Phenetic Analysis in Paleoanthropology: Phenogeography of Peoples of the World

Phenetic diversity of peoples of the world in a system of nonmetric, discrete variable traits has been studied. Sixty-two populations from North, Central, and Southeast Asia, Eastern and Western Europe, America, East Africa, Australia, and Melanesia have been examined. The estimates of phenetic diversity within regions (F_st) and the distances of the regions from the global means (d) proved to be comparable to the corresponding estimates inferred from genetic data. This means that differentiation of populations in discrete variable traits is related to the history of formation of their gene pools. A classification tree of the world peoples constructed using bootstrap implemented in the PHYLIP program package (Felsenstein, 1993) showed that the Australo-Melanesian populations were close to the East African ones but separated from those of the Eurasian region. The results of phylogenetic analysis of the reconstructed phene pools of the regional ancestral populations support the assumptions on the early colonization of Australia and Melanesia and on the later time of divergence of the ancestors of modern Caucasoids and North Asian Mongoloids.     

Native South American genetic structure and prehistory inferred from hierarchical modeling of mtDNA

Genetic diversity in Native South Americans forms a complexpattern at both the continental and local levels. In comparingthe West to the East, there is more variation within groupsand smaller genetic distances between groups. From this pattern,researchers have proposed that there is more variation in theWest and that a larger, more genetically diverse, founding populationentered the West than the East. Here, we question this characterizationof South American genetic variation and its interpretation.Our concern arises because others have inferred regional variationfrom the mean variation within local populations without takinginto account the variation among local populations within thesame region. This failure produces a biased view of the actualvariation in the East. In this study, we analyze the mitochondrial DNA sequence betweenpositions 16040 and 16322 of the Cambridge reference sequence.Our sample represents a total of 886 people from 27 indigenouspopulations from South (22), Central (3), and North America(2). The basic unit of our analyses is nucleotide identity bydescent, which is easily modeled and proportional to nucleotidediversity. We use a forward modeling strategy to fit a seriesof nested models to identity by descent within and between allpairs of local populations. This method provides estimates ofidentity by descent at different levels of population hierarchywithout assuming homogeneity within populations, regions, orcontinents. Our main discovery is that Eastern South America harbors moregenetic variation than has been recognized. We find no evidencethat there is increased identity by descent in the East relativeto the total for South America. By contrast, we discovered thatpopulations in the Western region, as a group, harbor more identityby descent than has been previously recognized, despite thefact that average identity by descent within groups is lower.In this light, there is no need to postulate separate foundingpopulations for the East and the West because the variabilityin the East could serve as a source for the Western gene pools.     

A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa

We have typed 275 men from five populations in Algeria, Tunisia, and Egypt with a set of 119 binary markers and 15 microsatellites from the Y chromosome, and we have analyzed the results together with published data from Moroccan populations. North African Y-chromosomal diversity is geographically structured and fits the pattern expected under an isolation-by-distance model. Autocorrelation analyses reveal an east-west cline of genetic variation that extends into the Middle East and is compatible with a hypothesis of demic expansion. This expansion must have involved relatively small numbers of Y chromosomes to account for the reduction in gene diversity towards the West that accompanied the frequency increase of Y haplogroup E3b2, but gene flow must have been maintained to explain the observed pattern of isolation-by-distance. Since the estimates of the times to the most recent common ancestor (TMRCAs) of the most common haplogroups are quite recent, we suggest that the North African pattern of Y-chromosomal variation is largely of Neolithic origin. Thus, we propose that the Neolithic transition in this part of the world was accompanied by demic diffusion of Afro-Asiatic-speaking pastoralists from the Middle East.     

Colonization history and introduction dynamics of capsella bursa-pastoris (Brassicaceae) in north america: isozymes and quantitative traits

Multilocus isozyme genotypic composition for aspartate aminotransferase (AAT), leucine aminopeptidase (LAP) and glutamate dehydrogenase (GDH) was studied for Capsella in the source continent, Europe (9000 plants from 593 populations), and in the colonized continent, North America (2700 plants from 88 populations). North America was depauperate in the number of genotypes (by approximately 50%), but in terms of frequencies, a few genotypes were common and shared by both continents. Although some, very rare, genotypes were, however, unique for North America, our data provided no evidence to indicate that the introduced gene pools were reconstructed on a multilocus genetic basis after introduction. Instead, they argued for a considerable number of independent introduction events. Geographical distribution patterns of multilocus genotypes in Europe and North America were pronounced and enabled us to trace the colonization history of Californian Capsella back to Spanish ancestral populations and those of temperate North America back to temperate European gene pools. A random-block field experiment with 14 Californian populations from different climatic regions revealed that variation patterns of quantitative traits reflect ecotypic variation, and the ecological amplitude of Capsella in North America is similar to that in Europe, which can be traced back to the introduction of preadapted genotypes. It appears that certain multilocus isozyme genotypes are associated with certain ecotypes. The variable European gene pool of Capsella was essentially introduced into North America without major genetic changes.     

