Molecular anthropology 3295330 225921675 2008-07-16T00:57:13Z Pdeitiker 2327450 /* The protein era */ '''Molecular anthropology''' is a field of [[anthropology]] in which [[molecular]] analysis is used to determine [[evolutionary]] links between peoples, ancient and modern populations, as well as between contemporary species. Generally, comparisons are made between sequence, either [[Deoxyribonucleic acid|DNA]] or [[protein]] sequence, however early studies used comparative serology. By examining [[DNA sequences]] in different populations, scientist can determine the closeness relationships between populations (or within populations). Certain similarities in genetic makeup let molecular anthropologists determine whether or not different groups of people belong to the same [[haplogroup]], and thus if they share a common [[geographical]] origin. This is significant because it allows anthropologists to trace patterns of [[Human migration|migration]] and [[town|settlement]], which gives helpful insight as to how contemporary populations have formed and progressed over time.<ref>Kottak, Conrad Phillip. ''Windows on Humanity''. New York: McGraw-Hill, 2005.</ref> Molecular anthropology has been extremely useful in establishing the evolutionary tree of humans and other [[primates]], including closely related species like chimps and gorillas. While there are clearly many [[Morphology (biology)|morphological]] similarities between humans and [[chimpanzee]]s, for example, not many would have guessed that the two have roughly 98 percent of their DNA in common.{{Fact|date=July 2008}} Such information is useful in searching for common ancestors and coming to a better understanding of how humans evolved. ==Haploid Loci in molecular anthropology== [[Image:diagram of an animal mitochondrion.svg|thumb|right|Image of mitochondria. There many mitochondrion within a cell, and DNA in these replicated independently of the chromosomes in the nucleus]] There are two continuous [[linkage group]]s in human that are carried by a single sex. The first is the Y-chromosome, which is passed from father to son. Rarely do anatomical females carry a Y chromosome as a result of genetic defect. The other linkage group is the mitochondrial DNA (mtDNA). MtDNA can only be passed to the next generation by females but only under highly exceptional circumstances is mtDNA passed through males. The non-recombinant portion of the Y chromosome and the mtDNA, under normal circumstances, do not undergo productive recombination. Part of Y chromosome can undergo recombination with X chromosome and within ape history the boundary has changed. Such recombinant changes in the non-recombinant region of Y are extremely rare.[Needs picture]{{Fact|date=July 2008}} ===Mitochondrial DNA=== [[Image:Mitochondrial DNA en.svg|thumb|left|300px|Illustration showing mitochondrial DNA, the control region (D-loop, hypervariable regions 1 and II are located on left and right side at the top, respectively)]] Mitochondrial DNA became an area of research in phylogenetics in the late 1970s. Unlike genomic DNA is offered advantages in that it did not undergo recombination. The process of recombination, if requent enough corrupts the ability to create parsimonious trees because stretches of amino acid subsititions (SNPs). When looking between distantly related species, recombination is less of a problem since recombination between branches from common ancestors is prevented after true speciation occurs. When examining closely related species, or branching within species recombination creates a large number of 'irrelevant SNPs' for cladistic analysis. MtDNA, through the process of organelle division, become clonal over time, very little, too often none, of that paternal mtDNA is passed. While recombination may occur in mtDNA, there is little risk that it will be passed to the next generation. As a result mtDNA become clonal copies of each other, except when a new mutation arises. As a result mtDNA does not have pitfalls of autosomal loci when studied in interbreeding groups. Another advantage of mtDNA is that the hyper-variable regions evolve very quickly, this exhibits that certain regions of mitochondrial DNA approach neutrality. This allowed the use of mitochondrial DNA to determine that the relative age of the human population was small having gone through a recent constriction at about 150,000 years ago (see Sources of error). Mitochondrial DNA has also been used to verify the proximity of chimpanzees to humans relative to gorilla, and to verify the relationship of these 3 species relative to