DNA dating: How molecular clocks are refining human evolution's timeline
Y chromosome is a superb tool for inferring human evolution and recent of mutation rate to be used in Y chromosome dating is controversial. (i) The evolutionary dynamics of the genome region is known in pattern and tempo. in some cases just part of the genetic information is being used, and analyses do The newly proposed age is much younger than dates consistent with . Coalescence theory is providing extremely useful tools for the. Population genetics has emerged as a powerful tool for unraveling human history . In some cases the Y chromosome, or any other locus, may be used to infer Y-chromosome genealogical depth was used to assess the date of origin of.
Analyzing DNA from present-day and ancient genomes provides a complementary approach for dating evolutionary events. Because certain genetic changes occur at a steady rate per generation, they provide an estimate of the time elapsed.
Molecular clocks are becoming more sophisticated, thanks to improved DNA sequencing, analytical tools and a better understanding of the biological processes behind genetic changes. By applying these methods to the ever-growing database of DNA from diverse populations both present-day and ancientgeneticists are helping to build a more refined timeline of human evolution.
How DNA accumulates changes Molecular clocks are based on two key biological processes that are the source of all heritable variation: DNA image via www. These changes will be inherited by future generations if they occur in eggs, sperm or their cellular precursors the germline. Most result from mistakes when DNA copies itself during cell division, although other types of mutations occur spontaneously or from exposure to hazards like radiation and chemicals.
In a single human genome, there are about 70 nucleotide changes per generation — minuscule in a genome made up of six billion letters. But in aggregate, over many generations, these changes lead to substantial evolutionary variation. Scientists can use mutations to estimate the timing of branches in our evolutionary tree.
Then, knowing the rate of these changes, they can calculate the time needed to accumulate that many differences. Comparison of DNA between you and your sibling would show relatively few mutational differences because you share ancestors — mom and dad — just one generation ago. However, there are millions of differences between humans and chimpanzees ; our last common ancestor lived over six million years ago. Bits of the chromosomes from your mom and your dad recombine as your DNA prepares to be passed on.
Chromosomes image via www. Recombinationalso known as crossing-over, is the other main way DNA accumulates changes over time. It leads to shuffling of the two copies of the genome one from each parentwhich are bundled into chromosomes. In humans, about 36 recombination events occur per generation, one or two per chromosome. As this happens every generation, segments inherited from a particular individual get broken into smaller and smaller chunks.
Based on the size of these chunks and frequency of crossovers, geneticists can estimate how long ago that individual was your ancestor. Gene flow between divergent populations leads to chromosomes with mosaic ancestry.
As recombination occurs in each generation, the bits of Neanderthal ancestry in modern human genomes becomes smaller and smaller over time. Bridget Alex, CC BY-ND Building timelines based on changes Genetic changes from mutation and recombination provide two distinct clocks, each suited for dating different evolutionary events and timescales.
Because mutations accumulate so slowly, this clock works better for very ancient events, like evolutionary splits between species. The recombination clock, on the other hand, ticks at a rate appropriate for dates within the lastyears. The case of Neanderthals illustrates how the mutation and recombination clocks can be used together to help us untangle complicated ancestral relationships.
Geneticists estimate that there are 1. Applying the mutation clock to this count suggests the groups initially split betweenandyears ago.
Evaluating the Y chromosomal timescale in human demographic and lineage dating
At that time, a population — the common ancestors of both human groups — separated geographically and genetically. Some individuals of the group migrated to Eurasia and over time evolved into Neanderthals. Those who stayed in Africa became anatomically modern humans.
An evolutionary tree displays the divergence and interbreeding dates that researchers estimated with molecular clock methods for these groups.
Modern humans eventually spread to Eurasia and mated with Neanderthals. Applying the recombination clock to Neanderthal DNA retained in present-day humans, researchers estimate that the groups interbred between 54, and 40, years ago. When scientists analyzed a Homo sapiens fossil, known as Oase 1, who lived around 40, years ago, they found large regions of Neanderthal ancestry embedded in the Oase genome, suggesting that Oase had a Neanderthal ancestor just four to six generations ago.
Comparing chromosome 6 from the 40,year-old Oase fossil to a present-day human. Second, the detected mutations must be true. In this regard, Xue et al. This pedigree-based rate has been widely used in Y chromosome demographic and lineage dating. Although this pedigree-based substitution rate is widely accepted, some concerns have also been raised. First, the mutation process of Y chromosome is highly stochastic, and the rate based on a single pedigree and only four mutations might not be suitable for all the situations.
For instance, the haplogroup of the pedigree used in rate estimation of Xue et al. Second, the substitution rate was estimated using two individuals separated only 13 generations, thus, the question is whether the substitution rate estimated at relatively short time spans could be used in long-term human population demographic analysis without considering natural selection and genetic drift.
Actually, many studies have noted that molecular rates observed on genealogical timescales are greater than those measured in long-term evolution scales [ 14 ]. This novel haplotype represents an out-group lineage to all other known Y haplotypes presently identified in human population. To estimate the time of origin of the novel haplotype, these authors neither used the existing rates for Y chromosome substitutions as estimated from human and chimpanzee comparisons [ 67 ] or from human deep-rooting pedigrees [ 8 ]; instead they developed a likelihood-based method that uses paternal autosomal mutation rates reported from an Icelandic data set of 78 parent-offspring trios.
Evaluating the Y chromosomal timescale in human demographic and lineage dating
Under the assumptions that mutation rates are equal to substitution rates, and the Y chromosomal substitution rate is linearly related to the autosomal rate, they obtained a Y chromosome estimate of 6. Strikingly, this substitution rate is only approximately half of the previous evolutionary rates and pedigree rate, although is very similar to estimates of autosomal rate [ 15 ].
In particular, it is unreasonable for the great disparity between Xue et al. While Mendez et al. Several reasons suggest that the Y chromosome mutation rate is expected to be higher than that of the autosomes. First it undergoes more rounds of replication in the male germline compared with autosomes [ 13 ].
In addition, long-term Y chromosomal substitution rates are not equal to single generation autosomal mutation rates, and purifying or advantageous selective pressures and genetic drift make it difficult to infer the correct Y chromosomal substitution rate from autosomal substitution rates [ 5 ]. Using the pedigree-based substitution rate results in a more reasonable estimate of TMRCA at about to kya [ 5 - 9 ], which is consistent with the earliest emergence of anatomically modern humans, and excludes the possibility of archaic introgression.
The generation time is actually a key parameter in paternal lineage dating, as male mutation rates have been shown to increase with increasing generation time [ 5 ]. The unreasonable generation times of Mendez et al. Y chromosome base-substitution rate based on archaeological evidence of founding migrations InPoznik et al. Instead of using previous evolutionary and pedigree-based substitution rates for Y chromosome dating, they estimated the rate using a within-human calibration point, the initial migration into and expansion throughout the Americas.
Well-dated archaeological sites indicate that humans first colonized the Americas about 15 kya [ 18 ].
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Using this, the authors obtained a mutation rate of 0. Thus the authors concluded that the coalescence times of Y chromosomes and mitochondrial genomes are not significantly different, which disagrees with the conventional suggestion the common ancestor of male lineages lived considerably more recently than that of female lineages [ 10 ].
The estimated Y-chromosomal substitution rate was subsequently applied to lineage dating within haplogroup R. The distribution of R1a and R1b, two main sublineages of haplogroup R, is suggested to be associated with recent episodes of population growth and movement in Europe. Similar to Poznik et al.
They used the initial expansion of the Sardinian population about 7. This rate is extremely low and only half of the pedigree-based rate. The main concern of the above two rates is the calibration point. In Poznik et al. An ancient genome of male infant about By direct counting the transversions accumulated in the past That is to say, the Y chromosomal substitution rate has been overestimated in Poznik et al.
In Francalacci et al. If the latter is true, Francalacci et al. Although using the archaeological evidence for calibration in Y chromosomal substitution rate estimation is correct in principle, we have to pay great attention to whether the calibration point is reliable and suitable or not. In addition, more calibration dates could lead to more robust estimates. Besides the initial peopling of Americas and the initial expansion of the Sardinian population, the peopling of Oceania might be another good calibration point.
The next most important split point is the out-of-Africa superhaplogroup CT, which we date here at However, the times estimated using rate based on archaeological evidence of initial Sardinian expansion is nearly two-fold of using pedigree rate, and almost three-fold of using rates obtained from human-chimpanzee comparisons.
The times using rate calibrated by initial peopling of Americas are very similar with those applying pedigree rate, but still 10 to 20 ky larger.
The rate adjusted from autosomal rates has inflated these time estimates by two-third as compared with pedigree rate. There are evidence for earliest modern human activities in Australia and neighboring New Guinea about 40 to 45 kya [ 23 ], in Southeast Asia about 37 to 38 kya [ 24 ], in China about 38 to 44 kya [ 2526 ], and in Europe about 40 [ 2728 ].