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Mitochondrial DNA "clock" for the Amerinds and its implications for timing their entry into North America.

Students of the time of entry of the ancestors of the Amerinds into the New World are divided into two camps, one favoring an "early" entry [more than approximately 30,000 years before the present (YBP)], the other favoring a "late" entry (less than approximately 13,000 YBP). An "intermediate" date is unlikely for geological reasons. The correlation of the appropriate data on mtDNA variation in Amerinds with linguistic, archaeological, and genetic data offers the possibility of establishing a time frame for mtDNA evolution in Amerinds. In this paper, we estimate that the separation of the Chibcha-speaking tribes of Central America from other linguistic groups/nascent tribes began approximately 8000-10,000 YBP. Characterization of the mtDNA of 110 Chibcha speakers with 14 restriction enzymes leads on the basis of their time depth to an estimated mtDNA nucleotide substitution rate for Amerinds of 0.022-0.029% per 10,000 years. As a first application of this rate, we consider the mtDNA variation observed in 18 Amerind tribes widely dispersed throughout the Americas and studied by ourselves with the same techniques, and we estimate that if the Amerinds entered the New World as a single group, that entry occurred approximately 22,000-29,000 YBP. This estimate carries a large but indeterminate error. The mtDNA data are thus at present equivocal with respect to the most likely times of entry of the Amerind into the New World mentioned above but favor the "early" entry hypothesis.

Anthropology↗

Molecular evidence for an African origin of the Hawaiian endemic Hesperomannia (Asteraceae).

Identification of the progenitors of plants endemic to oceanic islands often is complicated by extreme morphological divergence between island and continental taxa. This is especially true for the Hawaiian Islands, which are 3,900 km from any continental source. We examine the origin of Hesperomannia, a genus of three species endemic to Hawaii that always have been placed in the tribe Mutisieae of the sunflower family. Phylogenetic analyses of representatives from all tribes in this family using the chloroplast gene ndhF (where ndhF is the ND5 protein of chloroplast NADH dehydrogenase) indicate that Hesperomannia belongs to the tribe Vernonieae. Phylogenetic comparisons within the Vernonieae using sequences of both ndhF and the internal transcribed spacer regions of nuclear ribosomal DNA reveal that Hesperomannia is sister to African species of Vernonia. Long-distance dispersal northeastward from Africa to southeast Asia and across the many Pacific Ocean island chains is the most likely explanation for this unusual biogeographic connection. The 17- to 26-million-year divergence time between African Vernonia and Hesperomannia estimated by the DNA sequences predates the age of the eight existing Hawaiian Islands. These estimates are consistent with an hypothesis that the progenitor of Hesperomannia arrived at one of the low islands of the Hawaiian-Emperor chain between the late Oligocene and mid-Miocene when these islands were above sea level. Subsequent to its arrival the southeast Pacific island chains served as steppingstones for dispersal to the existing Hawaiian Islands.

Africa↗

RRNA and dnaK relationships of Bradyrhizobium sp. nodule bacteria from four papilionoid legume trees in Costa Rica.

Enzyme electrophoresis and sequencing of rRNA and dnaK genes revealed high genetic diversity among root nodule bacteria from the Costa Rican trees Andira inermis, Dalbergia retusa, Platymiscium pinnatum (Papilionoideae tribe Dalbergieae) and Lonchocarpus atropurpureus (Papilionoideae tribe Millettieae). A total of 21 distinct multilocus genotypes [ETs (electrophoretic types)] was found among the 36 isolates analyzed, and no ETs were shared in common by isolates from different legume hosts. However, three of the ETs from D. retusa were identical to Bradyrhizobium sp. isolates detected in prior studies of several other legume genera in both Costa Rica and Panama. Nearly full-length 16S rRNA sequences and partial 23S rRNA sequences confirmed that two isolates from D. retusa were highly similar or identical to Bradyrhizobium strains isolated from the legumes Erythrina and Clitoria (Papilionoideae tribe Phaseoleae) in Panama. rRNA sequences for five isolates from L. atropurpureus, P. pinnatum and A. inermis were not closely related to any currently known strains from Central America or elsewhere, but had affinities to the reference strains Bradyrhizobium japonicum USDA 110 (three isolates) or to B. elkanii USDA 76 (two isolates). A phylogenetic tree for 21 Bradyrhizobium strains based on 603 bp of the dnaK gene showed several significant conflicts with the rRNA tree, suggesting that genealogical relationships may have been altered by lateral gene transfer events.

Bacterial Proteins↗

TP53 polymorphisms and haplotypes in South Amerindians and neo-Brazilians.

