Reflections of Our Past: How Human History Is Revealed in Our Genes

Reflections of Our Past: How Human History Is Revealed in Our Genes. John H. Relethford. Boulder: Westview Press, 2004. 257 pp.     

Genetic variation in Native Americans, inferred from Latino SNP and resequencing data

Analyses of genetic polymorphism data have the potential to be highly informative about the demographic history of Native American populations, but due to a combination of historical and political factors, there are essentially no autosomal sequence polymorphism data from any Native American group. However, there are many resequencing studies involving Latinos, whose genomes contain segments inherited from their Native American ancestors. In this study, we introduce a new method for estimating local ancestry across the genomes of admixed individuals and show how this method, along with dense genotyping and targeted resequencing, can be used to assay genetic variation in ancestral Native American groups. We analyze roughly 6 Mb of resequencing data from 22 Mexican Americans to provide the first large-scale view of sequence level variation in Native Americans. We observe low levels of diversity and high levels of linkage disequilibrium in the Native American-derived sequences, consistent with a recent severe population bottleneck associated with the initial peopling of the Americas. Using two different computational approaches, one novel, we estimate that this bottleneck occurred roughly 12.5 Kya; when uncertainty in the estimation process is taken into account, our results are consistent with archeological estimates for the colonization of the Americas.     

Evolutionary History of the Vertebrate Period Genes

Circadian clock genes are remarkably conserved between eucoelomates. Although Drosophila has one copy of each major component, vertebrates have two or (in the case of the Period genes) three paralogs (Per1-3). We investigated the possibility that the vertebrate Per genes arose through two genome duplications during the emergence of vertebrates. Phylogenetic trees have placed zebrafish and mammalian Per1 and 2 together in a separate branch from Per3. The positions of four coding region splice sites were conserved between Drosophila per and the human paralogs, the fifth one being unique to Drosophila. The human PER genes shared the positions of all coding region splice sites, except the first two in PER1 and PER2 (which PER3 lacks). The phases of all splice sites were conserved between all four genes with two exceptions. Analysis of all genes within 10 Mb of the human PER1-3 genes, which are located 7.8—8.8 Mb from the telomeres on chromosomes 17, 2, and 1, identified several orthologous neighbors shared by at least two PER genes. Two gene families, HES (hairy and Enhancer of Split) and KIF1 (kinesin-like protein 1), were represented in all three of these paralogons. Although no functional fourth human PER paralog exists, five representatives from the same gene families were found close to the telomer of chromosome 3. We conclude that the ancestral chordate Per gene underwent two duplication events, giving rise to Per1—3 and a lost fourth paralog. [Reviewing Editor: Dr. John Onkeshott]     

Early Evolution of Immunoglobulin Genes

Considerable progress has been made in the characterizationof immunoglobulin genes from several lower vertebrate taxa.Isolation and identification of immunoglobulin genes in phylogeneticallyprimitive species is based predominantly on heterologous crosshybridization.The unit, clustered organization of heavy chain segmental elementsobserved in the germline of the horned shark (Hinds and Litman,1986) has also been found in another elasmobranch. Studies todetermine whether the clustered organization is universal throughoutthe entire cartilaginous fish assemblage are ongoing. In contrast,the ray-finned (bony)fishes appear to possess a mammalian-typeheavy chain gene organization. Additionally, immunoglobulingenes are being characterized in two relict fish species whoseexact systematic relationships are unknown. Isolation of putativeimmunoglobulin genes from the phylogenetically- ancient hagfishis being attempted using a PCR-based approach. Other ongoingor future research efforts involve characterization of lowervertebrate light chain genes, heavy chain isotype evolution,and the divergence of the immunoglobulins and T-cell antigenreceptors     

Genes, Tribes, and African History

Over the past 40 years, traditional perspectives on the constitution of human groups have been subjected to stringent critique within anthropology. This began with the dismantling of accepted "race" divisions after World War II and continued with analyses of the meaning and reality of African "tribal" distinctions from the 1960s until the present. Archaeologists, ethnographers, linguists, and historians of Africa now work within a research milieu where social interactions, cultural exchange, and the dynamic nature of group identifications are accepted as a normal part of the human experience. At the same time, new techniques have been developed for the examination of human history, techniques based upon an expanding repertoire of tools for the analysis of genetic variability in human populations. Perhaps the most striking result of this research has been Cavalli-Sforza, Menozzi, and Piazza's The History and Geography of Human Genes. Rather less attention has been paid, however, to the conceptual relationships between the human groups defined through such analyses, in Africa and elsewhere, and those defined through other kinds of research. This paper is a preliminary examination of the fit between genetic, archaeological, and ethnographic data on the African past.     

Genes, Tribes, and African History

Over the past 40 years, traditional perspectives on the constitution of human groups have been subjected to stringent critique within anthropology. This began with the dismantling of accepted "race" divisions after World War II and continued with analyses of the meaning and reality of African "tribal" distinctions from the 1960s until the present. Archaeologists, ethnographers, linguists, and historians of Africa now work within a research milieu where social interactions, cultural exchange, and the dynamic nature of group identifications are accepted as a normal part of the human experience. At the same time, new techniques have been developed for the examination of human history, techniques based upon an expanding repertoire of tools for the analysis of genetic variability in human populations. Perhaps the most striking result of this research has been Cavalli-Sforza, Menozzi, and Piazza's The History and Geography of Human Genes. Rather less attention has been paid, however, to the conceptual relationships between the human groups defined through such analyses, in Africa and elsewhere, and those defined through other kinds of research. This paper is a preliminary examination of the fit between genetic, archaeological, and ethnographic data on the African past.     

Genes, Tribes, and African History

Over the past 40 years, traditional perspectives on the constitution of human groups have been subjected to stringent critique within anthropology. This began with the dismantling of accepted "race" divisions after World War II and continued with analyses of the meaning and reality of African "tribal" distinctions from the 1960s until the present. Archaeologists, ethnographers, linguists, and historians of Africa now work within a research milieu where social interactions, cultural exchange, and the dynamic nature of group identifications are accepted as a normal part of the human experience. At the same time, new techniques have been developed for the examination of human history, techniques based upon an expanding repertoire of tools for the analysis of genetic variability in human populations. Perhaps the most striking result of this research has been Cavalli-Sforza, Menozzi, and Piazza's The History and Geography of Human Genes. Rather less attention has been paid, however, to the conceptual relationships between the human groups defined through such analyses, in Africa and elsewhere, and those defined through other kinds of research. This paper is a preliminary examination of the fit between genetic, archaeological, and ethnographic data on the African past.     

Evolutionary History and Functional Diversification of Phosphomannomutase Genes

Phosphomannomutases (PMMs) catalyze the interconversion of mannose-6-phosphate to mannose-1-phosphate. In humans, two PMM enzymes exist—PMM1 and PMM2; yet, they have different functional specificities. PMM2 presents PMM activity, and its deficiency causes a Congenital Disorder of Glycosylation (PMM2-CDG). On the other hand, PMM1 can also act as glucose-1,6-bisphosphatase in the brain after stimulation with inosine monophosphate and thus far has not been implicated in any human disease. This study aims to refine the evolutionary time frame at which gene duplication gave rise to PMM1 and PMM2, and to identify the most likely amino acid positions underlying the proteins’ different functions. The phylogenetic analysis using available protein sequences, allowed us to establish that duplication occurred early in vertebrate evolution. In order to understand the molecular basis underlying the functional divergence, conserved and most likely functional divergence-related sites were identified, through the analysis of site-specific evolutionary rates. This analysis indicates that most of the sites known to be important in the homodimer formation and in the catalytic activity are conserved in both proteins. Among those potentially related to functional divergence, two positions (183 and 186 in human PMM1) emerge as the most interesting ones. The residues at these positions have different side-chain conformations in the protein structure in the unbound and bound states, and are highly but differently conserved in PMM1 and in PMM2 proteins. Altogether, these results provide new data into the evolutionary history of PMM1 and PMM2 duplicates and highlight the most probable sites that evolved to distinct functional specificities.     

Analysis of the Exochelin Locus in Mycobacterium smegmatis: Biosynthesis Genes Have Homology with Genes of the Peptide Synthetase Family

Mycobacteria secrete the siderophore exochelin when grown under iron-limiting conditions. In order to understand iron uptake mechanisms in mycobacteria, we have taken a genetic approach to identify those genes involved in exochelin biosynthesis and transport in Mycobacterium smegmatis. Of the 6,000 chemically mutagenized clones of M. smegmatis mc²155 screened on agar plates containing chrome azural S, 19 mutants that had lost the ability to produce or secrete exochelin were identified. Thirteen of these mutants were complemented by a single M. smegmatis cosmid. Sequence analysis of this cosmid revealed nine open reading frames, three of which are homologous to genes encoding transporter proteins, which are likely involved in exochelin transport. Complementation and Tn10 mutagenesis analysis identified two new genes, fxbB and fxbC, which are required for exochelin biosynthesis. The fxbB and fxbC genes encode large proteins of 257 and 497 kDa, respectively, which are highly homologous to peptide synthetases, indicating that exochelin biosynthesis occurs by a nonribosomal mechanism.     

Early South Americans Cranial Morphological Variation and the Origin of American Biological Diversity

Recent South Americans have been described as presenting high regional cranial morphological diversity when compared to other regions of the world. This high diversity is in accordance with linguistic and some of the molecular data currently available for the continent, but the origin of this diversity has not been satisfactorily explained yet. Here we explore if this high morphological variation was already present among early groups in South America, in order to refine our knowledge about the timing and origins of the modern morphological diversity. Between-group (Fst estimates) and within-group variances (trace of within-group covariance matrix) of the only two early American population samples available to date (Lagoa Santa and Sabana de Bogotá) were estimated based on linear craniometric measurements and compared to modern human cranial series representing six regions of the world, including the Americas. The results show that early Americans present moderate within-group diversity, falling well within the range of modern human groups, despite representing almost three thousand years of human occupation. The between-group variance apportionment is very low between early Americans, but is high among recent South American groups, who show values similar to the ones observed on a global scale. Although limited to only two early South American series, these results suggest that the high morphological diversity of native South Americans was not present among the first human groups arriving in the continent and must have originated during the Middle Holocene, possibly due to the arrival of new morphological diversity coming from Asia during the Holocene.     

Evolution of Rh Blood Group Genes Have Experienced Gene Conversions and Positive Selection

There are two tightly linked loci (D and CE) for the human Rh blood group. Their gene products are membrane proteins having 12 transmembrane domains and form a complex with Rh50 glycoprotein on erythrocytes. We constructed phylogenetic networks of human and nonhuman primate Rh genes, and the network patterns suggested the occurrences of gene conversions. We therefore used a modified site-by-site reconstruction method by using two assumed gene trees and detected 9 or 11 converted regions. After eliminating the effect of gene conversions, we estimated numbers of nonsynonymous and synonymous substitutions for each branch of both trees. Whichever gene tree we selected the branch connecting hominoids and Old World monkeys showed significantly higher nonsynonymous than synonymous substitutions, an indication of positive selection. Many other branches also showed higher nonsynonymous than synonymous substitutions; this suggests that the Rh genes have experienced some kind of positive selection. Received: 16 March 1999 / Accepted: 17 June 1999     

A History of Dogs in the Early Americas

. History of Dogs in the Early Americas. Marion Schwartz. New Haven, CT: Yale University Press, 1997. 233 pp.     

How Venetians Think About Carnival and History

Carnival in Venice dates back to the the 11th century. After steadily efflorescing through to the 18th century and acquiring a grand reputation throughout Europe and beyond, carnival lapsed in the period after the conquest by Napoleon in 1797. Only in 1979 did it reemerge as an important Venetian event. This essay traces the important historical continuities and contexts of Venetian carnival to the present. Despite its hiatus, Venetians link themselves and their carnival to their glorious, remote past, demonstrating profound historical consciousness, politicising and debating the ‘real’ meaning of carnival and above all, defining and reaffirming their own identity through its performance.