orangutan. [[Image:Retrospective population bottleneck.PNG|thumb|right|A population bottleneck, as illustrated was detected by intrahuman mtDNA phylogenetic studies, the length of the bottleneck itself is indeterminant per mtDNA.]] More recently the mtDNA genome has been used to estimate branching patterns in peoples around the world, such as when the new world was settled and how. The problem with these studies have been that they rely heavily on mutations in the coding region. Researchers have increasingly discovered that as humans moved from africas south-eastern regions, that more mutations accumulated in the coding region than expected, and in passage to the new world some groups are believe to have passed from the Asian tropics to Siberia to an ancient land region called Beringia and quickly migrating to south America. Many of the mtDNA have far more mutations and at rarely mutated coding sites relative to expectations of neutral mutations. Mitochondrial DNA offers another advantage over autosomal DNA. There are generally 2 to 4 copies of each chromosome in each cell (1 to 2 from each parent chromosome). For mtDNA there can be dozens to hundreds in each cell. This increases the amount of each mtDNA loci by at least a magnitude. For ancient DNA, in which the DNA is highly degraded, the number of copies of DNA is helpful in extending and bridging short fragments together, and decreases the amount of bone extracted from highly valuable fossil/ancient remains. Unlike Y chromosome both male and female remains carry mtDNA in roughly equal quantities. [[Image:biological cell.svg|thumb|left|Schematic of typical animal cell, showing subcellular components. [[Organelle]]s: (1) [[nucleolus]] (2) [[nucleus]] (9) [[mitochondrion|mitochondria]]]] ===Y chromosome=== [[Image:Chromosome Y.svg|thumb|right|100px|Illustration of [[human Y chromosome]]]] Y chromosome is found in the nucleus of normal cells ([[Nuclear DNA]]). Unlike mtDNA has mutations in the non-recombinant portion (NRY) of the chromosome spaced widely apart, so far apart that finding the mutations on new Y chromosomes is labor intensive relative to mtDNA. Many studies rely on tandem repeats however tandem repeat can expand and retract rapidly and in some predictable patterns. Y chromosome only tracks male lines, and is not found in females, whereas mtDNA can be traced in males even though they fail to pass mtDNA. In addition it has been estimated that effective male populations in the prehistoric period were typically 2 females per male, and recent studies show that cultural hegemony plays a large role in the passage of Y. This has created disconcordance between the time to most recent common ancestor of males and females. The estimates for Y TMRCA range from 1/4th to less than 1/2 that of mtDNA TMRCA. It is unclear whether this is due to high male-to-female ratios in the passed coupled with repeat migrations from africa, as a result of mutational rate change, or some have even proposed that females of the LCA between chimps and humans continued to pass DNA millions after males ceased to pass DNA. At present the best evidence suggests that in migration the male to female ratio in humans may have declined causing a trimming of Y diversity on multiple occasions within and outside of Africa. [[Image:Chromosome X.svg|thumb|left|100px|Diagram of [[human X chromosome]] showing genetic map]] For short range molecular phylogenetics and molecular clocking Y chromosome is highly affective and creates a second perspective. One argument that arose was that the Moari by mtDNA appear to have migrated from Eastern China or Taiwan, by Y chromosome from Papua New Guinea region. When HLA haplotypes were used to evaluate the two hypothesis it was uncovered that both were right, that the Maori were an admixed population. Such admixtures appear to be common in the human population and thus the use of a single haploid loci can give a biased perspective. ==X-linked Studies== The X-chromosome is also a form of nuclear DNA. Since it is found as 1 copy in males and 2 non-identical chromsomes in females it has a [[ploidy]] of 1.5. However, in humans the effective ploidy is somewhat higher, ~1.7, as females in the breeding population have tended to outnumber males by 2:1 during a large portion of human prehistory. Like mtDNA, X-linked DNA tends to over emphasize female population history much more than male. There have been several studies of loci on X chromosome, in total 20 sites have been examined. These include PDHA1, PDHA1, Xq21.3, Xq13.3, [[Zfx]], Fix, Il2rg, Plp, Gk, Ids, Alas2, Rrm2p4, AmeIX, Tnfsf5, Licam, and