Mitochondrial DNA and the peopling of South America

The initial peopling of South America is largely unresolved, in part because of the unique distribution of genetic diversity in native South Americans. On average, genetic diversity estimated within Andean populations is higher than that estimated within Amazonian populations. Yet there is less genetic differentiation estimated among Andean populations than estimated among Amazonian populations. One hypothesis is that this pattern is a product of independent migrations of genetically differentiated people into South America. A competing hypothesis is that there was a single migration followed by regional isolation. In this study we address these hypotheses using mtDNA hypervariable region 1 sequences representing 21 South American groups and include new data sets for four native Peruvian communities from Tupe, Yungay, and Puno. An analysis of variance that compared the combined data from western South America to the combined data from eastern South America determined that these two regional data sets are not significantly different. As a result, a migration from a single source population into South America serves as the simplest explanation of the data.     

An ecological study of Caiman crocodilus crocodilus inhabiting savanna lagoons in the Venezuelan Guayana

Summary Mark and recapture studies were carried out for three and a half years on a population of Caiman c. crocodilus inhabiting a savanna lagoon system in the Venezuelan Guayana. Sub-adult and adult caimans migrated from permanent lagoon refuges to temporary lagoons during the wet season. A distinct homing response by artificially displaced caimans was observed.The wet season was the most significant time of the year for both feeding and growth. It was estimated that caimans take 6 years to reach a size of 97 cm. Thereafter the growth rate was variable. During a dry year there was little growth, but during a wet year a large caiman could increase in length by up to 10 cm.During the first 18 months of life, young caimans remained near the nest site. Older caimans dispersed and competed for territories which resulted in a high incidence of damage, particularly to the tails, as a result of intraspecific fighting.     

Mitochondrial DNA analysis of Sporothrix schenckii in North and South America

Mitochondrial DNA (mtDNA) types based on restriction fragment length polymorphism (RFLP) patterns with HaeIII were investigated in clinical isolates of Sporothrix schenckii in North and South America. In addition to 14 mtDNA types (Types 1–14) so far reported, six new mtDNA types, Types 15–20 were found in this study. Type 3 was divided into two subtypes, Subtype 3A and Subtype 3B based on RFLP with Msp1. Type 14 was also divided into three subtypes, Subtype 14A, Subtype 14B and Subtype 14C based on RFLP with Hha1. Nineteen isolates in the United States consisted of 1 isolate of Type 1, 12 of Type 2, 2 of Type 4, 3 of Type 14 (1 of Subtype 14B and 2 of Subtype 14C) and 1 of Type 15. Twenty nine isolates in Venezuela consisted of 13 of Type 3 (Subtype 3B), 6 of Type 4, 1 of Type 18, 3 of Type 19 and 6 of Type 20. Thirteen isolates in Argentina consisted of 2 of Type 3 (Subtype 3A), 4 of Type 4, 4 of Type 16 and 3 of Type 17. One isolate in Brazil was Type 3 (Subtype 3A). Based on the phylogeny of 20 mtDNA types (Types 1–20) constructed by estimating sequence divergences of mtDNA, mtDNA types were clustered into two groups: Group A (Types 1–3, Type 11 and Types 14–19) and Group B (Types 4–10, Types 12–13 and Type 20). These results suggest that S. schenckiiisolates in North and South America mainly belong to Group A. This revised version was published online in June 2006 with corrections to the Cover Date.     

Mitochondrial DNA phylogeography of European hedgehogs

European hedgehog populations belonging to Erinaceus europaeus and E . concolor have been investigated by mitochondrial DNA analysis. A 383 bp fragment of the cytochrome b gene has been sequenced and maximum parsimony and neighbour-joining trees of Tamura–Nei genetic distance values have been constructed. Similar topologies have been produced by both methods, showing a deep divergence between E . europaeus and E . concolor and a further subdivision of each species into a western and an eastern clade. A comparison with previously published allozyme data is made, and concordant and discordant patterns are discussed. The influence of Pleistocene glaciations on the observed pattern of divergence is inferred.     

