Most recent common ancestor

For lowest common ancestors in graph theory and computer science, see Lowest common ancestor.
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In biology, the most recent common ancestor (MRCA) of any set of organisms is the most recent individual from which all organisms in a group, for example a haplogroup, are directly descended. The term is often applied to human genealogy.

The MRCA of a set of individuals can sometimes be determined by referring to an established pedigree. However, in general, it is impossible to identify the exact MRCA of a large set of individuals, but an estimate of the time at which the MRCA lived can often be given. Such time to MRCA (TMRCA) estimates can be given based on DNA test results and established mutation rates as practiced in genetic genealogy, or by reference to a non-genetic, mathematical model or computer simulation. TMRCA is often given in years before current (ybc). A certain mutation can be assumed to have been formed at a time instant between the TMRCA of the previous branch in the phylogenetic tree, and the TMRCA of the mutation itself.

Assuming that no genetically isolated human populations remain, the human MRCA may have lived 2,000 to 4,000 years ago.[1] This estimate is based on a non-genetic, mathematical model that assumes random mating although it has taken into account important aspects of human population substructure such as assortative mating and historical geographical constraints on interbreeding.[1]

The term MRCA is usually used to describe a common ancestor of individuals within a species. It can also be used to describe a common ancestor between species. To avoid confusion, last common ancestor (LCA) or the equivalent term concestor is sometimes used in place of MRCA when discussing ancestry between species.

The term MRCA may also be used to identify a common ancestor between a set of organisms via specific gene pathways. The TMRCA in the case of gene pathways will be different depending on how restrictive the choice of genes is. Choosing a very restrictive gene such as mtDNA, which is inherited only along the female lineage Mitochondrial Eve or the male equivalent Y-chromosomal Adam are examples of such MRCAs, which yields TMRCA estimates orders of magnitude further back in time than TMRCA if any possible line of descendancy is allowed. Such genealogies in reality trace ancestry of individual genes, not organisms. As a result, TMRCA estimates for genetic MRCAs are necessarily greater than those for MRCAs of organisms.

MRCA of all living humans

Through random drift or selection lineage will trace back to a single person. In this example over 5 generations, the colors represent extinct matrilineal lines and black the matrilineal line descended from the MRCA.

Tracing one person's lineage back in time for a few generations in principle forms a binary tree of parents, grandparents, great-grandparents and so on. However, the number of individuals in such an ancestor tree grows exponentially and very soon exceeds the population from which the ancestors were drawn. A human alive today would, over 30 generations (going back to about the High Middle Ages), have 230 or about 1.07 billion ancestors, more than the world population at the time.[2] Thus it is obvious that there is multiple counting and the individual is descended from some of these ancestors through more than one line: pedigree collapse changes the binary tree to a directed acyclic graph.

Consider the formation, one generation at a time, of the ancestor graph of all living humans with no descendants. Start with living people with no descendants at the bottom of the graph. Adding the parents of all those individuals at the top of the graph will connect (half-) siblings via one or two common ancestors, their parent(s). Adding the next generation will connect all first cousins. As each of the following generations of ancestors is added to the top of the graph, some of the relationships between more and more people are mapped (second cousins, third cousins and so on). Eventually a generation may be reached where one of the many top-level ancestors is the MRCA from whom it is possible to trace a path of direct descendants all the way down to every living person in the bottom generations of the graph.

The MRCA of everyone alive could have co-existed with a large human population, each of whom either has no living descendants or is an ancestor of only some of the people alive today. Therefore, the existence of an MRCA does not imply the existence of a population bottleneck, let alone a "first couple".

The MRCA of the current population can change over time as people die.

It is incorrect to assume that the MRCA passed all of his or her genes (or indeed any gene) down to every person alive. Because of sexual reproduction at every generation, an ancestor passes half of his or her genes to each descendant in the next generation. Save for inbreeding, the percentage of genes inherited from the MRCA becomes smaller and smaller in individuals at each generation, sometimes decreasing to zero (at which point the Ship of Theseus paradox arises[3]), as genes inherited from contemporaries of MRCA are interchanged via sexual reproduction.[1][4]

Identical ancestors point

The MRCA of living humans may have had many companions of both sexes. Many of these contemporaries left direct descendants, but not an unbroken line of descendants all the way down to everyone in today's population. Some contemporaries of the MRCA are ancestors of no one in the current population. The remainder are ancestors of only some of the current population.