To evaluate the genetic diversity of Brazilian populations and contribute to the knowledge of their evolutionary history this study investigated three TP53 polymorphisms (BstUI and MspI RFLPs in exon 4 and intron 6, respectively, and a 16 bp duplication in intron 3). The populations studied were: 114 Amerindians from five Brazilian Indian tribes (Gavião, Surui, Zoró, Wai-Wai and Xavante), 95 Euro-Brazilians and 70 Afro-Brazilians. The polymorphisms were all analysed using PCR amplifications. Gene frequencies and haplotype prevalences were calculated using the ARLEQUIN software. The genetic affinities of these groups with other world populations were estimated by the D(A) distance and neighbour joining method, using the NJBAFD computer program. Neo-Brazilians (immigrants from Europe and Africa) generally presented more variability than Amerindians, Afro-Brazilians being the most variable population. Among Amerindians, Gavião is the only group polymorphic for the three markers. Wai-Wai showed variability in BstUI and MspI RFLPs, while the other tribes were monomorphic for the 16 bp A1 and MspI A2 alleles. A rare haplotype (1-2-1) was verified among the Wai-Wai. This haplotype was previously described in a Chinese sample only, but with low frequency. Therefore, either this combination was lost in the other tribes by genetic drift, recombination, or other factor, or it occurs in the Wai-Wai and Chinese by independent events. The Gavião also presented a haplotype (2-1-1) not observed in the other Amerindians; but since it is present in Euro- and Afro-Brazilians. its occurrence there is probably due to interethnic admixture. The relationships of several world populations obtained using TP53 indicates that this marker is very efficient in clustering populations of the same ethnic group.

Brazil↗

Genetic variation at three VNTR loci (D1S80, APOB, and D17S5) in two tribal populations of Andhra Pradesh, India.

This study reports the genetic variation at three variable number of tandem repeat (VNTR) loci (APOB, D17S5 and D1S80) in two tribes (Thoti and Kolam) of Andhra Pradesh, India. Kolams constitute 1% of the total scheduled tribal population of Andhra Pradesh, while Thoti is a numerically small tribe. All three genetic loci were genotyped using the polymerase chain reaction (PCR) technique and were polymorphic in both populations. At the D1S80 locus, both populations showed higher frequencies of allele *31 (9-14%) than other Indian populations. In the APOB system, Thoti showed a very high frequency of allele *37 (54%) and for D17S5 system allele *4 was the most common in Thoti (32%) and allele *2 in Kolam (28%). Both tribes differed statistically significantly from other tribal populations of the region. The level of gene differentiation was low (GST = 0.038) for Indian tribal populations. The allele frequency distribution, heterozygosity and genetic diversity analysis shows that the observed genetic variation is socially and geographically structured.

Alleles↗

Demographic and genetic relationships among Brazilian Wapishana Indians.

Demographic information is given and data on 25 genetic systems are reanalysed for six populations of Wapishana Indians living in northern Brazil. Despite 200 years of contact with non-Indians, the maximum amount of admixture that may be present in persons who claim 'pure' Indian ancestry is 3%. Historical sources mention considerable exchange with the Macushi, Taurepan and Atorai tribes, confirmed by our genealogies. Departures from the maximum amount of heterozygosity per locus are similar in putative 'full bloods' and admixed individuals, as well as among the first and members of other tribes. Demographically the Wapishana can be characterized as very mobile, with high fertility but moderate mortality for an agricultural group. The Index of Opportunity for Selection (0 x 57) is one of the lowest calculated so far among South American tribes. Despite the indicated high mobility, clustering of some alleles was observed in two localities.

Adolescent↗

Further blood genetic studies on Amazonian diversity--data from four Indian groups.

Information related to 31 protein genetic systems was obtained for 307 individuals affiliated with the Cinta Larga, Karitiana, Surui and Kararaô Indians of northern Brazil. In terms of genetic distances the Cinta Larga showed more similarities with the Karitiana (both are Tupi-speaking tribes), while at a more distant level the Surui clustered with the Kararaô. The latter, a Cayapo subgroup, showed a completely different genetic constitution from the other subgroups of this same tribe. Both the Kararaô and Karitiana are small, remnant populations, and their gene pools have presumably been severely affected by random and founder effects. These results were incorporated with those of 25 other Amazonian Indian tribes, and analysis by two multivariate techniques confirmed a previously observed geographical dichotomy, suggesting either that the Amazon river constitutes a barrier to north-south gene flow or that latitudinally different past migrations entered the region from the west.

Alleles↗

An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference.