Msn. The time to most recent common ancestor(TMRCA) ranges from fixed to ~1.8 million years, with a median around 700ky. These studies roughly plot to the expected fixation distribution of alleles, given linkage disequilibrium between adjacent sites. For some alleles the point of origin is elusive, for others, the point of origin points toward Sub-saharan Africa. There are some distinctions within SSA that suggest a smaller region, but there is not adequate enough sample size and coverage to define a place of most recent common ancestor. The TMRCA is consistent with and extends the bottleneck implied by mtDNA, confidently to about 500,000 years. ==Autosomal Loci== [[Image:Karyotype.png|thumb|right|300px|Diagram of [[human karyotype]]]] ==Rate variation== ==Ancient DNA sequencing== Since Krings Neandertal mtDNA have been sequenced, and the sequence similarity indicates an equally recent origin from a small population on the Neanderthal branch of late hominids. MCR1 gene has also been sequenced but the results are controversial, with one study claiming that contamination issues cannot be resolved from human Neandertal similarities. Critically however no DNA sequence has been obtained from Homo erectus, Homo floriensis, or any of the other late hominids. Some of the ancient sequences obtained have highly probable errors, and proper control to avoid contamination. [[Image:Human-Neandertal mtDNA.gif‎|thumb|left|Comparison of differences between human and Neanderthal mtDNA]] ==Causes of errors== {{underconstruction}} The molecular phylogenetics is based on quantitating substitutions and then comparing sequence with other species, there are several points in the process which create errors. The first and greatest challenge is finding "anchors" that allow the research to calibrate the system. In this example, there are 10 mutations between chimp and humans, but the researcher has no known fossils that are agreeably ancestral to both but not ancestral to the next species in the tree, gorilla. However, there are fossils believed to be ancestral to Orangutans and Humans, from about 14 million years ago. So that the researcher can use Orangutan and Human comparison and comes up with a difference of 24. Using this he can estimate (24/(14*2, the "2" is for the length of the branch to Human (14my) and the branch to Orangutan (14 my) from their last common ancestor (LCA). The mutation rate at 0.857 for a stretch of sequence. Mutation rates are given, however, as rate per nucleotide(nt)-site, so if the sequence were say 100 nt in length that rate would be 0.00857/nt per million years. Ten mutations*100nt/(0.00857*2) = 5.8 million years.</br> ===The problem of calibration=== There are several problems not seen in the above. First, mutations occur as random events. Second, the chance that any site in the genome varies is different from the next site, a very good example is the codons for amino acids, the first two nt in a codon may mutate at 1 per billion years, but the third nt may mutate 1 per million years. Unless scientist study the sequence of a great many animals, particularly those close to the branch being examined, they generally do not know what the rate of mutation for a given site. Mutations do occur at 1st and 2nd positions of codons, but in most cases these mutations are under negative selection and so are removed from the population over small periods of time. In defining the rate of evolution in the anchor one has the problem that random mutation creates. For example a rate of .005 or .010 can also explain 24 mutations according to the [[binomial probability distribution]]. Some of the mutations that did occur between the two have reverted, hiding an initially higher rate. Selection may play into this, a rare mutation may be selective at point X in time, but later climate may change or the species migrates and it is not longer selective, and pressure exerted on new mutations that revert the change, and sometimes the reversion of a nt can occur, the greater the distance between two species the more likely this is going to occur. In addition, from that ancestral species both species may randomly mutate a site to the same nucleotide. Many times this can be resolved by obtaining DNA samples from species in the branches, creating a parsimonious tree in which the order of mutation can be deduced, creating branch-length diagram. This diagram will then produce a more accurate estimate of mutations between two species. Statistically one can assign variance based on the problem of randomnicity, back mutations, and parallel mutations (homoplasies) in creating an error range. There is another problem in calibration however that has defied statistical analysis. There is a true/false designation of a fossil to an least common ancestor. In reality the odds of having the least common ancestor of two extant species as an anchor is low, often that fossil already lies in one branch (underestimating the age), lies in a third branch (underestimating the age) or in the case of being within the LCA species, may have been millions of years older than the branch. To date the only way to assess this variance is to apply molecular phylogenetics on species claimed to be branch points. This only, however identifies the 'outlying' anchor points. And since it is more likely the more abundant fossils are younger than the branch point the outlying fossil may simply be a rare older representative. These unknowns create uncertainty that is difficult to quantitate, and often not attempted. Recent papers have been able to estimate, roughly, variance. The general trend as new fossils are discovered, is that the older fossils underestimated the age of the branch point. In addition to this dating of fossils has had a history of errors and there have been many revised datings. The age assigned by researchers to some major branch points have almost doubled in age over the last 30 years. An excellent example of this is the debate over LM3 (Mungo lake 3) in Australia. Originally it was dated to around 30 ky by carbon dating, carbon dating has problems, however, for sampled over 20ky in age, and severe problems for samples around 30ky in age. Another study looked at the fossil and estimated the age to be 62 ky in age. At the point one has an estimation of mutation rate, given the above there must be two sources of variance that need to be cross-multiplied to generate an overall variance. This is infrequently done in the literature. ===Problems in estimating TMRCA=== Time to most recent common ancestor ('''TMRCA''') combines the errors in calibration with errors in determining the age of a local branch. ==History of Molecular Anthropology== ===The protein era=== [[Image:1GZX Haemoglobin.png|thumb|right|Structure of human hemoglobin. Hemoglobins from dozens of animals and even plants were sequenced in the 1960s and early 1970s}}]] With DNA newly discovered as the genetic material, in the early 1960s protein sequencing was beginning to take off.<ref>A.C.Wilson and N.O.Kaplan (1963) Enzymes and nucleic acids in systematics. Proceedings of the XVI International Congress of Zoology Vol.4, pp.125-127.</ref> Protein sequencing began on cytochrome C and Hemoglobin. [http://de.wikipedia.org/wiki/Gerhard_Braunitzer G. Braunizter] sequenced [[hemoglobin]] and [[myoglobin]], in total more than 100s of sequences from wide ranging species were done. In 1967 [[Allan Wilson|A.C. Wilson]] began to promote the idea of a "molecular clock". By 1969 molecular clocking was applied to anthropoid evolution and [[Vincent Sarich|V. Sarich]] and A.C. Wilson found that albumin and hemoglobin has comparable rates of evolution, indicating [[chimp]]s and humans split about 4 to 5 million years ago.<ref name="pmid4982244">{{cite journal |author=Wilson AC, Sarich VM |title=A molecular time scale for human evolution |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=63 |issue=4 |pages=1088–93 |year=1969 |month=August |pmid=4982244 |pmc=223432 |doi= |url=}}</ref> In 1970, [[Louis Leakey]] confronted this conclusion with arguing for improper calibration of molecular clocks.<ref name="pmid5002096">{{cite journal |author=Leakey LS |title=The relationship of African apes, man and old world monkeys |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=67 |issue=2 |pages=746–8 |year=1970 |month=October |pmid=5002096 |pmc=283268 |doi= |url=}}</ref> By 1975 [[protein sequencing]] and comparative [[serology]] combined were used to propose that humans closest living relative (as a [[species]]) was the [[chimpanzee]].<ref name="pmid1090005">{{cite journal |author=King MC, Wilson AC |title=Evolution at two levels in humans and chimpanzees |journal=Science (journal) |volume=188 |issue=4184 |pages=107–16 |year=1975 |month=April |pmid=1090005 |doi= |url=http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=1090005}}</ref> In hindsight, the [[last common ancestor]] (LCA) from humans and chimps appears to older than the ''Sarich and Wilson'' estimate, but not as old as Leakey claimed , either. However, Leakey was correct in the divergence of old and new world monkeys, the value Sarich and wilson used was a significant underestimate. This error in prediction capability highlights a common theme. (See [[#Causes of error|Causes of Error]]) ===The DNA era=== [[Image:Mitochondrial DNA en.svg|thumb|left|Restriction fragment length polymorphisms studies the cutting of mtDNA into fragements, Later the focus of PCR would be on the D 'contol'-loop, at the top of the circle]] ====RLFP and DNA hybridization==== In 1979. W.M.Brown and Wilson began looking at the evolution of [[mtDNA|mitochodrial DNA]] in animals, and found they were evolving rapidly.