DNA and recent human evolution

Geographical, environmental and pathophysiological influences on the human blood transcriptome

Gene expression variation provides a read-out of both genetic and environmental influences on gene activity. Geographical, genomic and sociogenomic studies have highlighted how life circumstances of an individual modify the expression of hundreds and in some cases thousands of genes in a co-ordinated manner. This review places such results in the context of a conserved set of 90 transcripts known as Blood Informative Transcripts (BIT) that capture the major conserved components of variation in the peripheral blood transcriptome. Pathophysiological states are also shown to associate with the perturbation of transcript abundance along the major axes. Discussion of false negative rates leads us to argue that simple significance thresholds provide a biased perspective on assessment of differential expression that may cloud the interpretation of studies with small sample sizes.

The revolution that didn't arrive: A review of Pleistocene Sahul

There is a "package" of cultural innovations that are claimed to reflect modern human behaviour. The introduction of the "package" has been associated with the Middle-to-Upper Palaeolithic transition and the appearance in Europe of modern humans. It has been proposed that modern humans spread from Africa with the "package" and colonised not only Europe but also southern Asia and Australia (McBrearty and Brooks, 2000; Mellars, 2006a). In order to evaluate this proposal, we explore the late Pleistocene archaeological record of Sahul, the combined landmass of Australia and Papua New Guinea, for indications of these cultural innovations at the earliest sites. It was found that following initial occupation of the continent by anatomically and behaviourally modern humans, the components were gradually assembled over a 30,000-year period. We discount the idea that the "package" was lost en route to Sahul and assess the possibility that the "package" was not integrated within the material culture of the initial colonising groups because they may not have been part of a rapid colonisation process from Africa. As the cultural innovations appear at different times and locations within Sahul, the proposed "package" of archaeologically visible traits cannot be used to establish modern human behaviour. Whilst the potential causal role of increasing population densities/pressure in the appearance of the "package" of modern human behaviour in the archaeological record is acknowledged, it is not seen as the sole explanation because the individual components of the "package" appear at sites that are widely separated in space and time.

Metric dental variation of major human populations

Mesiodistal and buccolingual crown diameters of all teeth recorded in 72 major human population groups and seven geographic groups were analyzed. The results obtained are fivefold. First, the largest teeth are found among Australians, followed by Melanesians, Micronesians, sub-Saharan Africans, and Native Americans. Philippine Negritos, Jomon/Ainu, and Western Eurasians have small teeth, while East/Southeast Asians and Polynesians are intermediate in overall tooth size. Second, in terms of odontometric shape factors, world extremes are Europeans, aboriginal New World populations, and to a lesser extent, Australians. Third, East/Southeast Asians share similar dental features with sub-Saharan Africans, and fall in the center of the phenetic space occupied by a wide array of samples. Fourth, the patterning of dental variation among major geographic populations is more or less consistent with those obtained from genetic and craniometric data. Fifth, once differences in population size between sub-Saharan Africa, Europe, South/West Asia, Australia, and Far East, and genetic drift are taken into consideration, the pattern of sub-Saharan African distinctiveness becomes more or less comparable to that based on genetic and craniometric data. As such, worldwide patterning of odontometric variation provides an additional avenue in the ongoing investigation of the origin(s) of anatomically modern humans.

MITOCHONDRIAL DNA AND HUMAN EVOLUTION

Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history.

Genetic variation in gorillas

This review summarizes what is currently known concerning genetic variation in gorillas, on both inter- and intraspecific levels. Compared to the human species, gorillas, along with the other great apes, possess greater genetic variation as a consequence of a demographic history of rather constant population size. Data and hence conclusions from analysis of mitochondrial DNA (mtDNA), the usual means of describing intraspecific patterns of genetic diversity, are limited at this time. An important task for future studies is to determine the degree of confidence with which gorilla mtDNA can be analyzed, in view of the risk that one will inadvertently analyze artifactual rather than genuine sequences. The limited information available from sequences of nuclear genomic segments does not distinguish western from eastern gorillas, and, in comparison with results from the two chimpanzee species, suggests a relatively recent common ancestry for all gorillas. In the near future, the greatest insights are likely to come from studies aimed at genetic characterization of all individual members of social groups. Such studies, addressing topics such as behavior of individuals with kin and non-kin, and the actual success of male reproductive strategies, will provide a link between behavioral and genetic studies of gorillas.