Mitochondrial DNA under siege in avian phylogeography

Mitochondrial DNA (mtDNA) has been the workhorse of research in phylogeography for almost two decades. However, concerns with basing evolutionary interpretations on mtDNA results alone have been voiced since the inception of such studies. Recently, some authors have suggested that the potential problems with mtDNA are so great that inferences about population structure and species limits are unwarranted unless corroborated by other evidence, usually in the form of nuclear gene data. Here we review the relative merits of mitochondrial and nuclear phylogeographical studies, using birds as an exemplar class of organisms. A review of population demographic and genetic theory indicates that mitochondrial and nuclear phylogeographical results ought to concur for both geographically unstructured populations and for populations that have long histories of isolation. However, a relatively common occurrence will be shallow, but geographically structured mtDNA trees--without nuclear gene corroboration--for populations with relatively shorter periods of isolation. This is expected because of the longer coalescence times of nuclear genes (approximately four times that of mtDNA); such cases do not contradict the mtDNA inference of recent isolation and evolutionary divergence. Rather, the nuclear markers are more lagging indicators of changes in population structure. A review of the recent literature on birds reveals the existence of relatively few cases in which nuclear markers contradict mitochondrial markers in a fashion not consistent with coalescent theory. Preliminary information from nuclear genes suggests that mtDNA patterns will prove to be robust indicators of patterns of population history and species limits. At equilibrium, mitochondrial loci are generally a more sensitive indicator of population structure than are nuclear loci, and mitochondrial estimates of F(ST)-like statistics are generally expected to exceed nuclear ones. Hence, invoking behavioural or ecological explanations of such differences is not parsimonious. Nuclear genes will prove important for quantitative estimates of the depths of haplotype trees, rates of population growth and values of gene flow.     

On the dependence on metabolism of the cochlear potentials in Caiman (Caiman crocodilus)

Summary Investigation of the cochlear potentials in a reptile shows that the microphonics contain 2 components as previously observed in birds. The potentials depend to varying degrees and in a similar way as in birds on metabolism; the time course is expanded by a factor of 20.Supported by the Deutsche Forschungsgemeinschaft.     

Mitochondrial DNA diversity in South America and the genetic history of Andean highlanders

We analyzed mtDNA sequence variation in 590 individuals from 18 south Amerindian populations. The spatial pattern of mtDNA diversity in these populations fits well the model proposed on the basis of Y-chromosome data. We found evidence of a differential action of genetic drift and gene flow in western and eastern populations, which has led to genetic divergence in the latter but not in the former. Although it is not possible to identify a pattern of genetic variation common to all South America, when western and eastern populations are analyzed separately, the mtDNA diversity in both regions fits the isolation-by-distance model, suggesting independent evolutionary dynamics. Maximum-likelihood estimates of divergence times between central and south Amerindian populations fall between 13,000 and 19,000 years, which is consistent with a Pleistocenic peopling of South America. Moreover, comparison of among-population variability of mtDNA and Y-chromosome DNA seems to indicate that South America is the only continent where the levels of differentiation are similar for maternal and paternal lineages.     

Kinematics of the jaw and hyolingual apparatus during feeding in Caiman crocodilus

Movements of the neck, jaws, and hyolingual apparatus during inertial feeding in Caiman crocodilus were studied by cineradiography. Analysis reveals two kinds of cycles: inertial bites (reposition, kill/crush, and transport) and swallowing cycles. They differ in their gape profile and in displacement of the neck, cranium, and hyolingual apparatus. Inertial bites are initiated by an elevation of the neck and cranium; the head is then retracted backward, the prey simultaneously being lifted by the hyolingual apparatus. Next the lower jaw is depressed, and the prey is rapidly pushed further upward by the hyolingual apparatus. Thereafter fast mouth-closure occurs with the neck and cranium being abruptly depressed, the lower jaw elevated, and the hyolingual apparatus rapidly retracted ventrally. Depression of the neck and cranium thrusts the head forward and impacts the backward moving prey more posteriorly in the oral cavity. Swallowing cycles initially involve movement of the hyoid in front of the prey followed by rapid posteroventrad retraction of the hyoid, forcing the prey into the esophagus during opening and closing of the mouth. After mouth-closure, the hyoid apparatus is again protracted. Jaws, neck, tongue, and hyoid apparatus play an active role during intertial feeding sequences. At the beginning of a feeding sequence, the hyolingual apparatus mainly moves dorsoventrally, whereas toward the end of a sequence anteroposterior displacements of the hyoid are prominent. © 1992 Wiley-Liss, Inc.     