Because ancestors of the MRCA are by definition also common ancestors, we can find (less recent) common ancestors by pushing further back in time to ancient common ancestors of all people alive. Eventually we reach a point in the past where all humans can be divided into two groups: those who left no descendants today and those who are common ancestors of all living humans. This point in time is termed the identical ancestors point (IAP). Even though each living person receives genes (in original or mutated forms) in dramatically different proportions from these ancestors from the identical ancestors point,[1] from this point back, all living people share the same set of ancestors, all the way to the first single-celled organism.[2]

Note that at the IAP, we had many common ancestors. At some very much earlier time, it may be that there was a single organism such that its only contemporaries who were ancestors of all current humans were either its descendants or its own ancestors, in the way that there is a single Mitochondrial Eve and a single Y chromosome Adam. However, if such a time existed, it would substantially predate the IAP.

Estimating the identical ancestor point is complicated by uncertainty in interbreeding between geographically separated groups. However, it presumably occurred before Aboriginal Australians split from Europeans and Asians 65,000-75,000 years ago, since they remained relatively isolated after that point, until the recent arrival of Europeans.

MRCA of different species

Euryarchaeota Nanoarchaeota Crenarchaeota Protozoa Algae Plantae Slime molds Animal Fungus Gram-positive bacteria Chlamydiae Chloroflexi Actinobacteria Planctomycetes Spirochaetes Fusobacteria Cyanobacteria Thermophiles Acidobacteria Proteobacteria
Evolutionary tree showing the divergence of modern species from the last universal ancestor in the center.[1] The three domains are colored, with bacteria blue, archaea green, and eukaryotes red.
  1. ^ Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P; Doerks; von Mering; Creevey; Snel; Bork (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science 311 (5765): 1283–7. Bibcode:2006Sci...311.1283C. doi:10.1126/science.1123061. PMID 16513982. 

It is also possible to use the term MRCA to describe the common ancestor of two or more different species. In the past, the term MRCA was used interchangeably with last common ancestor (LCA) to denote both the common ancestor within a species and that between species. But MRCA is now more frequently used to describe common ancestors within a species. On the other hand, LCA now describes the common ancestor between two species.

The concept of the last common ancestor is described in Richard Dawkins' book, The Ancestor's Tale, in which he imagines a 'pilgrimage' backwards in time, during which we humans travel back through our own evolutionary history and as we do so are joined at each successive stage by all the other species of organism with which we share each respective common ancestor. Dawkins uses the word "concestor" (coined by Nicky Warren) as an alternative to LCA.

In The Ancestor's Tale, following the human evolutionary tree backward, we first meet the concestor that we share with the species that are our closest relatives, the chimpanzee and bonobo. Dawkins estimates this to have occurred between 5 and 7 million years ago. Another way of looking at this is to say that our (approximately) 250,000-greats-grandparent was a creature from which all humans, chimpanzees, and bonobos are directly descended. Further on in Dawkins' imaginary journey (imaginary, in that the journey is going backwards in time), we meet the concestor we share with the gorilla, our next nearest relative, then the orangutan, and so on, until we finally meet the concestor of all living organisms, known as the last universal ancestor.

A common mistake made by the public as well as some authors is to refer to a proposed last common ancestor as an earliest ancestor. Examples include the book The Link: Uncovering Our Earliest Ancestor by Colin Tudge,[5] and a documentary of the same name screened on the History Channel (US) and BBC One (UK),[6] both referring to the primate fossil dubbed Ida.

MRCA of a population identified by a single genetic marker

Main article: Coalescent theory

It is also possible to consider the ancestry of individual genes (coalescent theory), instead of a person (an organism) as a whole. Unlike organisms, a gene is passed down from a generation of organisms to the next generation either as perfect replicas of itself or as slightly mutated descendant genes. While organisms have ancestry graphs and progeny graphs via sexual reproduction, a gene has a single chain of ancestors and a tree of descendants. An organism produced by sexual cross-fertilization (allogamy) has at least two ancestors (its immediate parents), but a gene always has one ancestor per generation.

Given any gene in the body of a person, we can trace a single chain of human ancestors back in time, following the lineage of this one gene. Because a typical organism is built from tens of thousands of genes, there are numerous ways to trace the ancestry of organisms using this mechanism. But all these inheritance pathways share one common feature. If we start with all humans alive now and trace their ancestry by one particular gene (actually a locus), we find that the farther we move back in time the smaller the number of ancestors becomes. The pool of ancestors continues to shrink until we find the most recent common ancestor (MRCA) of all humans who were alive today, via this particular gene pathway.[2]

Patrilineal and matrilineal MRCA

Mitochondrial DNA (mtDNA) is nearly immune to sexual mixing, unlike the nuclear DNA whose chromosomes are shuffled and recombined in Mendelian inheritance. Mitochondrial DNA, therefore, can be used to trace matrilineal inheritance and to find the Mitochondrial Eve (also known as the African Eve), the most recent common ancestor of all humans via the mitochondrial DNA pathway.