Characterization of biological diversity through analysis of discrete cranial traits

In the present study, the frequency distributions of 20 discrete cranial traits in 70 major human populations from around the world were analyzed. The principal-coordinate and neighbor-joining analyses of Smith's mean measure of divergence (MMD), based on trait frequencies, indicate that 1). the clustering pattern is similar to those based on classic genetic markers, DNA polymorphisms, and craniometrics; 2). significant interregional separation and intraregional diversity are present in Subsaharan Africans; 3). clinal relationships exist among regional groups; 4). intraregional discontinuity exists in some populations inhabiting peripheral or isolated areas. For example, the Ainu are the most distinct outliers of the East Asian populations. These patterns suggest that founder effects, genetic drift, isolation, and population structure are the primary causes of regional variation in discrete cranial traits. Our results are compatible with a single origin for modern humans as well as the multiregional model, similar to the results of Relethford and Harpending ([1994] Am. J. Phys. Anthropol. 95:249-270). The results presented here provide additional measures of the morphological variation and diversification of modern human populations.

Mitochondrial DNA sequence analysis in Sicily

This study reports data on the sequences of the first hypervariable segment of a sample of the Sicilian population from Alia (Palermo, Italy). The results show the presence of 32 different haplotypes in the 49 individuals examined. The average number of pairwise nucleotide differences was 4.04, i.e., 1.17% per nucleotide. The distribution of the nucleotide differences matches the theoretical distribution and indicates only one major episode of expansion that occurred between 20,732 and 59,691 years ago, between the Middle Paleolithic and Upper Paleolithic. Compared with the other populations, parameters of the Sicilian sample lie in an intermediate position between the eastern and western Mediterranean populations. This is due to numerous contacts that Sicily has had with the Mediterranean area since prehistoric times. At the same time, the singularity of some of the haplotypes present in the sample studied indicates the persistence of some characteristics caused by genetic drift and isolation that the population has endured in the course of its history.

The revolution that wasn't: a new interpretation of the origin of modern human behavior

Proponents of the model known as the "human revolution" claim that modern human behaviors arose suddenly, and nearly simultaneously, throughout the Old World ca. 40-50 ka. This fundamental behavioral shift is purported to signal a cognitive advance, a possible reorganization of the brain, and the origin of language. Because the earliest modern human fossils, Homo sapiens sensu stricto, are found in Africa and the adjacent region of the Levant at >100 ka, the "human revolution" model creates a time lag between the appearance of anatomical modernity and perceived behavioral modernity, and creates the impression that the earliest modern Africans were behaviorally primitive. This view of events stems from a profound Eurocentric bias and a failure to appreciate the depth and breadth of the African archaeological record. In fact, many of the components of the "human revolution" claimed to appear at 40-50 ka are found in the African Middle Stone Age tens of thousands of years earlier. These features include blade and microlithic technology, bone tools, increased geographic range, specialized hunting, the use of aquatic resources, long distance trade, systematic processing and use of pigment, and art and decoration. These items do not occur suddenly together as predicted by the "human revolution" model, but at sites that are widely separated in space and time. This suggests a gradual assembling of the package of modern human behaviors in Africa, and its later export to other regions of the Old World. The African Middle and early Late Pleistocene hominid fossil record is fairly continuous and in it can be recognized a number of probably distinct species that provide plausible ancestors for H. sapiens. The appearance of Middle Stone Age technology and the first signs of modern behavior coincide with the appearance of fossils that have been attributed to H. helmei, suggesting the behavior of H. helmei is distinct from that of earlier hominid species and quite similar to that of modern people. If on anatomical and behavioral grounds H. helmei is sunk into H. sapiens, the origin of our species is linked with the appearance of Middle Stone Age technology at 250-300 ka.

