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.     

Phylogeography of the harlequin beetle-riding pseudoscorpion and the rise of the Isthmus of Panamá

Molecular and geological evidence indicates that the emergence of the Isthmus of Panamá influenced the historical biogeography of the Neotropics in a complex, staggered manner dating back at least 9 Myr bp. To assess the influence of Isthmus formation on the biogeography of the harlequin beetle-riding pseudoscorpion, Cordylochernes scorpioides, we analysed mitochondrial COI sequence data from 71 individuals from 13 locations in Panamá and northern South America. Parsimony and likelihood-based phylogenies identified deep divergence between South American and Panamanian clades. In contrast to low haplotype diversity in South America, the Panamanian Cordylochernes clade is comprised of three highly divergent lineages: one clade consisting predominantly of individuals from central Panamá (PAN A), and two sister clades (PAN B1 and PAN B2) of western Panamanian pseudoscorpions. Breeding experiments demonstrated a strictly maternal mode of inheritance, indicating that our analyses were not confounded by nuclear-mitochondrial pseudogenes. Haplotype diversity is striking in western Atlantic Panamá, where all three Panamanian clades can occur in a single host tree. This sympatry points to the existence of a cryptic species hybrid zone in western Panamá, a conclusion supported by interclade crosses and coalescence-based migration rates. Molecular clock estimates yield a divergence time of approximately 3 Myr between the central and western Panamanian clades. Taken together, these results are consistent with a recent model in which a transitory proto-Isthmus enabled an early wave of colonization out of South America at the close of the Miocene, followed by sea level rise, inundation of the terrestrial corridor and then a second wave of colonization that occurred when the Isthmus was completed approximately 3 Myr bp.     

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.     

The genetic structure of a tribal population, the Yanomama Indians XI. Gene frequencies for 10 blood groups and the ABH-Le secretor traits in the Yanomama and their neighbors; the uniqueness of the tribe.

In this paper we present the results of blood group typings for a total of 33 villages distributed among five South American Indian tribes--Yanomama (21 villages), Makiritare (eight villages), Macushi (two villages), Piaroa (one village), and Wapishana (one village). These new results for the Yanomama and Makiritare tribes have been combined with those previously reported to allow a better appreciation of the distribution of allelic frequencies in the tribes. The relationship of the Yanomama to other South American Indian tribes is investigated using data on six polymorphic loci (Rh, MNS, Fy, Jk, Di, Hp). By use of four genetic measures (two of genetic relationship and two of genetic diversity), we demonstrate that the Yanomama are genetically unique among a sample of 20 South American tribes. In addition, the Yanomama show somewhat less genetic diversity for the six loci analyzed than the average South American tribe. Taken together, these results indicate a rather long period of isolation for the population antecedent to the Yanomama--perhaps since the time of entry of man into the South American continent. The pattern of genetic relationships and genetic diversity for the 20 tribes is consistent with the hypothesis that evolution in South America proceeded by a process of fission-fusion leading to isolation of subpopulations with subsequent genetic differentiation as a consequence of population isolation. The uniqueness of the Yanomama appears to stem entirely from such a process, there being no evidence of any selective differential for the loci analyzed.     

HLA antigens (A,B,C and D) among two groups of Guahiboan speaking Indians in Colombia. “Results of expedicion humana”

The serological HLA types (A,B,C and D loci) were studied in the Sikuani and Guayabero, two Guahiboan speaking Indian groups inhabiting the eastern lowlands of Colombia. Besides restricted polymorphism, the results show significant differences only in two antigens, A2 and B35, suggesting genetic similarity among these tribes which belong to the same linguistic family. Genetic distances were calculated for comparison with other Colombian groups so far studied, showing the lowest distance between the two tribes under study. The Guayabero were closer to the urban population of Bogota, which suggests that the genetic structure of the present day Amerindians of South America may be significantly influenced by the European populations.     

Blood genetic systems in four Amazonian tribes.

Data on 31 genetic systems were obtained for 421 individuals belonging to the Arara, Araweté, Mundurucu, and Jamamadi tribes of northern Brazil. The Jamamadi depart farthest, and the Mundurucu least, from South American Indian averages. These data are analyzed together with those of 24 other Amazonian groups. Genetic distances and corresponding dendrograms indicate a cluster of 14 related tribes living north of the Amazon river. These genetic results show only a modest correlation with linguistic and geographic relationships among these groups.     