Melanesian mtDNA complexity

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at approximately 30-50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval approximately 3,500-8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved.     

A population genetic characterization of Estonians

This paper discusses the genetic characterization of Estonians on the basis of eight blood group systems, and the traits of PTC tasting and colour blindness in 40 Estonian population samples from various parts of the country. The allele frequencies for the total Estonian population and for the four most different regions are presented. The survey shows genetic heterogeneity within the Estonians; the greatest genetic differences were observed in West-East direction. The West-Islands, West, and North Estonia differ from the other regions (East, South-East, also South-West and Central Estonia--which form a compact cluster). The mean allele frequencies of the Estonians are comparable to those typical for populations from North and East Europe, but the allele frequencies of Estonians are characterized by tendencies in two opposite (western and eastern) directions, like in other Finno-Ugric populations and concerning other anthropological traits. Estonians reveal closest similarities to the nearest neighbouring populations, regardless of their language group. The genetic heterogeneity and antagonistic traits in Estonians seem to be traces of the original genetic structure of Finno-Ugric ancestor populations which were neither Mongoloid nor Caucasoid.     

Female gene pools of Berber and Arab neighboring communities in central Tunisia: microstructure of mtDNA variation in North Africa

North African populations are considered genetically closer to Eurasians than to sub-Saharans. However, they display a considerably high mtDNA heterogeneity among them, namely in the frequencies of the U6, East African, and sub-Saharan haplogroups. In this study, we describe and compare the female gene pools of two neighboring Tunisian populations, Kesra (Berber) and Zriba (non-Berber), which have contrasting historical backgrounds. Both populations presented lower diversity values than those observed for other North African populations, and they were the only populations not showing significant negative Fu's F(S) values. Kesra displayed a much higher proportion of typical sub-Saharan haplotypes (49%, including 4.2% of M1 haplogroup) than Zriba (8%). With respect to U6 sequences, frequencies were low (2% in Kesra and 8% in Zriba), and all belonged to the subhaplogroup U6a. An analysis of these data in the context of North Africa reveals that the emerging picture is complex, because Zriba would match the profile of a Berber Moroccan population, whereas Kesra, which shows twice the frequency of sub-Saharan lineages normally observed in northern coastal populations, would match a western Saharan population except for the low U6 frequency. The North African patchy mtDNA landscape has no parallel in other regions of the world and increasing the number of sampled populations has not been accompanied by any substantial increase in our understanding of its phylogeography. Available data up to now rely on sampling small, scattered populations, although they are carefully characterized in terms of their ethnic, linguistic, and historical backgrounds. It is therefore doubtful that this picture truly represents the complex historical demography of the region rather than being just the result of the type of samplings performed so far.     

On the origin of the invasive olives (Olea europaea L., Oleaceae)

The olive tree (Olea europaea) has successfully invaded several regions in Australia and Pacific islands. Two olive subspecies (subspp. europaea and cuspidata) were first introduced in these areas during the nineteenth century. In the present study, we determine the origin of invasive olives and investigate the importance of historical effects on the genetic diversity of populations. Four invasive populations from Australia and Hawaii were characterized using eight nuclear DNA microsatellites, plastid DNA markers as well as ITS-1 sequences. Based on these data, their genetic similarity with native populations was investigated, and it was determined that East Australian and Hawaiian populations (subsp. cuspidata) have originated from southern Africa while South Australian populations (subsp. europaea) have mostly derived from western or central Mediterranean cultivars. Invasive populations of subsp. cuspidata showed significant loss of genetic diversity in comparison to a putative source population, and a recent bottleneck was evidenced in Hawaii. Conversely, invasive populations of subsp. europaea did not display significant loss of genetic diversity in comparison to a native Mediterranean population. Different histories of invasion were inferred for these two taxa with multiple cultivars introduced restoring gene diversity for europaea and a single successful founder event and sequential introductions to East Australia and then Hawaii for cuspidata. Furthermore, one hybrid (cuspidata x europaea) was identified in East Australia. The importance of hybridizations in the future evolution of the olive invasiveness remains to be investigated.     