Mitochondrial control-region sequence variation in the Corsican population, France

The mtDNA sequence variation of the hypervariable segment I of the control region was studied in 47 unrelated individuals of Corsican origin from Corte (Corsica, France). Thirty-one different sequences were identified by 40 variable sites, of which five involve transversions. The nucleotide diversity among the sequences was estimated as 1.03%. The pairwise difference agreed with the model proposed by Rogers and Harpending ([1992] Mol Biol Evol 9:552-569) and appeared bell-shaped, with only one peak at 3.71, indicating the occurrence of a single episode of demographic expansion roughly 14,443 to 41,584 years ago. From our results it seems that the ancestral Corsican population expanded more recently than all other studied European populations. Compared to other populations by genetic distances and a neighbor-joining tree, Corsicans appear most closely linked to the Basques and Sardinians than to other populations. Although the results substantiate an east-to-west migration, some problems are evident: 1) the estimates of demographic expansion are not in agreement with paleontological data; 2) the expansion occurred later than the expansion of the Sardinian population; and 3) the genetic affinity between Corsicans, Basques, and Sardinians. Answers will need to come from archaeological, paleontological, genetic, geological, and climatological observations. Finally, the study of mtDNA confirms what had already been shown with classic genetic markers. Am. J. Hum. Biol. 12:339-351, 2000. Copyright 2000 Wiley-Liss, Inc.

The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data

We report a comparison of worldwide genetic variation among 255 individuals by using autosomal, mitochondrial, and Y-chromosome polymorphisms. Variation is assessed by use of 30 autosomal restriction-site polymorphisms (RSPs), 60 autosomal short-tandem-repeat polymorphisms (STRPs), 13 Alu-insertion polymorphisms and one LINE-1 element, 611 bp of mitochondrial control-region sequence, and 10 Y-chromosome polymorphisms. Analysis of these data reveals substantial congruity among this diverse array of genetic systems. With the exception of the autosomal RSPs, in which an ascertainment bias exists, all systems show greater gene diversity in Africans than in either Europeans or Asians. Africans also have the largest total number of alleles, as well as the largest number of unique alleles, for most systems. GST values are 11%-18% for the autosomal systems and are two to three times higher for the mtDNA sequence and Y-chromosome RSPs. This difference is expected because of the lower effective population size of mtDNA and Y chromosomes. A lower value is seen for Y-chromosome STRs, reflecting a relative lack of continental population structure, as a result of rapid mutation and genetic drift. Africa has higher GST values than does either Europe or Asia for all systems except the Y-chromosome STRs and Alus. All systems except the Y-chromosome STRs show less variation between populations within continents than between continents. These results are reassuring in their consistency and offer broad support for an African origin of modern human populations.

Direct radiocarbon dates for Vindija G(1) and Velika Pecína late Pleistocene hominid remains

New accelerator mass spectrometry radiocarbon dates taken directly on human remains from the Late Pleistocene sites of Vindija and Velika Pecina in the Hrvatsko Zagorje of Croatia are presented. Hominid specimens from both sites have played critical roles in the development of current perspectives on modern human evolutionary emergence in Europe. Dates of approximately 28 thousand years (ka) before the present (B.P.) and approximately 29 ka B.P. for two specimens from Vindija G(1) establish them as the most recent dated Neandertals in the Eurasian range of these archaic humans. The human frontal bone from Velika Pecina, generally considered one of the earliest representatives of modern humans in Europe, dated to approximately 5 ka B.P., rendering it no longer pertinent to discussions of modern human origins. Apart from invalidating the only radiometrically based example of temporal overlap between late Neandertal and early modern human fossil remains from within any region of Europe, these dates raise the question of when early modern humans first dispersed into Europe and have implications for the nature and geographic patterning of biological and cultural interactions between these populations and the Neandertals.