Genetic relationships between Amerindian populations of Argentina

A total of 495 individuals from five different Argentinian tribes was examined for variation in 23 blood group and protein genetic systems, and the results were integrated with previous data on some of these systems. These tribes generally present RH * R1, PGM1 * 1, and ACP * A frequencies lower and RH * R2, ESD * 1, and GLO * 1 prevalences higher than those observed in other South American Indian groups. Earlier studies with mitochondrial DNA showed that haplogroup A was present in low frequencies in these tribes, but haplogroup B showed a high prevalence among the Mataco. Average heterozygosities are very similar in the five tribes, while estimates of non-Indian ancestry are generally low. Both the blood group and protein, as well as the mtDNA data sets, divide the five tribes into two groups, and the relationships obtained with the blood group and protein systems are exactly those expected on the basis of geography and language. However, the topology obtained with the mtDNA results was different, possibly due to sampling effects or diverse patterns of exchange between the groups related to sex.     

Intra- and inter-tribal genetic variability in South American Indians

A review was made of all studies to date concerning the genetic polymorphisms of South American Indians. The observed inter-tribal variability was then compared with the intra-tribal variation encountered in seven Caingang and three Xavante Indian communities. The differing pattern of genetic variability observed within these two tribes was afterwards correlated with the information available about their breeding structure.     

Mutant allele frequencies in domestic cat populations in Catalonia,Spain, and their genetic relationships with Spanish and English colonial cat populations

Two Catalan cat populations (Spain) were analyzed. The genetic profiles of these Catalan populations are very homogeneous. The low q (t ^b) values are the most outstanding factor. These populations and two British cat populations were compared with different colonial settlement cat populations. A close genetic relationship was found between Catalan populations and those of California, Texas, Colorado, Mexico and the North of South America (Caracas and Willemstad (Curaçao)).     

Population Histories and Genomic Diversity of South American Natives

South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation by distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in precontact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated precontact population reductions and demic expansions in South America.     

Microevolution in lower Central America: genetic characterization of the Chibcha-speaking groups of Costa Rica and Panama, and a consensus taxonomy based on genetic and linguistic affinity.

There is evidence that Amerindians have continuously occupied the lower Central American Isthmus for as long as 10,000 years. There remains some doubt about the relationships of these original colonizers to the resident peoples of this zone at the time of European contact (approximately A.D. 1500). We present new genetic data for up to 48 genetic loci for 570 members of six Chibcha-speaking tribes of lower Central America--the Boruca, Bribri, Cabecar, and Guatuso of Costa Rica and the Kuna and Teribe of Panama--and delineate the genetic affinities among the various groups (these six tribes and the Guaymi and Bokota) of lower Central America. We convert standard genetic distance metrics into a form that is linear with the effective time since divergence, and we compare the genetic distances with linguistic distances for the same groups (r = .74, P less than .001). Geographic affinity accounts for some of the genetic divergence among groups (r = .49, P less than .084) and for some of the linguistic divergence (r = .53, P less than .037), but the correspondence between geographic position and taxonomic affinity is not high. We combine all of the genetic and linguistic data to construct a synthetic overview taxonomy of the lower Central American Chibcha. Both the genetic and linguistic data exhibit hierarchical organization of tribal groups, showing a general east-to-west pattern of grouping, with greater affinities between close neighbors. The presence of private genetic variants of some antiquity within the region and their absence outside the zone, coupled with the essential absence of the DI*A polymorphism of mongoloid origin that is widespread outside the zone, argue for a relatively isolated development of the Central American Chibcha. Our results do not support the old view of lower Central America as a frontier between more advanced cultures to the north and south. Any such explanation would require recent waves of migration from outside the region, migration that is not compatible with either the genetic or linguistic data or with the archaeological history of the region.     

Molecular diversification of salamanders of the tropical American genus Bolitoglossa (Caudata: Plethodontidae) and its evolutionary and biogeographical implications

The largest genus of salamanders, Bolitoglossa (Plethodontidae), is widespread in tropical America, where it occurs in diverse habitats and elevations, from high elevation grasslands to lowland rain forest . It has the most extensive geographical range of any salamander genus. While most species occur in Middle America, it ranges throughout most of tropical South America as well. Phylogenetic analysis of 1196 bp of two mitochondrial genes (cytochrome b , 16S RNA) from 55 species offers strong support for the monophyly of the genus and sorts the species into a number of clades. Taking into account morphology, distribution, general ecology, and prior systematic and taxonomic studies, we recognize seven subgenera, four of them new: Bolitoglossa Duméril, Bibron et Duméril, 1854, Eladinea Miranda Ribeiro, 1937, Magnadigita Taylor, 1944, Mayamandra , Nanotriton , Oaxakia and Pachymandra . All South American and some lower Middle American species are included in a single well -supported clade, Eladinea . At the species level our analyses uncover the existence of large genetic diversity within morphologically homogeneous taxa. We propose the new combination: B. (Eladinea) paraensis (Unterstein, 1930) stat. nov. , for Brazilian salamanders previously included under B. altamazonica . We evaluate evidence for the multiple colonization of the tropical lowlands by morphologically derived species groups. South America was invaded by members of one clade, Eladinea , which we infer to have dispersed to South America prior to closure of the Panamanian Portal. Despite the relatively long history of salamanders in South America, that continent now accounts for a relatively small proportion of the lineages and species of neotropical salamanders.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81 , 325–346.     