The objective of this study was to obtain a quantitative assessment of the monophyly of morning glory taxa, specifically the genus Ipomoea and the tribe Argyreieae. Previous systematic studies of morning glories intimated the paraphyly of Ipomoea by suggesting that the genera within the tribe Argyreieae are derived from within Ipomoea; however, no quantitative estimates of statistical support were developed to address these questions. We applied a Bayesian analysis to provide quantitative estimates of monophyly in an investigation of morning glory relationships using DNA sequence data. We also explored various approaches for examining convergence of the Markov chain Monte Carlo (MCMC) simulation of the Bayesian analysis by running 18 separate analyses varying in length. We found convergence of the important components of the phylogenetic model (the tree with the maximum posterior probability, branch lengths, the parameter values from the DNA substitution model, and the posterior probabilities for clade support) for these data after one million generations of the MCMC simulations. In the process, we identified a run where the parameter values obtained were often outside the range of values obtained from the other runs, suggesting an aberrant result. In addition, we compared the Bayesian method of phylogenetic analysis to maximum likelihood and maximum parsimony. The results from the Bayesian analysis and the maximum likelihood analysis were similar for topology, branch lengths, and parameters of the DNA substitution model. Topologies also were similar in the comparison between the Bayesian analysis and maximum parsimony, although the posterior probabilities and the bootstrap proportions exhibited some striking differences. In a Bayesian analysis of three data sets (ITS sequences, waxy sequences, and ITS + waxy sequences) no supoort for the monophyly of the genus Ipomoea, or for the tribe Argyreieae, was observed, with the estimate of the probability of the monophyly of these taxa being less than 3.4 x 10(-7).

Bayes Theorem↗

Validity of the SMAST in two American Indian tribal populations.

The standardized evaluation of alcoholism and other psychopathologies in minority populations, particularly American Indians, has long been questioned. This study investigated the validity of one of the most commonly applied assessments for alcoholism--the Short Michigan Alcohol Screening Test (SMAST)--in two distinct American Indian tribal groups. We analyzed data collected from 1989 to 1995 from largely community representative samples of 456 Southwestern and 214 Plains Indians ages 21 or older. For comparison, alcohol dependence was diagnosed using Diagnostic and Statistical Manual of Mental Disorders, Third Edition-Revised (DSM-III-R) criteria from a detailed, modified version of the Schedule for Affective Disorders and Schizophrenia--Lifetime (SADS-L). Accuracy of the SMAST was quantified as sensitivity, specificity, likelihood ratios, and the area under the curve for receiver operating characteristics, using the DSM-III-R diagnosis as the reference. The standard SMAST cutoff score of > or = 3 had a demonstrated sensitivity 86% to 95%, but did not perform well in terms of specificity (23%-47%). Significantly higher cutoff scores (> or = 5 for both genders in the Southwestern tribe and 8 and > or = 6 for men and women in the Plains tribe) were required to demonstrate acceptable levels of specificity in both tribes. The findings suggest that the SMAST is not a valid tool to screen for alcohol misuse in these two tribal populations. The highly elevated and different thresholds required from one population to the next and from one gender to the next constitute a significant obstacle to the use of the instrument.

Adult↗

Morphological and ultrastructural diversity of orbicules in Gentianaceae.

Minute granules of sporopollenin, called orbicules, can be observed on the innermost tangential and/or radial walls of secretory tapetum cells. Orbicules were investigated in 53 species of 34 Gentianaceae genera using light microscopy, scanning electron microscopy and transmission electron microscopy. This selection covered all different tribes and subtribes recognized in Gentianaceae (87 genera, +/-1650 species). Orbicules were found in 38 species (23 genera) distributed among the six tribes recognized in Gentianaceae. The orbicule typology is based on those described previously in Rubiaceae. Of the six orbicule types described previously, Type II orbicules are lacking. Type III orbicules are most common (17 species). Hockinia Gardner is the only representative with Type I orbicules. The number of representatives with orbicules belonging to the other orbicule types are equally distributed among the species studied: seven species possess Type IV orbicules, six species Type V and six species Type VI. The systematic usefulness of this typology is discussed in comparison with the latest systematic insights within the family, and palynological trends in Gentianaceae. Orbicule data have proven to be useful for evaluating tribal delimitation within Rubiaceae and Loganiaceae s.l.; however, they seem not to be useful for tribal delimitation in Gentianaceae. In the tribes Potalieae and Gentianeae orbicule data may be useful at subtribal level.

Cytoplasmic Granules↗

Phenotypic correlations among plant parts in Iberian Papilionoideae (Fabaceae).