Molecular characterization of HLA class I in Colombians carrying HLA-A2: high allelic diversity and frequency of heterozygotes at the HLA-B locus

Polymerase chain reaction using sequence-specific oligonucleotide probes (PCR-SSOP) typing was used to analyze HLA class I A, B and C alleles in three different Colombian populations. Fifty-nine samples were from Hispano-American Mestizos living in the urban areas of Cali (referred to here as Aso population). Forty-four and thirty samples were from the African Black populations of Zacarias (Zac) and Punta Soldado (PS), respectively. Samples were selected for expression of HLA-A2 by monoclonal antibody staining and allele-specific hybridization, and their HLA-A2 subtype distribution has been reported previously. Although only a limited number of samples was analyzed, the data suggest the existence of a remarkable degree of HLA class I polymorphism in the populations studied, with representatives of most serological classes. Despite their common African origin, the populations Zac and PS, both resident in malaria endemic regions, showed some striking differences in allelic distribution for all three class I loci. Furthermore, the samples from Aso and PS, but not Zac, showed a low percentage of blank alleles at the HLA-B locus (0 and 0.4%, respectively), suggesting the possibility of a heterozygote advantage for HLA-B alleles in Colombian populations.

Towards a theory of modern human origins: geography, demography, and diversity in recent human evolution

The origins of modern humans have been the central debate in palaeoanthropology during the last decade. We examine the problem in the context of the history of anthropology, the accumulating evidence for a recent African origin, and evolutionary mechanisms. Using a historical perspective, we show that the current controversy is a continuation of older conflicts and as such relates to questions of both origins and diversity. However, a better fossil sample, improved dates, and genetic data have introduced new perspectives, and we argue that evolutionary geography, which uses spatial distributions of populations as the basis for integrating contingent, adaptive, and demographic aspects of microevolutionary change, provides an appropriate theoretical framework. Evolutionary geography is used to explore two events: the evolution of the Neanderthal lineage and the relationship between an ancestral bottleneck with the evolution of anatomically modern humans and their diversity. We argue that the Neanderthal and modern lineages share a common ancestor in an African population between 350,000 and 250,000 years ago rather than in the earlier Middle Pleistocene; this ancestral population, which developed mode 3 technology (Levallois/Middle Stone Age), dispersed across Africa and western Eurasia in a warmer period prior to independent evolution towards Neanderthals and modern humans in stage 6. Both lineages would thus share a common large-brained ancestry, a technology, and a history of dispersal. They differ in the conditions under which they subsequently evolved and their ultimate evolutionary fate. Both lineages illustrate the repeated interactions of the glacial cycles, the role of cold-arid periods in producing fragmentation of populations, bottlenecks, and isolation, and the role of warmer periods in producing trans-African dispersals.

Late Pleistocene human population bottlenecks, volcanic winter, and differentiation of modern humans

The "Weak Garden of Eden" model for the origin and dispersal of modern humans (Harpending et al., 1993) posits that modern humans spread into separate regions from a restricted source, around 100 ka (thousand years ago), then passed through population bottlenecks. Around 50 ka, dramatic growth occurred within dispersed populations that were genetically isolated from each other. Population growth began earliest in Africa and later in Eurasia and is hypothesized to have been caused by the invention and spread of a more efficient Later Stone Age/Upper Paleolithic technology, which developed in equatorial Africa. Climatic and geological evidence suggest an alternative hypothesis for Late Pleistocene population bottlenecks and releases. The last glacial period was preceded by one thousand years of the coldest temperatures of the Later Pleistocene (approximately 71-70 ka), apparently caused by the eruption of Toba, Sumatra. Toba was the largest known explosive eruption of the Quaternary. Toba's volcanic winter could have decimated most modern human populations, especially outside of isolated tropical refugia. Release from the bottleneck could have occurred either at the end of this hypercold phase, or 10,000 years later, at the transition from cold oxygen isotope stage 4 to warmer stage 3. The largest populations surviving through the bottleneck should have been found in the largest tropical refugia, and thus in equatorial Africa. High genetic diversity in modern Africans may thus reflect a less severe bottleneck rather than earlier population growth. Volcanic winter may have reduced populations to levels low enough for founder effects, genetic drift and local adaptations to produce rapid population differentiation. If Toba caused the bottlenecks, then modern human races may have differentiated abruptly, only 70 thousand years ago.