Phylogenetic relationships in the cactus family (Cactaceae) based on evidence from trnK/ matK and trnL-trnF sequences

Cacti are a large and diverse group of stem succulents predominantly occurring in warm and arid North and South America. Chloroplast DNA sequences of the trnK intron, including the matK gene, were sequenced for 70 ingroup taxa and two outgroups from the Portulacaceae. In order to improve resolution in three major groups of Cactoideae, trnL-trnF sequences from members of these clades were added to a combined analysis. The three exemplars of Pereskia did not form a monophyletic group but a basal grade. The well-supported subfamilies Cactoideae and Opuntioideae and the genus Maihuenia formed a weakly supported clade sister to Pereskia. The parsimony analysis supported a sister group relationship of Maihuenia and Opuntioideae, although the likelihood analysis did not. Blossfeldia, a monotypic genus of morphologically modified and ecologically specialized cacti, was identified as the sister group to all other Cactoideae. The tribe Cacteae was found to be sister to a largely unresolved clade comprising the genera Calymmanthium, Copiapoa, and Frailea, as well as two large and well-supported clades. Browningia sensu stricto (excluding Castellanosia), the two tribes Cereeae and Trichocereeae, and parts of the tribes Notocacteae and Rhipsalideae formed one clade. The distribution of this group is largely restricted to South America. The other clade consists of the columnar cacti of Notocacteae, various genera of Browningieae, Echinocereeae, and Leptocereeae, the tribes Hylocereeae and Pachycereeae, and Pfeiffera. A large portion of this latter group occurs in Central and North America and the Caribbean.     

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 hierarchical 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.     

Further data on the microsatellite locus D12S67 in worldwide populations: an unusual distribution of D12S67 alleles in Native Americans

We report the frequencies of alleles at the microsatellite locus D12S67 in 2 widely separated ethnic groups of the world: 2 populations from Sulawesi, an island in the Indonesian archipelago, and 5 Native American tribes of Colombia, South America. The allele frequencies in the Minihasans and Torajans of Sulawesi are similar to each other (but the modal class allele is different) and in general agreement with those reported in mainland Asian groups, but different from both Europeans and Chinese Han of Taiwan. The 5 Native American tribes (Arsario, Kogui, Ijka, Wayuu, and Coreguaje) display different allele frequencies from those seen in Sulawesi populations, in other groups from Europe and mainland Asia, and in Chinese Han of Taiwan. Native Americans exhibit a bimodal distribution of alleles, unlike other groups, with significant differences among the tribes. The Arsario and Kogui have no admixture with Europeans or Africans and are the most distinctive, while the Wayuu have the most admixture and show most similarity to other groups. The data suggest that nonadmixed Native Americans may be quite distinctive with respect to this marker. The most common allele varies across the 5 tribes, from 249 base pairs to 261 base pairs. All samples exhibit Hardy-Weinberg genotype proportions; heterozygosities are lowest in the 2 nonadmixed Native American tribes. Examination of all the available data indicates that some east Asian and southeast Asian groups are characterized by a high frequency of smaller sized D12S67 alleles, while other populations have a greater proportion of the larger sized alleles. The cumulative, though still highly restricted, population data on locus D12S67 demonstrate that it may be of considerable value in anthropological genetic studies of ethnic groups. Data are required on Native Americans outside Colombia before this marker can be used in admixture studies of this group.     

Genetic distances among the Ho tribe and other groups of Central Indians

The Ho, a settled tribal group of Chota Nagpur, India, were tested for five genetic characters. Genetic distance among eleven tribal groups of Bihar, Orissa and Madhya Pradesh are calculated according to Edwards ('71). Affinities of these tribes are discussed taking into consideration the languages spoken by them. These breeding groups may have drifted apart along the paths of their dialect differentiations. Cultural and geographical factors further enhanced their isolation.     

Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): Systematics, morphology, and biogeography

The family Cervidae includes 40 species of deer distributed throughout the northern hemisphere, as well as in South America and Southeast Asia. Here, we examine the phylogeny of this family by analyzing two mitochondrial protein-coding genes and two nuclear introns for 25 species of deer representing most of the taxonomic diversity of the family. Our results provide strong support for intergeneric relationships. To reconcile taxonomy and phylogeny, we propose a new classification where the family Cervidae is divided in two subfamilies and five tribes. The subfamily Cervinae is composed of two tribes: the tribe Cervini groups the genera Cervus, Axis, Dama, and Rucervus, with the Père David's deer (Elaphurus davidianus) included in the genus Cervus, and the swamp deer (Cervus duvauceli) placed in the genus Rucervus; the tribe Muntiacini contains Muntiacus and Elaphodus. The subfamily Capreolinae consists of the tribes Capreolini (Capreolus and Hydropotes), Alceini (Alces), and Odocoileini (Rangifer + American genera). Deer endemic to the New World fall in two biogeographic lineages: the first one groups Odocoileus and Mazama americana and is distributed in North, Central, and South America, whereas the second one is composed of South American species only and includes Mazama gouazoubira. This implies that the genus Mazama is not a valid taxon. Molecular dating suggests that the family originated and radiated in central Asia during the Late Miocene, and that Odocoileini dispersed to North America during the Miocene/Pliocene boundary, and underwent an adaptive radiation in South America after their Pliocene dispersal across the Isthmus of Panama. Our phylogenetic inferences show that the evolution of secondary sexual characters (antlers, tusk-like upper canines, and body size) has been strongly influenced by changes in habitat and behaviour.     

Genetic differences between Chibcha and Non-Chibcha speaking tribes based on mitochondrial DNA (mtDNA) haplogroups from 21 Amerindian tribes from Colombia

We analyzed the frequency of four mitochondrial DNA haplogroups in 424 individuals from 21 Colombian Amerindian tribes. Our results showed a high degree of mtDNA diversity and genetic heterogeneity. Frequencies of mtDNA haplogroups A and C were high in the majority of populations studied. The distribution of these four mtDNA haplogroups from Amerindian populations was different in the northern region of the country compared to those in the south. Haplogroup A was more frequently found among Amerindian tribes in northern Colombia, while haplogroup D was more frequent among tribes in the south. Haplogroups A, C and D have clinal tendencies in Colombia and South America in general. Populations belonging to the Chibcha linguistic family of Colombia and other countries nearby showed a strong genetic differentiation from the other populations tested, thus corroborating previous findings. Genetically, the Ingano, Paez and Guambiano populations are more closely related to other groups of south eastern Colombia, as also inferred from other genetic markers and from archeological data. Strong evidence for a correspondence between geographical and linguistic classification was found, and this is consistent with evidence that gene flow and the exchange of customs and knowledge and language elements between groups is facilitated by close proximity.     

Global Genetics and Invasion History of the Potato Powdery Scab Pathogen,Spongospora subterranea f.sp. subterranea

Spongospora subterranea f. sp. subterranea (Sss) causes two diseases on potato (Solanum tuberosum), lesions on tubers and galls on roots, which are economically important worldwide. Knowledge of global genetic diversity and population structure of pathogens is essential for disease management including resistance breeding. A combination of microsatellite and DNA sequence data was used to investigate the structure and invasion history of Sss. South American populations (four countries, 132 samples) were consistently more diverse than those from all other regions (15 countries, 566 samples), in agreement with the hypothesis that Sss originated in South America where potato was domesticated. A substantial genetic differenciation was found between root and tuber-derived samples from South America. Estimates of past and recent gene flow suggested that Sss was probably introduced from South America into Europe. Subsequently, Europe is likely to have been the recent source of migrants of the pathogen, acting as a “bridgehead” for further global dissemination. Quarantine measures must continue to be focussed on maintaining low global genetic diversity and avoiding exchange of genetic material between the native and introduced regions. Nevertheless, the current low global genetic diversity of Sss allows potato breeders to select for resistance, which is likely to be durable.     

Karyotypic evolution and phylogeny of Mexican Passalidae (Coleoptera: Polyphaga: Scarabaeoidea)

The chromosomes of 26 taxa from Mexico of the tribes Passalini (three species) and Proculini (23 species) have been studied, increasing the karyotypically known species of the family Passalidae to 56. Karyotypic dynamism is high since the diploid number varies from 18 to 44 in the tribe Proculini. and from 25 to 31 in the tribe Passalini. In addition, supernumerary chromosomes, chromosome heteromorphism, translocations and possible sex multivalents have been found. These results contrast with the numerical conservatism found in related families of the superfamily Scarabaeoidea. However, both tribes are conservative with regard to sex determination, as all species of Proculini have male XY chromosomes whereas species of the Passalini have male XO chromosomes. It is postulated that differences in patterns shown by these two tribes are mainly due to population structure, because many species of Proculini are endemic to restricted areas of Meso and South America, favouring the settlement of karyotypic changes, whereas species of Passalini are distributed over large areas in the lowlands. It is also postulated that the ancestral karyotypic formula of the family is close to 12–14 pairs of autosomes although the ancestral male sex determination may be either XY or XO. At present only a weak relationship between morphological and karyotypic evolution has been found, which together with the marked numerical variability found within and between genera make it difficult to obtain phylogenetic conclusions from karyotypic results.