<ref name="pmid109836">{{cite journal |author=Brown WM, George M, Wilson AC |title=Rapid evolution of animal mitochondrial DNA |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=76 |issue=4 |pages=1967–71 |year=1979 |month=April |pmid=109836 |pmc=383514 |doi= |url=}}</ref> The technique they used was [[restriction fragment length polymorphism]]('''RFLP''') which was more affordable at the time compared to sequencing. In 1980, W.M. Brown, looking at the relative variation between human and other species, recognizes there was a recent [[Population constriction|constriction]] (180,000 years ago) in the human population.<ref name="pmid6251473">{{cite journal |author=Brown WM |title=Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=77 |issue=6 |pages=3605–9 |year=1980 |month=June |pmid=6251473 |pmc=349666 |doi= |url=}}</ref> A year later Brown and Wilson were looking at RFLP fragments and determined the human population expanded more recently than other ape populations.<ref name="pmid6273863">{{cite journal |author=Ferris SD, Brown WM, Davidson WS, Wilson AC |title=Extensive polymorphism in the mitochondrial DNA of apes |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=78 |issue=10 |pages=6319–23 |year=1981 |month=October |pmid=6273863 |pmc=349030 |doi= |url=}}</ref>. In 1984 the first DNA sequence from an extinct animal was done.<ref name="pmid6504142">{{cite journal |author=Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC |title=DNA sequences from the quagga, an extinct member of the horse family |journal=Nature |volume=312 |issue=5991 |pages=282–4 |year=1984 |pmid=6504142 |doi= |url=}}</ref> Sibley and Ahlquist apply DNA-DNA hybridization technology to anthropoid phylogeny, and see pan/human split closer than gorilla/pan or gorilla/human split, a highly controversial claim.<ref name="pmid6429338">{{cite journal |author=Sibley CG, Ahlquist JE |title=The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization |journal=J. Mol. Evol. |volume=20 |issue=1 |pages=2–15 |year=1984 |pmid=6429338 |doi= |url=}}</ref><ref name="pmid3939706">{{cite journal |author=Templeton AR |title=The phylogeny of the hominoid primates: a statistical analysis of the DNA-DNA hybridization data |journal=Mol. Biol. Evol. |volume=2 |issue=5 |pages=420–33 |year=1985 |month=September |pmid=3939706 |doi= |url=http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=3939706}}</ref> However, in 1987 they were able to support their claim.<ref name="pmid3125341">{{cite journal |author=Sibley CG, Ahlquist JE |title=DNA hybridization evidence of hominoid phylogeny: results from an expanded data set |journal=J. Mol. Evol. |volume=26 |issue=1-2 |pages=99–121 |year=1987 |pmid=3125341 |doi= |url=}}</ref> In 1987, Cann, Stoneking and Wilson suggest, by RFLP analysis of human mitochondrial DNA, that humans evolved from a constrict in Africa of a single female in a small populations, ~10,00 individuals, 200,000 years ago.<ref name="pmid3025745">{{cite journal |author=Cann RL, Stoneking M, Wilson AC |title=Mitochondrial DNA and human evolution |journal=Nature |volume=325 |issue=6099 |pages=31–6 |year=1987 |pmid=3025745 |doi=10.1038/325031a0 |url=}}</ref> ====The era of PCR==== [[Image:PCR.svg|thumb|right|PCR could rapidly amplify DNA from 1 molecule to billions allowing sequencing from human hairs or ancient DNA]] In 1987, PCR-amplification of mtDNA was first used to determine sequences.<ref name="pmid2881260">{{cite journal |author=Wrischnik LA, Higuchi RG, Stoneking M, Erlich HA, Arnheim N, Wilson AC |title=Length mutations in human mitochondrial DNA: direct sequencing of enzymatically amplified DNA |journal=Nucleic Acids Res. |volume=15 |issue=2 |pages=529–42 |year=1987 |month=January |pmid=2881260 |pmc=340450 |doi= |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=2881260}}</ref> In 1991 Vigilante et al. published the seminal work on mtDNA phylogeny implicating sub-saharan africa as the place of humans most recent common ancestors for all mtDNAs.