Using mitochondrial and nuclear DNA markers to reconstruct human evolution

Molecular genetic-data have greatly improved our ability to test hypotheses about human evolution. During the past decade, a large amount of nuclear and mitochondrial data have been collected from diverse human populations. Taken together, these data indicate that modern humans are a relatively young species. African populations show the largest amount of genetic diversity, and they are the most genetically divergent population. Modern human populations expanded in size first on the African continent. These findings support a recent African origin of modern humans, but this conclusion should be tempered by the possible effects of factors such as gene flow, population size differences, and natural selection.

Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa

Alu insertion polymorphisms (polymorphisms consisting of the presence/absence of an Alu element at a particular chromosomal location) offer several advantages over other nuclear DNA polymorphisms for human evolution studies. First, they are typed by rapid, simple, PCR-based assays; second, they are stable polymorphisms-newly inserted Alu elements rarely undergo deletion; third, the presence of an Alu element represents identity by descent-the probability that different Alu elements would independently insert into the exact same chromosomal location is negligible; and fourth, the ancestral state is known with certainty to be the absence of an Alu element. We report here a study of 8 loci in 1500 individuals from 34 worldwide populations. African populations exhibit the most between-population differentiation, and the population tree is rooted in Africa; moreover, the estimated effective time of separation of African versus non-African populations is 137,000 +/- 15,000 years ago, in accordance with other genetic data. However, a principal coordinates analysis indicates that populations from Sahul (Australia and New Guinea) are nearly as close to the hypothetical ancestor as are African populations, suggesting that there was an early expansion of tropical populations of our species. An analysis of heterozygosity versus genetic distance suggests that African populations have had a larger effective population size than non-African populations. Overall, these results support the African origin of modern humans in that an earlier expansion of the ancestors of African populations is indicated.

The founding mitochondrial DNA lineages of Tristan da Cunha Islanders

Genealogical histories show that the inhabitants of Tristan da Cunha are derived from a known number of founders. Using the transmission of mitochondrial DNA (mtDNA) from mother to offspring pairs, we traced the mtDNA types found in 161 extant individuals to five female founders. Although the historical data claimed that two pairs of sisters were among the founding females, mtDNA data showed support for only one pair of sisters. We also studied the fidelity of mtDNA transmission in conjunction with the genealogical data. We did not detect any mutations from 698 base pairs of sequence data from 75 individuals, which together accounted for 108 independent transmissions of mtDNA from mother to offspring. Based on this observation, we estimate that the mtDNA mutation rate is no more than one new mutation every 36 transmissions. These results indicate a high fidelity of maternal mtDNA transmission and support the utility of mtDNA in evolutionary and forensic studies.

Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography

Y chromosome haplotypes are particularly useful in deciphering human evolutionary history because they accentuate the effects of drift, migration, and range expansion. Significant acceleration of Y biallelic marker discovery and subsequent typing involving heteroduplex detection has been achieved by implementing an innovative and cost-efficient method called denaturing high-performance liquid chromatography (DHPLC). The power of the method resides in its sensitivity and ability to rapidly compare amplified sequences in an automated manner. We have determined the allelic states of 22 Y polymorphisms; 19 of which are unreported, in 718 diverse extant chromosomes; established haplotype frequencies; and deduced a phylogeny. All major geographic regions, including Eurasia, are characterized by mutations reflecting episodes of genetic drift and expansion. Most biallelic markers are localized regionally. However, some show wider dispersal and designate older, core haplotypes. One transversion defines a major haplogroup that distinguishes a previously unknown deep, apparently non-African branch. It provides evidence of an ancient bottleneck event. It is now possible to anticipate the inevitable detailed reconstruction of human Y chromosome genealogy based on several tens to even hundreds of these important polymorphisms.

Genetic Diversity in Hominoid Primates

Humans are only one of the species produced by the hominoid evolutionary radiation. Common and pygmy chimpanzees (our closest relatives), gorillas, orangutans, and the lesser apes also belong to this group. In humans, patterns of genetic variation are becoming increasingly better characterized by modern molecular methods. Understanding human variation in an evolutionary context, however, requires comparison of human patterns with those of other hominoids, to reveal features shared among hominoids and those unique to humans. Genetic variation among chimpanzees, gorillas, and orangutans is beginning to be characterized, so that comparisons are now possible.