BACKGROUND AND AIMS: Different plant organs may show varying degrees of form diversification or conservatism across phylogenetically related taxa. The present study uses data from a recent systematic study of Iberian Papilionoideae to investigate diversification and covariation in reproductive and vegetative plant parts. The appropriateness of imprecise (but comprehensive) taxonomic quantitative information is tested. METHODS: Organ size covariation and phenotypic correlations were studied among tribes, genera and species. Scale relationships were investigated by Reduced Major Axis regression. Variables used were the maximum dimensions of calyx, corolla, keel petal, fruit, seed, stipule, leaflet and petiole. KEY RESULTS: As regards tribe averages, the length of the corolla and that of calyx correlated positively and significantly. In contrast, pod length was unrelated to corolla size and largely tribe-specific. Within genera, the sizes of calyx, corolla and fruit sometimes covaried linearly (e.g. Lathyrus species) and other times did not (Genista, Astragalus). CONCLUSIONS: Information from taxonomic studies can be useful to establish major phenotypic correlations in plants. Results underscore the implications of tribal ownership in the Papilionoideae and illustrate the extensive morphological diversification of pods relative to flowers in this group.

Fabaceae↗

The genetic structure of a tribal population, the Yanomama Indians. VI. Analysis by F-statistics (including a comparison with the Makiritare and Xavante).

The infra-structure of three relatively undisturbed tribes of American Indians (Yanomama, Makiritare, Xavante) has been investigated by means of the F-statistics of Wright, using 8, 9 and 6 codominant systems respectively. The data for the first two mentioned tribes are much more extensive (37 and 7 villages) than for the third (3 villages), and much of the argument is based on the first two. An additive model partitioning F(IS) into an average effect (F(A)) and deviations due to deme size, systems effects, village effects, and random error has been employed. The Cannings-Edwards formulation suggests that the small size of the demes alone would result in an F(IS) of -0.008 for the Yanomama and -0.007 for the Makiritare. There is no evidence for significant village or systems effects. Despite considerable scatter, F(A) values are not significantly heterogeneous and tend to be negative (-0.012 to -0.023). On the basis of a computer simulation model, it appears that there is an excess of consanguineous marriage over random expectation, i.e. the negative F(A) values are probably not due to avoidance of close inbreeding in a subdivided population in which demes are small. Aspects of population structure which could contribute to negative F(A) values are identified. These include unequal gene frequencies in the sexes and occasional marked differential fertility. It is at this point unnecessary to introduce overdominance as a cause of the negative F(A) values, since a computer simulation program which does not incorporate selection satisfactorily reproduces the observed F(IS) values. If population breeding structure alone can result in negative F(IS) values, then this may constitute a mechanism for retarding random fixation.-Mean F(ST) values are 0.063 for the Yanomama and 0.036 for the Makiritare. While truly comparable data are lacking, it seems likely these will be found to be relatively high values for human populations. F(IT) values have been calculated by both direct and indirect approaches. The direct approach yields a value of 0.045 for the Yanomama and -0.009 for the Makiritare; the respective indirect values are 0.085 and 0.017. The primary identifiable reason for this difference between tribes is the greater genetic heterogeneity among Yanomama villages. The assumptions underlying the indirect approach to the calculation of F(IT) do not appear to be met in these populations.

Analysis of Variance↗

The genetic structure of a tribal population, the Yanomama Indians. XIV. Clines and their interpretation.

The Yanomama Indians are a South American tribe distributed over an irregular area approximately 200 X 300 miles. The gene frequencies observed at 12 loci in 47 villages within this area have been analyzed for the occurrence of clines. Apparently significant clines are observed for alleles of the Rh, MNSs, Kidd, Gm, Inv and serum albumin system. Available data concerning recent tribal expansion and admixture permit a tentative analysis of the causes of these clines. Although the action of selection cannot be rigorously excluded, it seems unlikely to be the major couse. Admixture with surrounding tribes plays a role which can be quantified because of the fortuitous cicumstance of two genetic markers for admixture. It is suggested that an important factor in the origin of these clines is the manner in which the tribe has recently expanded through successive village fissionings and a predominantly centrifugal pattern of village migration.

Alleles↗

A comparison of the genetic infrastructure of the Ye'cuana and the Yanomama: a likelihood analysis of genotypic variation among populations.