Bayesian phylogeography of the Arawak expansion in lowland South America

Phylogenetic inference based on language is a vital tool for tracing the dynamics of human population expansions. The timescale of agriculture-based expansions around the world provides an informative amount of linguistic change ideal for reconstructing phylogeographies. Here we investigate the expansion of Arawak, one of the most widely dispersed language families in the Americas, scattered from the Antilles to Argentina. It has been suggested that Northwest Amazonia is the Arawak homeland based on the large number of diverse languages in the region. We generate language trees by coding cognates of basic vocabulary words for 60 Arawak languages and dialects to estimate the phylogenetic relationships among Arawak societies, while simultaneously implementing a relaxed random walk model to infer phylogeographic history. Estimates of the Arawak homeland exclude Northwest Amazonia and are bi-modal, with one potential homeland on the Atlantic seaboard and another more likely origin in Western Amazonia. Bayesian phylogeography better supports a Western Amazonian origin, and consequent dispersal to the Caribbean and across the lowlands. Importantly, the Arawak expansion carried with it not only language but also a number of cultural traits that contrast Arawak societies with other lowland cultures.     

Mitochondrial DNA phylogeography of Glyptothorax fokiensis and Glyptothorax hainanensis in Asia

Whole mitochondrial DNA cytochrome b sequences in 62 fish from 13 locations in Southeast China identified two major clades corresponding to two allopatric taxa, Glyptothorax fokiensis fokiensis and Glyptothorax fokiensis hainanensis . Reciprocal monophyly and a molecular clock separation between these two taxa of 2·3 million years indicate these taxa should be elevated to species. Mismatch distributions and Fu's F _S statistic suggest that both G. fokiensis and G. hainanensis have experienced recent population expansions. Analysis of molecular variance indicates that most of the genetic variation resides among populations within both species, with Φ _ST= 0·645 for G. fokiensis and 0·801 for G. hainanensis , suggesting restricted gene flow among populations. Significant correlations between the geographic and the genetic distances provide support for the importance of geographic isolations between populations. Nested clade analysis also confirms low levels of genetic exchanges between the two major groups and between populations within each group. The phylogeographical pattern among populations of Glyptothorax in East Asia can be attributed to historical fragmentations, demographic expansions and occasional long-distance dispersals stimulated by tectonic activity and Ice Age climate changes.     

Annual and inter-annual variability of the present climate in northern South America and southern Mesoamerica

Present climate of northwestern South America and the southern Isthmus is detailed in terms of major hydro-climatic controls, supported by evidence from station records, reanalysis data and satellite information. In this tropical region, precipitation is the principal hydro-climatological variable to display great variability. The primary objective is to view the controls that operate at intra-seasonal to inter-decadal time scales. This is a topographical complex region whose climate influences range in provenance from the South Atlantic to the Canadian Prairies, and from the North Atlantic to the Eastern Pacific. The situation is further complicated by interactions and feedbacks, in time and space, between these influences, which are interconnected over various scales. The greatest single control on the annual cycle is the meridional migration of the Inter-tropical Convergence Zone and its pattern of associated trade winds. Consideration of these alone and their interaction with the Cordilleras of the Andes and Central America produce a variety of unimodal and bimodal regimes. Regionally, two low level jet streams, the westerly Choco jet (5°N) and the easterly San Andrés jet (12-14°N), and their seasonal variability, have tremendous significance, as do mesoscale convective storms and mid-latitude cold fronts from both the northern (“nortes”) and southern (“friagems”) hemispheres. There are many examples of hydro-climatological feedbacks within the region. Of these the most notable is the interaction between evaporation over the Amazon, precipitation onto the eastern Andes and streamflow from the headwaters of the Amazon. This is further compounded by the high percentages of recycled precipitation over large areas of the tropics and the potential impacts of anthropogenic modification of the land surface. The El Niño-Southern Oscillation phenomenon (ENSO) is the greatest single cause of interannual variability within the region, yet its effects are not universal in their timing, sign or magnitude. A set of regional physical connections to ENSO are established and their varying local manifestations are viewed in the context of the dominant precipitation generating mechanisms and feedbacks at that location. In addition, some potential impacts of longer run variations within the ocean-atmosphere system of the Atlantic are examined independently and in conjunction with ENSO. This review of the climatic controls and feedbacks in the region provides a spatial and temporal framework within which the highly complex set of factors and their interactions may be interpreted from the past.     