From genetic data, several different kinds of information can be reconstructed, including the evolutionary relatedness of subspecies and populations, time estimates for evolutionary divergences, past population dynamics, extent of gene flow over geographical landscapes, and group social structure. Knowledge of hominoid genetic variation is also relevant to applied fields such as primate conservation and medicine.

Mitochondrial footprints of human expansions in Africa

mtDNA studies support an African origin for modern Eurasians, but expansion events within Africa have not previously been investigated. We have therefore analyzed 407 mtDNA control-region sequences from 13 African ethnic groups. A number of sequences (13%) were highly divergent and coalesced on the "mitochondrial Eve" in Africans. The remaining sequences also ultimately coalesced on this sequence but fell into four major clusters whose starlike phylogenies testify to demographic expansions. The oldest of these African expansions dates to approximately 60,000-80,000 years ago. Eurasian sequences are derived from essentially one sequence within this ancient cluster, even though a diverse mitochondrial pool was present in Africa at the time.

Ancient DNA is thirteen years old

The first successful recovery of ancient DNA, from quagga and human mummies inspired significant enough interest to open an entire field of research. Efforts from many research groups, often in a hunt for the oldest sequences, showed that ancient DNA was a poor substrate for the enzymes used in molecular biology; it is present in tiny amounts, hard to purify, and frequently damaged. These obstacles have been partially overcome by the use of drastic laboratory precautions and by the introduction of polymerase chain reaction and phylogenetic studies. Ancient DNA analysis now finds applications in many research domains.

Ancient and modern mitochondrial DNA sequences and the colonization of the Pacific

Mitochondrial DNA (mtDNA) is a valuable tool for the study of recent human evolution because it is easy to analyse, is inherited uniparentally and has a relatively rapid rate of evolution. mtDNA analysis has been used extensively for the elucidation of the pattern of migrations of human populations. Several studies have focused on the Pacific because Polynesia was settled by humans for the first time relatively recently and there is a wealth of archaeological and linguistic data to complement genetic data on the region. Results of mtDNA analyses on modern-day Pacific populations indicate reduced genetic variability, and suggest that the Polynesians descend from people who migrated relatively recently from island Southeast Asia and that a population bottleneck occurred during the settlement of the central Pacific. Several informative polymorphisms have been identified in the hypervariable control region of mtDNA in modern-day Pacific populations that are helpful in tracing the ancestral affinities of these people. Studies of these mtDNA polymorphisms in ancient bones of prehistoric Pacific islanders indicate that the proto-Polynesian colonizers may have descended from the early settlers of island Melanesia. Although fraught with technical difficulties, studies of ancient DNA can provide valuable evidence on the genetic affinities of past peoples.

Applications of microsatellite-based Y chromosome haplotyping

Y-chromosomal microsatellites have been investigated for the purposes of application to male identification, population genetics and population history. With nine markers, every male in a German population sample (n = 70) could be identified by an individual-specific Y microsatellite haplotype. The analysis of 474 unrelated males of nine human populations with seven markers revealed 301 different Y haplotypes. The analysis of molecular variance (AMOVA) approach was used to detect male population characteristics of Y microsatellite haplotypes. With pairwise comparisons of inter-population variance, most of the populations could be distinguished significantly. Sixty individuals from different male populations in Asia and Northern Europe carrying a novel Y-chromosomal T-->C transition show reduced microsatellite variability together with haplotype similarities. Microsatellite data suggest that the mutation occurred recently in Asia, supporting the hypothesis of Asian ancestry of some northern European populations.

Dispersion of human Y chromosome haplotypes based on five microsatellites in global populations

We have analyzed five microsatellite loci from the nonrecombining portion of the human Y chromosome in 15 diverse human populations to evaluate their usefulness in the reconstruction of human evolution and early male migrations. The results show that, in general, most populations have the same set of the most frequent alleles at these loci. Hypothetical ancestral haplotypes, reconstructed on the basis of these alleles and their close derivatives, are shared by multiple populations across racial and geographical boundaries. A network of the observed haplotypes is characterized by a lack of clustering of geographically proximal populations. In spite of this, few distinct clusters of closely related populations emerged in the network, which are associated with population-specific alleles. A tree based on allele frequencies also shows similar results. Lack of haplotypic structure associated with the presumed ancestral haplotypes consisting of individuals from almost all populations indicate a recent common ancestry and/or extensive male migration during human evolutionary history. The convergent nature of microsatellite mutation confounds population relationships. Optimum resolution of Y chromosome evolution will require the use of additional microsatellite loci and diallelic genetic markers with lower mutation rates.