A general procedure is described for measuring and testing population differences in gametic frequencies. The total dispersion among populations is subdivided in hierachical fashion. The multiple-locus treatment is simply the sum of the single-locus analyses, provided gametic equilibrium obtains among the loci. In the event that gametic equilibrium does not obtain, correlations among loci need to be dealt with.--The analysis is then used to examine the genetic infrastructure of two Indian tribes from South America, the Ye'cuana (Makiritare) and the Yanomama. From historical evidence, we may identify several "clusters" of villages within each tribe. The demographic and cultural practices affecting village formation and the maintenance of peer integrity are rather different in these tribes, however, and lead us to postulate rather different patterns of genetic variation among villages. Analyses of five codominant two-allele loci, four dominant two-allele loci and two complex loci (with four codominant haplotypes each) demonstrate that Yanomama clusters are more disparate than Ye'cuana clusters, as would have been predicted on sociocultural grounds.

Blood Group Antigens↗

Endemic human T cell lymphotropic virus type II infection among isolated Brazilian Amerindians.

Evidence for human T cell lymphotropic viruses (HTLV) was sought in sera and cells collected from adults in 13 isolated South and Central American Indian tribes. Serologic tests identified frequent HTLV-II-like reactivity among the Cayapo and Kraho tribes, who live 330 km apart in Central Brazil. Polymerase chain reaction analyses of viral DNA in cell pellet and plasma fractions confirmed the virus as HTLV-II. Both tribes speak Gé and, at the time of blood collection (1974), subsisted as hunter/gatherers and slash and burn agriculturalists. Further testing of plasma from Cayapo and Kraho of all ages revealed overall HTLV-II prevalence rates of 33.3% and 12.2%, respectively, with increasing prevalence associated with age and female gender. These data reveal for the first time a high prevalence of HTLV-II infection in remote South American Indians with little contact with non-Indians. Thus, HTLV-II is postulated to be an ancient human virus in the New World.

Adult↗

Hepatitis B epidemiology and its relation to immunogenetic traits in South American Indians.

Serologic tests for hepatitis B prevalence and immunogenetic characterizations were carried out on a sample of 800 persons from several isolated tribes of the lower Amazon basin and the southern Andes. The prevalence of hepatitis B antigen carriers and of antibody to the surface antigen varied from one tribe to another, but were high in all the forest tribes. The serologic evidence indicated high infection rates early in life, but also an increasing proportion showing evidence of infection with increasing age. The frequency of past infections was not differentially associated with the antigen status of the mother or father. A higher proportion of infected males than females had antigenemia. Contrary to published reports, no association of antigenemia was found with any HLA-A, B or C antigen or immunoglobulin allotype, individually or interactively. Antibody prevalence, however, did differ in persons with different HLA haplotypes.

Adolescent↗

Molecular evolution of the teosinte branched gene among maize and related grasses.

Several authors have proposed that changes in a small number of regulatory genes may be sufficient for the evolution of novel morphologies. Recent analyses have indicated that teosinte branched1 (tb1), a putative bHLH transcription factor, played such a role during the morphological evolution of maize from its wild ancestor, teosinte. To address whether or not tb1 played a similar role during the evolution of the Andropogoneae, the tribe to which maize belongs, and to examine the rate and pattern of tb1 evolution within this tribe, we analyzed tb1-like sequences from 23 members of the Andropogoneae and five other grasses. Our analysis revealed that the TB1 protein evolves slowly within three conserved domains but rapidly outside these domains. The nonconserved regions of the gene are characterized by both a high nonsynonymous substitution rate and frequent indels. The ratio of nonsynonymous substitutions per nonsynonymous site (d(N)) to synonymous substitutions per synonymous site (d(S)) was not significantly greater than 1.0, providing no evidence for positive selection. However, the d(N)/d(S) ratio varied significantly among lineages and was high compared with those of other plant nuclear genes. Variation in the d(N)/d(S) ratio among the Andropogoneae could be explained by unequal levels of purifying selection among lineages. Consistent with this interpretation, the rate of nonsynonymous substitution differed along several lineages, while the synonymous substitution rate did not differ significantly. Finally, using tb1, we examined phylogenetic relationships within the Andropogoneae. The phylogeny suggests that the tribe underwent a rapid radiation during its early history and that the monoecious Andropogoneae are polyphyletic.

Amino Acid Sequence↗

Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences.

Portions of the 12S and 16S mitochondrial ribosomal genes for 16 species representing nine tribes in the mammal family Bovidae were compared with six previously published orthologous sequences. Phylogenetic analysis of variable nucleotide positions under different constraints and weighting schemes revealed no robust groupings among tribes. Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae. However, the basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data. The intractability of this systematic problem is consistent with a rapid radiation of the major bovid groups. Several analyses of our data show that monophyly of the Bovidae, which was weakly supported by previous morphological and molecular work, is questionable.

Animals↗