<ref name="pmid1840702">{{cite journal |author=Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC |title=African populations and the evolution of human mitochondrial DNA |journal=Science (journal) |volume=253 |issue=5027 |pages=1503–7 |year=1991 |month=September |pmid=1840702 |doi= |url=http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=1840702}}</ref> The war between out-of-africa and multiregionalism, already simmering with the critiques of Allan Templeton, soon escalated with the paleoanthropologist, like Milford Wolpoff, getting involved.<ref>Templeton AR. ''The 'Eve' Hypothesis: A genetic critique and reanalysis''. American Anthropologist 95: 51-72.</ref><ref>Thorne A and Wolpoff M. ''The multiregional evolution of Humans''.Scientific American (April) pp.28-33 (1992)</ref><ref>Wolpoff M and Thorne A. The case against Eve. New Scientist (1991) pp.37-41.</ref> In 1995, F. Ayala published his critical Science article 'The Myth about Eve', which relied on [[HLA-DR]] sequence.<ref name="pmid8533083">{{cite journal |author=Ayala FJ |title=The myth of Eve: molecular biology and human origins |journal=Science (journal) |volume=270 |issue=5244 |pages=1930–6 |year=1995 |month=December |pmid=8533083 |doi= |url=http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=8533083}}</ref> At the time, however Ayala was not aware of rapid evolution of HLA loci via recombinatory process. In 1996, Parham and Ohta published their finds on the rapid evolution of HLA by short-distance recombination ('gene conversion' or 'abortive recombination'), weakening Ayala's claim (Parham had actually written a review a year earlier, but this had gone unnoticed).<ref name="pmid8600539">{{cite journal |author=Parham P, Ohta T |title=Population biology of antigen presentation by MHC class I molecules |journal=Science (journal) |volume=272 |issue=5258 |pages=67–74 |year=1996 |month=April |pmid=8600539 |doi= |url=http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=8600539}}</ref><ref name="pmid7558075">{{cite journal |author=Parham P, Adams EJ, Arnett KL |title=The origins of HLA-A,B,C polymorphism |journal=Immunol. Rev. |volume=143 |issue= |pages=141–80 |year=1995 |month=February |pmid=7558075 |doi= |url=}}</ref> A stream of papers would follow from both sides, many with highly flawed methods and sampling. One of the more interesting was Harris and Hey, 1998 which showed that the TMCRA (time to most recent common ancestor) for the PDHA1 gene was well in excess of 1 million years. Given a [[ploidy]] at this locus of 1.5 (3 fold higher then mtDNA) the TMRCA was more than double the expectation. While this falls into the 'fixation curve' of 1.5 ploidy (Averaging 2 female and 1 male) the suggested age of 1.8 my is close a significantly deviant p-value for the population size, possibly indicating that the human population shrank or split off of another population.<ref name="pmid10077682">{{cite journal |author=Harris EE, Hey J |title=X chromosome evidence for ancient human histories |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=96 |issue=6 |pages=3320–4 |year=1999 |month=March |pmid=10077682 |pmc=15940 |doi= |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=10077682}}</ref> Oddly, the next X-linked loci they examined, Factor IX, showed a TMRCA of less than 300,000 years. <ref name="pmid11378388">{{cite journal |author=Harris EE, Hey J |title=Human populations show reduced DNA sequence variation at the factor IX locus |journal=Curr. Biol. |volume=11 |issue=10 |pages=774–8 |year=2001 |month=May |pmid=11378388 |doi= |url=http://linkinghub.elsevier.com/retrieve/pii/S0960-9822(01)00223-8}}</ref> [[Image:Ancient DNA.png|thumb|left|Cross-linked DNA extracted from the 4,000 year-old liver of an Ancient Egyptian priest Called Nekht-Ankh.]] ====Ancient DNA==== Ancient DNA sequencing had been conducted on a limited scale up to the late 1990s when the folks at the Max Plank Institute would shock the anthropology world by sequencing DNA from an estimated 40,000 year old [[Neanderthal]].