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.     

Dental perspectives on the population history of Southeast Asia

This article uses metric and nonmetric dental data to test the "two-layer" or immigration hypothesis whereby Southeast Asia was initially occupied by an "Australo-Melanesian" population that later underwent substantial genetic admixture with East Asian immigrants associated with the spread of agriculture from the Neolithic period onwards. We examined teeth from 4,002 individuals comprising 42 prehistoric and historic samples from East Asia, Southeast Asia, Australia, and Melanesia. For the odontometric analysis, dental size proportions were compared using factor analysis and Q-mode correlation coefficients, and overall tooth size was also compared between population samples. Nonmetric population affinities were estimated by Smith's distances, using the frequencies of 16 tooth traits. The results of both the metric and nonmetric analyses demonstrate close affinities between recent Australo-Melanesian samples and samples representing early Southeast Asia, such as the Early to Middle Holocene series from Vietnam, Malaysia, and Flores. In contrast, the dental characteristics of most modern Southeast Asians exhibit a mixture of traits associated with East Asians and Australo-Melanesians, suggesting that these populations were genetically influenced by immigrants from East Asia. East Asian metric and/or nonmetric traits are also found in some prehistoric samples from Southeast Asia such as Ban Kao (Thailand), implying that immigration probably began in the early Neolithic. Much clearer influence of East Asian immigration was found in Early Metal Age Vietnamese and Sulawesi samples. Although the results of this study are consistent with the immigration hypothesis, analysis of additional Neolithic samples is needed to determine the exact timing of population dispersals into Southeast Asia.     

GM haplotype diversity of 82 populations over the world suggests a centrifugal model of human migrations

This study investigates the GM genetic relationships of 82 human populations, among which 10 represent original data, within and among the main broad geographic areas of the world. Different approaches are used: multidimensional scaling analysis and test for isolation by distance, to assess the correlation between genetic variation and spatial distributions; analysis of variance, to investigate the genetic structure at different hierarchical levels of population subdivision; genetic similarity map (geographic map distorted by available genetic information), to identify regions of high and low genetic variation; and minimal spanning network, to point out possible migration routes across continental areas. The results show that the GM polymorphism is characterized by one of the highest amounts of genetic variation observed so far among populations of different continents (Fct=0.3915, P < 0.0001). GM diversity can be explained by a model of isolation by distance (IBD) at most continental levels, with a particularly significant fit to IBD for the Middle East and Europe. Five peripheral regions of the world (Europe, west and south sub-Saharan Africa, Southeast Asia, and America) exhibit a low level of genetic diversity both within and among populations. By contrast, East and North African, Southwest Asian, and Northeast Asian populations are highly diverse and interconnected genetically by large genetic distances. Therefore, the observed GM variation can be explained by a "centrifugal model" of modern humans peopling history, involving ancient dispersals across a large intercontinental area spanning from East Africa to Northeast Asia, followed by recent migrations in peripheral geographic regions.     

Geography of HFE C282Y and H63D mutations

Hereditary hemochromatosis (HH) is a common autosomal recessive disorder causing inappropriate dietary iron absorption that affects North Europeans. HH is associated with the C282Y mutation of the HFE gene, and the H63D mutation to a lesser degree. Both mutations are abundant in Europe, with H63D also appearing in North Africa, the Middle East, and Asia. Emigration from Europe over the past 500 years has introduced C282Y and H63D to America, Australia, New Zealand, and South Africa in an essentially predictable fashion. The distinctive characteristics of the population genetics of HH are the confined racial distribution and high frequency in North European peoples. C282Y frequencies in North Europeans are typically between 5% and 10%, with homozygotes accounting for between 1/100 and 1/400 of these populations. The scarcity of the C282Y mutation in other populations accounts for the lack of HH in non-Europeans.     