Likewise, Y chromosome is present as a single sex chromosome in the male individual and is passed on to male descendants without recombination. It can be used to trace patrilineal inheritance and to find the Y-chromosomal Adam, the most recent common ancestor of all humans via the Y-DNA pathway.

Mitochondrial Eve and Y-chromosomal Adam have been established by researchers using genealogical DNA tests. Mitochondrial Eve is estimated to have lived about 200,000 years ago. A paper published in March 2013 determined that, with 95% confidence and that provided there are no systematic errors in the study's data, Y-chromosomal Adam lived between 237,000 and 581,000 years ago.[7][8]

The MRCA of humans alive today would, therefore, need to have lived more recently than either.[4][9]

It is more complicated to infer human ancestry via autosomal chromosomes. Although an autosomal chromosome contains genes that are passed down from parents to children via independent assortment from only one of the two parents, genetic recombination (chromosomal crossover) mixes genes from non-sister chromatids from both parents during meiosis, thus changing the genetic composition of the chromosome.

Time to MRCA estimates

Different types of MRCAs are estimated to have lived at different times in the past. These time to MRCA (TMRCA) estimates are also computed differently depending on the type of MRCA being considered. Patrilineal and matrilineal MRCAs (Mitochondrial Eve and Y-chromosomal Adam) are traced by single gene markers, thus their TMRCA are computed based on DNA test results and established mutation rates as practiced in genetic genealogy. Time to genealogical MRCA of all living humans is computed based on non-genetic, mathematical models and computer simulations.

Since Mitochondrial Eve and Y-chromosomal Adam are traced by single genes via a single ancestral parent line, the time to these genetic MRCAs will necessarily be greater than that for the genealogical MRCA. This is because single genes will coalesce more slowly than tracing of conventional human genealogy via both parents. The latter considers only individual humans, without taking into account whether any gene from the computed MRCA actually survives in every single person in the current population.[10]

TMRCA via genetic markers

Mitochondrial DNA can be used to trace the ancestry of a set of populations. In this case, populations are defined by the accumulation of mutations on the mtDNA, and special trees are created for the mutations and the order in which they occurred in each population. The tree is formed through the testing of a large number of individuals all over the world for the presence or lack of a certain set of mutations. Once this is done it is possible to determine how many mutations separate one population from another. The number of mutations, together with estimated mutation rate of the mtDNA in the regions tested, allows scientists to determine the approximate time to MRCA (TMRCA) which indicates time passed since the populations last shared the same set of mutations or belonged to the same haplogroup.

In the case of Y-Chromosomal DNA, TMRCA is arrived at in a different way. Y-DNA haplogroups are defined by single-nucleotide polymorphism in various regions of the Y-DNA. The time to MRCA within a haplogroup is defined by the accumulation of mutations in STR sequences of the Y-Chromosome of that haplogroup only. Y-DNA network analysis of Y-STR haplotypes showing a non-star cluster indicates Y-STR variability due to multiple founding individuals. Analysis yielding a star cluster can be regarded as representing a population descended from a single ancestor. In this case the variability of the Y-STR sequence, also called the microsatellite variation, can be regarded as a measure of the time passed since the ancestor founded this particular population. The descendants of Genghis Khan or one of his ancestors represents a famous star cluster that can be dated back to the time of Genghis Khan.[11]

TMRCA calculations are considered critical evidence when attempting to determine migration dates of various populations as they spread around the world. For example, if a mutation is deemed to have occurred 30,000 years ago, then this mutation should be found amongst all populations that diverged after this date. If archeological evidence indicates cultural spread and formation of regionally isolated populations then this must be reflected in the isolation of subsequent genetic mutations in this region. If genetic divergence and regional divergence coincide it can be concluded that the observed divergence is due to migration as evidenced by the archaeological record. However, if the date of genetic divergence occurs at a different time than the archaeological record, then scientists will have to look at alternate archaeological evidence to explain the genetic divergence. The issue is best illustrated in the debate surrounding the demic diffusion versus cultural diffusion during the European Neolithic.[12]

TMRCA of all living humans

Estimating time to MRCA of all humans based on the common genealogical usage of the term 'ancestor' is much harder and less accurate compared to estimates of patrilineal and matrilineal MRCAs. Researchers must trace ancestry along both female and male parental lines, and rely on historical and archaeological records.

