn, Thomas; Schrack, Bonnie; Krahn, Astrid-Maria; Veeramah, Krishna R.; Woerner, August E.; Fomine, Forka Leypey Mathew; Bradman, Neil; Thomas, Mark G.; Karafet, Tatiana M.; Hammer, Michael F
An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree The American Journal of Human Genetics, 92(3), 454-459; DOI: 10.1016/j.ajhg.2013.02.002
Copyright: © 2013 The authors.
Published by Elsevier. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
It may be the second example of a new species of Homo being discovered in the genetic record or modern humans. Recently scientists at the Max Planck Institute for Evolutionary Anthropology identified evidence of the DNA of an unknown Hominid in modern humans. This probably become incorporated into the modern human genome in addition to that of Neanderthals and the newly-discovered 'Denisovans' when humans appeared to form a ring species in Euro-Asia as Homo sapiens coming out of Africa came into contact with the descendants of their common ancestor, H. heidelbergensis who had migrated out in an earlier wave and had diversified into Neanderthals, Denisovans, and probably at least one other subspecies as they spread out into Europe and Asia.
See also A Human Ring Species? and More Evidence For A Human Ring Species
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