Physical variation and history in Melanesia and Australia

Local biological variation is marked in Melanesia. Some of it may result from gene flow from Micronesia, but the essential variation appears to result from isolation due to social fragmentation, and to genetic drift in place. In different regions, the variation may correspond well with language relationships, and probably constitutes differentiation which has been preserved over a considerable period, especially since the arrival of horticulture and development of village farming. However, none of this patterning suggests distinct waves of migration into Melanesia. Variation among Australian aboriginal groups is smaller, though far from absent. It may reflect a hunting culture together with social customs allowing more intertribal marriage than is typical of Melanesia. While phenotypically Australians and Melanesians differ, cranially they are closely allied, as against other major human groups. It is suggested that the genetic and phenotypic variety is old, that it existed in the previous home of the Australo-Melanesians (Old Melanesia, comprising present Indonesia and the Phillipines) at least back to 40,000 years ago, and that much of the variation in Melanesia and Australia, including their differences, results from the sampling process involved when different groups out of the original populations made early crossings of the water barriers from Old Melanesia.     

A comparison of the incidence of minor nonmetrical cranial variants in Australian aborigines with those of Melanesia and Polynesia

The incidence of 30 minor non-metrical cranial variants in Australian Aborigines discussed in a previous publication is compared with incidence in crania from Melanesia and Polynesia. With the qualification that the sample sizes from Melanesia and Polynesia are rather small, the data indicate that the differences between Australia and Melanesia and Polynesia exceed those between the three areas into which Australia was divided. The area of Australia made up of the Northern Territory and northern Western Australia has more association with Melanesia than Polynesia as expected, while the more southern regions of Australia have more association with Polynesia than Melanesia perhaps by migrations from Asia. Because the southern Australian Aborigines are now largely extinct, it seems difficult to prove this.     

Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps

Altitudinal gradients in mountain regions are short‐range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19–29 individuals from each population. The sample includes two pairs of low‐ and high‐altitude populations from two different valleys. High‐altitude populations showed a lower nucleotide diversity and negative Tajima's D values and were more closely related to each other than to low‐altitude populations from the same valley. Despite their close geographic proximity, demographic analysis revealed that low‐ and high‐altitude populations split between 260 000 and 15 000 years before present. Single nucleotide polymorphisms whose allele frequencies were highly differentiated between low‐ and high‐altitude populations identified genomic regions of up to 50 kb length where patterns of genetic diversity are consistent with signatures of local selective sweeps. These regions harbour multiple genes involved in stress response. Variation among populations in two putative adaptive phenotypic traits, frost tolerance and response to light/UV stress was not correlated with altitude. Taken together, the spatial distribution of genetic diversity reflects a potentially adaptive differentiation between low‐ and high‐altitude populations, whereas the phenotypic differentiation in the two traits investigated does not. It may resemble an interaction between adaptation to the local microhabitat and demographic history influenced by historical glaciation cycles, recent seed dispersal and genetic drift in local populations.     

The origins of subsistence agriculture in Oceania and the potentials for future tropical food crops

Subsistence agriculture in the Pacific Islands has a complex prehistory centered on western Melanesia. Based on an analysis of cultigen provenience, a sequential model of a three-tiered crop structure of indigenous agricultural systems has been derived: (1) The independent early domestication of endemic species in the New Guinea region; (2) introduction of species from Southeast Asia; (3) the advent of American crop plants. The temporal sequence has archaeological and linguistic confirmation of 10 000 years ago for the beginnings of agriculture, 6000 years for Southeast Asian introduction, with the sweet potato contributing in Polynesia in prehistory, and in Melanesia only in post-Columbian times. Recent research directed toward issues of domestication in New Guinea and subsistence prehistory in Australia on three genera,Canarium, Colocasia andIpomoea, exemplify under-recognized resources with quite different potentials for economic botany. Unlike past exploitation of indigenous plant resources, future users of plants such as those exemplified, and especially where commercialization is involved, cannot avoid addressing intellectual property rights that pertain to species domesticated, selected or conserved by peoples of the non-industri-alized world.     

Genetic variation in central and peripheral populations of Excoecaria agallocha from Indo-West Pacific

Genetic diversity and differentiation were studied in Excoecaria agallocha L., a mangrove species growing on the coastlines of the Indo-West Pacific region. Twenty natural populations of E. agallocha were sampled from the Malay Peninsula (central population), and in Southern China, North Australia, Sri Lanka and Southern Japan (peripheral populations). Our results showed that central populations from Malay Peninsula possessed significantly higher genetic diversity than the peripheral ones (P < 0.05). Analysis of molecular variation (AMOVA) revealed that genetic variability was partitioned at 22.9% among regions, 23.6% among populations within regions, and 53.5% within populations. Genetic differentiation (G_ST = 0.300) among the six central populations was stronger than those from peripheral regions. Populations from North Australia clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Southern Japan, Southern China and Sri Lanka also clustered closely together, respectively. However, populations from Malay Peninsula did not cluster by region. The east coast populations of Malay Peninsula (including Pasir population) were more genetically similar to the populations from Southern China than those from the west coastline of Malay Peninsula. Our study suggests that ocean currents, land barriers, limited dispersal ability of seeds, and founder effect may play important roles in the distribution of genetic diversity in E. agallocha.     

Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific

The human settlement of the Pacific Islands represents one of the most recent major migration events of mankind. Polynesians originated in Asia according to linguistic evidence or in Melanesia according to archaeological evidence. To shed light on the genetic origins of Polynesians, we investigated over 400 Polynesians from 8 island groups, in comparison with over 900 individuals from potential parental populations of Melanesia, Southeast and East Asia, and Australia, by means of Y chromosome (NRY) and mitochondrial DNA (mtDNA) markers. Overall, we classified 94.1% of Polynesian Y chromosomes and 99.8% of Polynesian mtDNAs as of either Melanesian (NRY-DNA: 65.8%, mtDNA: 6%) or Asian (NRY-DNA: 28.3%, mtDNA: 93.8%) origin, suggesting a dual genetic origin of Polynesians in agreement with the "Slow Boat" hypothesis. Our data suggest a pronounced admixture bias in Polynesians toward more Melanesian men than women, perhaps as a result of matrilocal residence in the ancestral Polynesian society. Although dating methods are consistent with somewhat similar entries of NRY/mtDNA haplogroups into Polynesia, haplotype sharing suggests an earlier appearance of Melanesian haplogroups than those from Asia. Surprisingly, we identified gradients in the frequency distribution of some NRY/mtDNA haplogroups across Polynesia and a gradual west-to-east decrease of overall NRY/mtDNA diversity, not only providing evidence for a west-to-east direction of Polynesian settlements but also suggesting that Pacific voyaging was regular rather than haphazard. We also demonstrate that Fiji played a pivotal role in the history of Polynesia: humans probably first migrated to Fiji, and subsequent settlement of Polynesia probably came from Fiji.     

Genomic evidence for an African expansion of anatomically modern humans by a Southern route

There is general agreement among scientists about a recent (less than 200,000 yrs ago) African origin of anatomically modern humans, whereas there is still uncertainty about whether, and to what extent, they admixed with archaic populations, which thus may have contributed to the modern populations' gene pools. Data on cranial morphology have been interpreted as suggesting that, before the main expansion from Africa through the Near East, anatomically modern humans may also have taken a Southern route from the Horn of Africa through the Arabian peninsula to India, Melanesia and Australia, about 100,000 yrs ago. This view was recently supported by archaeological findings demonstrating human presence in Eastern Arabia >90,000 yrs ago. In this study we analyzed genetic variation at 111,197 nuclear SNPs in nine populations (Kurumba, Chenchu, Kamsali, Madiga, Mala, Irula, Dalit, Chinese, Japanese), chosen because their genealogical relationships are expected to differ under the alternative models of expansion (single vs. multiple dispersals). We calculated correlations between genomic distances, and geographic distances estimated under the alternative assumptions of a single dispersal, or multiple dispersals, and found a significantly stronger association for the multiple dispersal model. If confirmed, this result would cast doubts on the possibility that some non-African populations (i.e., those whose ancestors expanded through the Southern route) may have had any contacts with Neandertals.     

Genetic differentiation between Australian and North American populations of the monarch butterfly Danaus plexippus (L.) (Lepidoptera: Nymphalidae): an exploration using allozyme electrophoresis

Allozyme analysis was used to address the question of the source of the Australian populations of the monarch butterfly Danaus plexippus (L.). The study had three major aims: (1) To compare the levels of diversity of Australian and Hawaiian populations with potential source populations. (2) To determine whether eastern and western North American populations were sufficiently divergent for the Australian populations to be aligned to a source population. (3) To compare the differentiation among regions in Australia and North America to test the prediction of greater genetic structure in Australia, as a consequence of reduced migratory behaviour. The reverse was found, with F _ST values an order of magnitude lower in Australia than in North America. Predictably, Australian and Hawaiian populations had lower allelic diversity, but unexpected higher heterozygosity values than North American populations. It was not possible to assign the Australian populations to a definitive source, although the high levels of similarity of Australian populations to each other suggest a single colonization event. The possibility that the Australian populations have not been here long enough to reach equilibrium is discussed. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 437–452.