Mitochondrial DNA phylogeography of red deer (Cervus elaphus)

In order to understand the origin, phylogeny, and phylogeography of the species Cervus elaphus, we examined the DNA sequence variation of the mitochondrial cytochrome b gene of 51 populations of deer from the entire distribution area of Cervinae with an emphasis on Europe and Asia. Several methods, including maximum parsimony, maximum likelihood, and nested clade analysis, revealed that red deer originated from the area between Kyrgyzstan and Northern India. We found two distinct groups of red deer: a western group consisting of four subgroups and an eastern group consisting of three subgroups. Our mtDNA data do not support the traditional classification of red deer as only one species nor its division into numerous subspecies. The discrepancies between the geographical pattern of differentiation based on mtDNA cytochrome b and the existing specific and subspecific taxonomy based on morphology are discussed.     

Women in Prehistory: North America and Mesoamerica

Women in Prehistory: North America and Mesoamerica. Cheryl Claassen and Rosemary A. Joyce. eds. Philadelphia: University of Pennsylvania Press, 1997. 300 pp.     

Organization of motoneurons innervating the axial musculature of the brown caiman (Caiman crocodilus fuscus)

The primary divisions of the spinal nerve in the brown caiman characteristically show the following features: (1) the medial ramus was lies in the thoraco-lumbar and caudal regions, and (2) the first cervical and hypoglossal nerves form a single nerve complex from which the ventral and dorsal rami extend. Intramuscular injections of horseradish peroxidase (HRP) established the positions of motoneurons whose axons followed the primary rami. In the ventral horn of the thoracic and caudal spinal cord, the motoneurons of the medial ramus lie ventrally. These motoneurons lie between the epaxial and hypaxial motoneurons. At the spinomedullary junction, the pools of motoneurons innervating the infrahyoid, lingual, and dorsal muscles have a somatotopic organization similar to that observed in the thoraco-lumbar and caudal regions. Thus clear somatotopic organization of the motoneurons that innervate the axial musculature exists at all spinal levels. © 1994 Wiley-Liss, Inc.     

Mitochondrial and nuclear DNA phylogeography of Crassostrea angulata, the Portuguese oyster endangered in Europe

The respective status of the Portuguese oyster, Crassostrea angulata, and the Pacific oyster, Crassostrea gigas, has long been a matter of controversy. Morphological and physiological similarities, homogeneity of allozyme allelic frequencies between populations of the two taxa and the demonstration of hybridization lead most authors to suggest that they should be regrouped within the same species. The risk of introgression and the present expansion of C. gigas aquaculture in Europe raises the question of the need for preservation of C. angulata in Europe, as only a few populations remain. We studied European and Asian populations of C. gigas and C. angulata using microsatellite and mitochondrial DNA markers to estimate their genetic diversity and differentiation. The analysis of genetic distances and the distribution of allelic and haplotype frequencies revealed significant genetic differences between taxa, showing two clusters: (1) C. gigas French and Japanese populations and (2) C. angulata Portuguese and Taiwanese populations. The Asian origin of the Crassostrea angulata taxa is therefore confirmed. Unlike previous studies based on allozymes, significant nuclear genome differences were noted between C. angulata and C. gigas. Despite the presumed history of the introduction of C. angulata into Southern Europe, these populations did not show any significant reduction of variability compared to Taiwanese populations. Any conservation plans for European C. angulata populations should take its non-native origin into account. They represent a valuable genetic resources for European breeding program.     

Mitochondrial DNA phylogeography of the red fox (Vulpes vulpes) in northern Japan

Mitochondrial DNA variation in the cytochrome b (cyt b) gene and the control region was examined in the red fox Vulpes vulpes from Japan, with special focus on the population divergence between Hokkaido and northern Honshu. Resultant haplotypes from Hokkaido were subdivided into two distinct groups (I and II), with an average genetic distance of 0.027 for cyt b. Divergence time is roughly estimated to be 1-2 million years ago, given that the conventional divergence rate of the mammalian cyt b gene is 2% per million years. Notably, Group II was only found in Hokkaido, whereas Group I comprised haplotypes from Honshu, Kyushu (Japan), eastern Russia, and Europe, as indicated by a comparison of our own data to the literature. On the other hand, judging from constructed trees, Group I haplotypes from Hokkaido appeared to differ from those from other parts of Japan, i.e., Honshu and Kyushu. This implies that Blakiston's Line, which demarcates the boundary between Hokkaido and Honshu, has been an effective barrier and has allowed the structuring of genetic variation in maternal lineages. Thus, these results suggest that the Hokkaido population, which is sometimes referred to as the distinct subspecies V. v. schrencki, has its own genetic background with multiple migration events and differs from the parapatric subspecies V. v. japonica found in Honshu and Kyushu.     