Depending on the survival of isolated lineages without admixture from modern migrations and taking into account long-isolated peoples, such as historical societies in central Africa, Australia and remote islands in the South Pacific, the human MRCA is generally assumed to have lived in the Upper Paleolithic period. Simplistic mathematical models, even those published in the highly regarded journal Nature,[1] can yield wildly inaccurate values for the MRCA, as recent as a few thousand years ago.

Such recent values would be possible if the following occurred: Humanity's MRCA was indeed a Paleolithic individual up to early modern times, but the European explorers of the 16th and 17th centuries fathered enough offspring so that some "mainland" ancestry by today pervades remote habitats. However, this was not part of the simple model mentioned above,[1] and such an explanation does not permit the similarly recent estimates of the identical ancestors point also given in that paper. The possibility remains that an isolated population with no recent "mainland" admixture persists somewhere, which would immediately push back the date of humanity's MRCA by many millennia.

An assumption that there are no isolated populations is questionable in view of the existence of various uncontacted peoples, who are suspected to have been isolated for many millennia, including the Sentinelese, who have been isolated from the rest of the world.

See also

References

  1. 1 2 3 4 5 6 Rohde DL, Olson S, Chang JT; Olson; Chang (September 2004). "Modelling the recent common ancestry of all living humans" (PDF). Nature 431 (7008): 562–6. Bibcode:2004Natur.431..562R. doi:10.1038/nature02842. PMID 15457259.
  2. 1 2 3 See the chapter All Africa and her progenies in Dawkins, Richard (1995). River Out of Eden. New York: Basic Books. ISBN 0-465-06990-8.
  3. ↑ Zhaxybayeva, Olga; Lapierre, Pascal; Gogarten, J. Peter (May 2004). "Genome mosaicism and organismal lineages" (PDF). Trends in Genetics (Department of Molecular and Cell Biology, University of Connecticut: Elsevier) 20 (5): 254–260. doi:10.1016/j.tig.2004.03.009. PMID 15109780. Retrieved 2009-02-19. The Ship of Theseus paradox […] is frequently invoked to illustrate this point […]. Even moderate levels of gene transfer will make it impossible to reconstruct the genomes of early ancestors; …
  4. 1 2 Dawkins, Richard (2004). The Ancestor's Tale, A Pilgrimage to the Dawn of Life. Boston: Houghton Mifflin Company. ISBN 0-618-00583-8.
  5. ↑ Tudge, Colin. (2009). The Link: Uncovering Our Earliest Ancestors. Little Brown.
  6. ↑ Elizabeth Cline (May 22, 2009). "Ida-lized! The Branding of a Fossil". Seed Magazine.
  7. ↑ Mendez, Fernando; Krahn, Thomas; Schrack, Bonnie; Krahn, Astrid-Maria; Veeramah, Krishna; Woerner, August; Fomine, Forka Leypey Mathew; Bradman, Neil; Thomas, Mark; Karafet, Tatiana M.; Hammer, Michael F. (7 March 2013). "An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree" (PDF). American Journal of Human Genetics 92 (3): 454–9. doi:10.1016/j.ajhg.2013.02.002. PMC 3591855. PMID 23453668. (primary source)
  8. ↑ Barrass, Colin (6 March 2013). "The father of all men is 340,000 years old". New Scientist. Retrieved 13 March 2013.
  9. ↑ Notions such as Mitochondrial Eve and Y-chromosomal Adam yield common ancestors that are more ancient than for all living humans (Hartwell 2004:539).
  10. ↑ Chang, Joseph T.; Donnelly, Peter; Wiuf, Carsten; Hein, Jotun; Slatkin, Montgomery; Ewens, W. J.; Kingman, J. F. C. (1999). "Recent common ancestors of all present-day individuals" (PDF). Advances in Applied Probability 31 (4): 1002–26, discussion and author's reply, 1027–38. doi:10.1239/aap/1029955256. Retrieved 2008-01-29.
  11. ↑ Tatiana Zerjal (2003), The Genetic Legacy of the Mongols, http://web.unife.it/progetti/genetica/Giorgio/PDFfiles/ajhg2003.pdf
  12. ↑ Morelli L, Contu D, Santoni F, Whalen MB, Francalacci P; Contu; Santoni; Whalen; Francalacci; Cucca; et al. (2010). Lalueza-Fox, Carles, ed. "A Comparison of Y-Chromosome Variation in Sardinia and Anatolia Is More Consistent with Cultural Rather than Demic Diffusion of Agriculture". PLoS ONE 5 (4): e10419. Bibcode:2010PLoSO...510419M. doi:10.1371/journal.pone.0010419. PMC 2861676. PMID 20454687.

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