<ref name="pmid8020612">{{cite journal |author=Handt O, Höss M, Krings M, Pääbo S |title=Ancient DNA: methodological challenges |journal=Experientia |volume=50 |issue=6 |pages=524–9 |year=1994 |month=June |pmid=8020612 |doi= |url=}}</ref><ref name="pmid8755923">{{cite journal |author=Handt O, Krings M, Ward RH, Pääbo S |title=The retrieval of ancient human DNA sequences |journal=Am. J. Hum. Genet. |volume=59 |issue=2 |pages=368–76 |year=1996 |month=August |pmid=8755923 |pmc=1914746 |doi= |url=}}</ref><ref name="pmid9230299">{{cite journal |author=Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S |title=Neandertal DNA sequences and the origin of modern humans |journal=Cell |volume=90 |issue=1 |pages=19–30 |year=1997 |month=July |pmid=9230299 |doi= |url=http://linkinghub.elsevier.com/retrieve/pii/S0092-8674(00)80310-4}}</ref> The results of that experiment is that the differences between humans living in Europe, many of which were derived from haplogroup H (CRS), Neandertals branched from humans more than 300,000 years before haplogroup H reached Europe. While the mtDNA and other studies continued to support a unique recent african origin, this new study basically answered critiques from the Neandertal side. ====Genomic Sequencing==== Significant progress has been made in genomic sequencing since Ingman and colleage published their finding on mitochondrial genome.<ref name="pmid11130070">{{cite journal |author=Ingman M, Kaessmann H, Pääbo S, Gyllensten U |title=Mitochondrial genome variation and the origin of modern humans |journal=Nature |volume=408 |issue=6813 |pages=708–13 |year=2000 |month=December |pmid=11130070 |doi=10.1038/35047064 |url=}}</ref> Several papers on genomic mtDNA have been published, there is considerable variability in the rate of evolution, and rate variation and selection are evident at many sites. In 2007 Gonder et al, proposed that a core population of humans, with greatest level of diversity and lowest selection once lived in the region of Tanzania and proximal parts of southern Africa, since humans left this part of Africa, mitochondria have been selectively evolving to new regions.<ref name="pmid17194802">{{cite journal |author=Gonder MK, Mortensen HM, Reed FA, de Sousa A, Tishkoff SA |title=Whole-mtDNA genome sequence analysis of ancient African lineages |journal=Mol. Biol. Evol. |volume=24 |issue=3 |pages=757–68 |year=2007 |month=March |pmid=17194802 |doi=10.1093/molbev/msl209 |url=}}</ref> ===Critical Progress=== Critical in the history of molecular anthropology. * That molecular phylogenetics could compete with comparative anthropology for determining the proximity of species to humans. * Wilson and King realized in 1975, that while there was equity between the level of molecular evolution branching from chimp to human to putative LCA, that there was an inequity in morphological evolution. Comparative morphology based on fossils could be biased by different rates of change.<ref name="pmid1090005">{{cite journal |author=King MC, Wilson AC |title=Evolution at two levels in humans and chimpanzees |journal=Science (journal) |volume=188 |issue=4184 |pages=107–16 |year=1975 |month=April |pmid=1090005 |doi= |url=http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=1090005}}</ref> * Realization that in DNA there are multiple independent comparisons. Two techniques, mtDNA and hybridization converge on a single answer, chimps as a species are most closely related to humans. * The ability to resolve population sizes based on the 2N rule, proposed by Kimura in the 1950s.<ref name="pmid17247483">{{cite journal |author=Kimura M |title=Process Leading to Quasi-Fixation of Genes in Natural Populations Due to Random Fluctuation of Selection Intensities |journal=Genetics |volume=39 |issue=3 |pages=280–95 |year=1954 |month=May |pmid=17247483 |pmc=1209652 |doi= |url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=17247483}}</ref> To use that information to compare relative sizes of population and come to a conclusion about abundance that contrasted observations based on the paleontological record. While human fossils in the early and middle stone age are far more abundant than Chimpazee or Gorilla, there are few unambiguous chimpanzee or gorilla fossils from the same period Loci that have been used in molecular phylogenetics. :[[Cytochrome C]] :[[Serum Albumin]] :[[Hemoglobin]] - Braunitizer, 1960s, Harding et al. 1997 :[[D-loop|Mitochondrial D-loop]] - Wilson group, 1980, 1981, 1984, 1987, 1989, 1991(posthumously) - TMRCA about 170 kya. :[[Y-chromosome]] :[[HLA-DR]] - Ayala 1995 - TMRCA for locus is 60 million years. :[[CD4]] (Intron) - Tishkoff, 1996 - most of the diversity is in Africa. :[[PDHA1]] (X-linked) Harris and Hey - TMRCA for locus greater than 1.5 million years. Xlinked loci: PDHA1, Xq21.3, Xq13.3, [[Zfx]], Fix, Il2rg, Plp, Gk, Ids, Alas2, Rrm2p4, AmeIX, Tnfsf5, Licam, and Msn Autosomal:Numerous. == References == {{reflist|2}} == Links == * [http://authors.library.caltech.edu/5456/01/hrst.mit.edu/hrs/evolution/public/profiles/wilson.html Allan Wilson - Recent History of Science and Technology] * [http://tech.groups.yahoo.com/group/DNAanthro/ DNAanthro - Molecular Anthropology - Tech groups - Yahoo (a free discussion group)] [[Category:Genetic genealogy]]