Mitochondrial DNA sequence variation and phylogeography of the scarlet kingsnake (Lampropeltis elapsoides)

BACKGROUND AND AIMS. With the goal of assessing population structure and geographic distribution of haplotype lineages among Lampropeltis elapsoides, we sequenced the ND4 mitochondrial DNA locus from 96 specimens of this snake across its area of distribution. MATERIALS AND METHODS. We relied heavily on formalin-fixed museum specimens to accomplish this analysis. RESULTS. The sequence alignment consisted of 491 bp of the selected gene, with 28% missing data. A simulation used to assess the effect of missing data on population genetic and phylogenetic resolution indicated increased character conflict, but with minimal loss of phylogenetic structure. CONCLUSION. This limited dataset suggests that L. elapsoides constitutes a largely unstructured population, with both widespread haplotypes and large number of private haplotypes, a moderate level of nucleotide diversity, and a low, but significant, degree of north-south population differentiation. Haplotype structure and frequency, nucleotide frequency, and values for Tajima's D and Fu's F(S) indicate a recent range or population expansion following a historic bottleneck.     

Peasantries and Other Topics: South and Mesoamerica

The Peasant Marketing System of Oaxaca, Mexico. Ralph L. Beals .
Pyramids of Sacrifice: Political Ethics and Social Change. Peter L. Berger .
Struggle in the Andes: Peasant Political Mobilization in Peru. Howard Handelman .
The Moving Frontier: Social and Economic Change in a Southern Brazilian Community. Maxine L. Margolis .
Peasants, Politics, and Revolution: Pressures toward Political and Social Change in the Third World. Joel S. Migdal .
Formaciones economicas y politicas del mundo andino. John V. Murra .
The Shaman and the Jaguar: A Study of Narcotic Drugs among the Indians of Colombia. Gerardo Reichel-Dolmatoff .
Brazilian Society. T. Lynn Smith .     

Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America

Molecular studies of plants from the Pacific Northwest of North America suggest a recurrent pattern of genetic differentiation and geographic structuring. In each of five angiosperms and one fern species representing diverse life histories, cpDNA data indicate two clades of populations that are geographically structured. A northern group comprises populations from Alaska to central or southern Oregon, whereas populations from central Oregon southward to northern California form a southern group. In several of these species, a few populations having southern genotypes may have survived in glacial refugia further north in the Olympic Peninsula, Queen Charlotte Islands, and Prince of Wales Island. Allozyme data reveal a similar pattern of differentiation in several other plants from the Pacific Northwest. North-south partitioning of genotypes has also been reported for several animal species from this region. On a broader geographic scale, northsouth partitioning of genotypes has also been observed in other plants from western North America having a variety of geographic distributions. Some species also display a reduction of genetic variability in the northern portion of their range compared to the south. The data suggest strongly that past glaciation profoundly influenced the genetic architecture of the flora and fauna of the Pacific Northwest. Two alternative hypotheses are advanced to explain the geographic structuring of genotypes. First, past glaciation may have created discontinuities in the geographic distributions of plant species, with populations surviving in several well-isolated northern and southern refugia. Following glaciation, migration of genetically differentiated, once-isolated populations resulted in the formation of a continuous geographic distribution with a major genetic discontinuity. Alternatively, plants survived and subsequently migrated northward from a southern refugium, and a genotype became fixed in one or a few populations at the leading edge of recolonization. Subsequent long-distance dispersal from this leading edge resulted in a relatively uniform northern genotype that differs from the southern genotype(s). Whatever the underlying mechanism, Pleistocence glaciation may have molded the intraspecific genetic architecture of both plants and animals from the Pacific Northwest in a geographically similar manner. Future studies should seek to obtain a comprehensive phylogeography for regions that includes a diversity of both plants and animals.Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday