Joseph G. Lorenz

Distribution of mtDNA haplogroup X among Native North Americans.

Mitochondrial DNA (mtDNA) samples of 70 Native Americans, most of whom had been found not to belong to any of the four common Native American haplogroups (A, B, C, and D), were analyzed for the presence of Dde I site losses at np 1715 and np 10394. These two mutations are characteristic of haplogroup X which might be of European origin. The first hypervariable segment (HVSI) of the non-coding control region (CR) of mtDNA of a representative selection of samples exhibiting these mutations was sequenced to confirm their assignment to haplogroup X. Thirty-two of the samples exhibited the restriction site losses characteristic of haplogroup X and, when sequenced, a representative selection (n = 11) of these exhibited the CR mutations commonly associated with haplogroup X, C --> T transitions at np 16278 and 16223, in addition to as many as three other HVSI mutations. The wide distribution of this haplogroup throughout North America, and its prehistoric presence there, are consistent with its being a fifth founding haplogroup exhibited by about 3% of modern Native Americans. Its markedly nonrandom distribution with high frequency in certain regions, as for the other four major mtDNA haplogroups, should facilitate establishing ancestor/descendant relationships between modern and prehistoric groups of Native Americans. The low frequency of haplogroups other than A, B, C, D, and X among the samples studied suggests a paucity of both recent non-Native American maternal admixture in alleged fullblood Native Americans and mutations at the restriction sites that characterize the five haplogroups as well as the absence of additional (undiscovered) founding haplogroups.

Distribution of four founding mtDNA haplogroups among Native North Americans

The mtDNA of most Native Americans has been shown to cluster into four lineages, or haplogroups. This study provides data on the haplogroup affiliation of nearly 500 Native North Americans including members of many tribal groups not previously studied. Phenetic cluster analysis shows a fundamental difference among 1) Eskimos and northern Na-Dene groups, which are almost exclusively mtDNA haplogroup A, 2) tribes of the Southwest and adjacent regions, predominantly Hokan and Uto-Aztecan speakers, which lack haplogroup A but exhibit high frequencies of haplogroup B, 3) tribes of the Southwest and Mexico lacking only haplogroup D, and 4) a geographically heterogeneous group of tribes which exhibit varying frequencies of all four haplogroups. There is some correspondence between language group affiliations and the frequencies of the mtDNA haplogroups in certain tribes, while geographic proximity appears responsible for the genetic similarity among other tribes. Other instances of similarity among tribes suggest hypotheses for testing with more detailed studies. This study also provides a context for understanding the relationships between ancient and modern populations of Native Americans.

The Structure of Diversity within New World Mitochondrial DNA Haplogroups: Implications for the Prehistory of North America

The mitochondrial DNA haplogroups and hypervariable segment I (HVSI) sequences of 1,612 and 395 Native North Americans, respectively, were analyzed to identify major prehistoric population events in North America. Gene maps and spatial autocorrelation analyses suggest that populations with high frequencies of haplogroups A, B, and X experienced prehistoric population expansions in the North, Southwest, and Great Lakes region, respectively. Haplotype networks showing high levels of reticulation and high frequencies of nodal haplotypes support these results. The haplotype networks suggest the existence of additional founding lineages within haplogroups B and C; however, because of the hypervariability exhibited by the HVSI data set, similar haplotypes exhibited in Asia and America could be due to convergence rather than common ancestry. The hypervariability and reticulation preclude the use of estimates of genetic diversity within haplogroups to argue for the number of migrations to the Americas.

The problems and promise of DNA barcodes for species diagnosis of primate biomaterials.

The Integrated Primate Biomaterials and Information Resource (www.IPBIR.org) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome c oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of ‘DNA barcodes’ for many species of primates. However, this quality control process is complicated by taxon specific patterns of ‘universal primer’ failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics.

Implications of the Distribution of Albumin Naskapi and Albumin Mexico for New World Prehistory

The known distributions of two mutational variants of the albumin gene that are restricted to Mexico and/or North America, Albumin Mexico (AL*Mexico) and Albumin Naskapi (AL*Naskapi), were expanded by the electrophoretic analysis of sera collected from more than 3, 500 Native Americans representing several dozen tribal groups. With a few exceptions that could be due to recent, isolated cases of admixture, AL*Naskapi is limited to groups that speak Athapaskan and Algonquian, two widely distributed language families not thought to be related, and to several linguistically unrelated groups geographically proximate to its probable ancestral homeland. Similarly, AL*Mexico is limited to groups that speak Yuman or Uto-Aztecan, two language groups in the American Southwest and Baja California not thought to be closely related to each other, and to several linguistically unrelated groups throughout Mexico. The simultaneous consideration of genetic, historical, linguistic, and archaeological evidence suggests that AL*Naskapi probably originated on the northwestern coast of North America, perhaps in some group ancestral to both Athapaskans and Algonquians, and then spread by migration and admixture to contiguous unrelated, or distantly related, tribal groups. AL*Mexico probably originated in Mexico before 3,000 years BP then spread northward along the Tepiman corridor together with cultural influences to several unrelated groups that participated in the Hohokam culture.

Mitochondrial DNA and Prehistoric Settlements: Native Migrations on the Western Edge of North America

We analyzed previously reported mtDNA haplogroup frequencies of 577 individuals and hypervariable segment 1 (HVS1) sequences of 265 individuals from Native American tribes in western North America to test hypotheses regarding the settlement of this region. These data were analyzed to determine whether Hokan and Penutian, two hypothesized ancient linguistic stocks, represent biological units as a result of shared ancestry within these respective groups. Although the pattern of mtDNA variation suggests regional continuity and although gene flow between populations has contributed much to the genetic landscape of western North America, some evidence supports the existence of both the Hokan and Penutian phyla. In addition, a comparison between coastal and inland populations along the west coast of North America suggests an ancient coastal migration to the New World. Similarly high levels of haplogroup A among coastal populations in the Northwest and along the California coast as well as shared HVS1 sequences indicate that early migrants to the New World settled along the coast with little gene flow into the interior valleys.

Using the Stable Carbon and Nitrogen Isotope Compositions of Vervet Monkeys (Chlorocebus pygerythrus) to Examine Questions in Ethnoprimatology

This study seeks to understand how humans impact the dietary patterns of eight free-ranging vervet monkey (Chlorocebus pygerythrus) groups in South Africa using stable isotope analysis. Vervets are omnivores that exploit a wide range of habitats including those that have been anthropogenically-disturbed. As humans encroach upon nonhuman primate landscapes, human-nonhuman primate interconnections become increasingly common, which has led to the rise of the field of ethnoprimatology. To date, many ethnoprimatological studies have examined human-nonhuman primate associations largely in qualitative terms. By using stable carbon (δ13C) and nitrogen (δ15N) isotope analysis, we use quantitative data to understand the degree to which humans impact vervet monkey dietary patterns. Based on initial behavioral observations we placed the eight groups into three categories of anthropogenic disturbance (low, mid, and high). Using δ13C and δ15N values we estimated the degree to which each group and each anthropogenically-disturbed category was consuming C4 plants (primarily sugar cane, corn, or processed foods incorporating these crops). δ13C values were significantly different between groups and categories of anthropogenic-disturbance. δ15N values were significantly different at the group level. The two vervet groups with the highest consumption of C4 plants inhabited small nature reserves, appeared to interact with humans only sporadically, and were initially placed in the mid level of anthropogenic-disturbance. However, further behavioral observations revealed that the high δ13C values exhibited by these groups were linked to previously unseen raiding of C4 crops. By revealing these cryptic feeding patterns, this study illustrates the utility of stable isotopes analysis for some ethnoprimatological questions.

Variation in vervet (Chlorocebus aethiops) hair cortisol concentrations reflects ecological disturbance by humans

AbstractVervet monkeys (Chlorocebus aethiops) often live in close proximity to humans. Vervets are known to raid crops, homes and gardens in suburban areas leading to human–vervet conflict. In general, primate groups with access to human foods experience increased population densities and intra-group aggression. This suggests high stress loads for vervets living in environments with high levels of human habitat disturbance and close proximity to humans. We tested the hypothesis that populations characterized by high levels of human impact are more physiologically stressed than low human impact populations, and that this increased stress would be reflected in higher concentrations of hair cortisol. We predicted that because females would be less likely to engage in high risk foraging activities, and hence keep more distance from humans than males, their hair cortisol levels should be lower than those in males. We quantified cortisol in the hair of wild caught individuals from populations that experienced different degrees of human habitat disturbance and differences in access to human food. We found that males in high human impact groups had significantly higher hair cortisol concentrations than those in low human impact groups, although this difference was not observed in female vervets. Human impacts on vervet behavioral ecology appear to be a significant source of stress for male animals in particular.

Variation in scrotal color among widely distributed vervet monkey populations (Chlorocebus aethiops pygerythrus and Chlorocebus aethiops sabaeus).

Vervet monkeys (Chlorocebus aethiops) exhibit bright blue scrotal skin which may function to mediate social interactions by acting as a socio‐sexual signal. Previous research on scrotal coloration among vervet monkeys was limited to experimental work on captive Ch. a. sabaeus, the least colorful vervet subspecies, and two field studies of the more colorful Ch. a. pygerythrus. In a study of free‐ranging and captive vervet monkeys in South Africa (Ch. pygerythrus), West Africa (Ch. a. sabaeus) and the Caribbean (Ch. a. sabaeus), we examined scrotal color variation across geographically distant subspecies. We provide an exploration of how digital photographs may be used to quantify and analyze blue and green skin coloration by examining the blue–yellow opponency channel and luminance channel as color measures. We found that that at all ages the scrotal color of Ch. a. pygerythrus males was always bluer and darker than that of Ch. a. sabaeus males. Among Ch. a. pygerythrus scrotal color becomes bluer and lightens with increasing age, while the color of Ch. a. sabaeus males also lightens, but becomes less blue with increasing age. We suggest that color variation is related to maturation and may function as an age‐related signal among Ch. a. pygerythrus and Ch. a. sabaeus. We also found color was related to three morphological features among adults. For Ch. a. pygerythrus, higher body weight is associated with more blue color and longer canine length is associated with lighter color. Lighter color was associated with longer body lengths among Ch. a. sabaeus. Future studies focused on color variation within age classes are needed to examine the potential signal content of color in this species. Am. J. Primatol. 75:752–762, 2013.

Worldwide Distribution of Allelic Variation at the Progesterone Receptor Locus and the Incidence of Female Reproductive Cancers

Global patterns of the incidence of cancer are often attributed to environmental and lifestyle differences between regions. Less attention has been given to global patterns of allelic variation of genes that may contribute to the risk of developing cancer.