Results of Expedicion Humana. II. Analysis of HLA class II alleles in three African American populations from Colombia using the PCR/SSOP: identification of a novel DQB1*02 (*0203) allele

PCR/SSOP typing methods were used to analyze the HLA Class II DRB1, DQA1, DQB1 and DPB1 loci of samples from three African American populations of Colombia. Forty samples from the Cauca (Pacific), and twenty samples each from the Choco (North Pacific Coast) and the Providencia (Caribbean island) populations, were collected and the Class II loci analyzed under the auspices of the Expedicion Humana. Despite the limited number of samples analyzed, the African Colombian populations exhibit a very high degree of class II polymorphism. A great diversity of DRB1 alleles was found, with representatives from all serological classes, including 19 DRB1 alleles in the Providencia, 16 in the Cauca and 14 in the Choco groups. In addition, a novel DQB1*02 allele (*0203) was found in two individuals from the Cauca population of the Pacific Coast. The sequence of the DQB1*0203 allele, associated with DR3, differs from DQB1*0201 by only one nucleotide substitution (C-->A) in the second position of codon 57, resulting in an Ala to Asp change. The addition of DQB1*0203 brings the total number of DQB1 alleles identified to date to 26. HLA class II diversity is much greater in these African Colombian populations than that seen in nearby Amerindian populations. Analysis of regional Colombian African American HLA population genetics is discussed with respect to the Colombian Amerindian HLA genetics described in an accompanying paper.

Genetic admixture in the late pleistocene

The replacement hypothesis of modern human origins holds that the original population of modern humans expanded throughout the world, replacing existing archaic populations as it went. If this expanding population interbred with the peoples it replaced, then some archaic mitochondria might have been introduced into the early modern gene pool. Such mitochondria would be recognizable today because they should differ from other modern mitochondria at several times the number of sites that we are used to seeing in pairwise comparisons. In this paper we ask what can be inferred from the absence of these "divergent" mitochondria from modern samples. We show that if the effective number of females in our species has been large for the past 40,000 years, then the level of admixture must have been low. For example, if this effective number exceeded 1.6 million, then we can reject the hypothesis that more more than 2/1,000 of the mitochondria in the early modern population derived from admixture with archaic peoples. We argue elsewhere that regional continuity would be detectable in the fossil record only if the rate of admixture exceeded 76%. Here, we show that this level of admixture would require the effective female size of the human population to have been less than 1,777 for the past 40,000 years.

A recent common ancestry for human Y chromosomes

The male-specific portion of the Y chromosome is especially useful for studies of human origins. Patterns of nucleotide variation that are neutral with respect to fitness should permit estimates of when and where ancestral Y chromosomes existed. However, variation on the human Y chromosome has been observed to be greatly reduced relative to the autosomes and the X chromosome. One explanation is that selection for a favourable mutation on the non-recombining portion of the Y chromosome has resulted in the recent fixation of a single Y haplotype. A 2.6-kilobase fragment encompassing a polymorphic Alu insertion was sequenced from 16 human and four chimpanzee Y chromosomes. Patterns of nucleotide sequence diversity and divergence provide no evidence for a recent, strong selective sweep on the human Y chromosome. The time back to a common ancestral human Y chromosome is estimated to be 188,000 years, with a 95% confidence interval from 51,000 to 411,000 years. These results are consistent with autosomal and mitochondrial DNA studies that suggest a long-term human effective population size of 10,000 and a sex ratio of 1 (ref. 7). These inferences contradict predictions of the multiregional hypothesis positing a widespread transformation of Homo erectus populations into Homo sapiens.