Origin and evolution of Native American mtDNA variation: a reappraisal.

The timing and number of prehistoric migrations involved in the settlement of the American continent is subject to intense debate. Here, we reanalyze Native American control region mtDNA data and demonstrate that only an appropriate phylogenetic analysis accompanied by an appreciation of demographic factors allows us to discern different migrations and to estimate their ages. Reappraising 574 mtDNA control region sequences from aboriginal Siberians and Native Americans, we confirm in agreement with linguistic, archaeological and climatic evidence that (i) the major wave of migration brought one population, ancestral to the Amerinds, from northeastern Siberia to America 20,000-25,000 years ago and (ii) a rapid expansion of a Beringian source population took place at the end of the Younger Dryas glacial phase approximately 11,300 years ago, ancestral to present Eskimo and Na-Dene populations.     

Mitochondrial genome diversity of Native Americans supports a single early entry of founder populations into America

There is general agreement that the Native American founder populations migrated from Asia into America through Beringia sometime during the Pleistocene, but the hypotheses concerning the ages and the number of these migrations and the size of the ancestral populations are surrounded by controversy. DNA sequence variations of several regions of the genome of Native Americans, especially in the mitochondrial DNA (mtDNA) control region, have been studied as a tool to help answer these questions. However, the small number of nucleotides studied and the nonclocklike rate of mtDNA control-region evolution impose several limitations to these results. Here we provide the sequence analysis of a continuous region of 8.8 kb of the mtDNA outside the D-loop for 40 individuals, 30 of whom are Native Americans whose mtDNA belongs to the four founder haplogroups. Haplogroups A, B, and C form monophyletic clades, but the five haplogroup D sequences have unstable positions and usually do not group together. The high degree of similarity in the nucleotide diversity and time of differentiation (i.e., approximately 21,000 years before present) of these four haplogroups support a common origin for these sequences and suggest that the populations who harbor them may also have a common history. Additional evidence supports the idea that this age of differentiation coincides with the process of colonization of the New World and supports the hypothesis of a single and early entry of the ancestral Asian population into the Americas.     

Native South American genetic structure and prehistory inferred from hierarchical modeling of mtDNA

Genetic diversity in Native South Americans forms a complexpattern at both the continental and local levels. In comparingthe West to the East, there is more variation within groupsand smaller genetic distances between groups. From this pattern,researchers have proposed that there is more variation in theWest and that a larger, more genetically diverse, founding populationentered the West than the East. Here, we question this characterizationof South American genetic variation and its interpretation.Our concern arises because others have inferred regional variationfrom the mean variation within local populations without takinginto account the variation among local populations within thesame region. This failure produces a biased view of the actualvariation in the East. In this study, we analyze the mitochondrial DNA sequence betweenpositions 16040 and 16322 of the Cambridge reference sequence.Our sample represents a total of 886 people from 27 indigenouspopulations from South (22), Central (3), and North America(2). The basic unit of our analyses is nucleotide identity bydescent, which is easily modeled and proportional to nucleotidediversity. We use a forward modeling strategy to fit a seriesof nested models to identity by descent within and between allpairs of local populations. This method provides estimates ofidentity by descent at different levels of population hierarchywithout assuming homogeneity within populations, regions, orcontinents. Our main discovery is that Eastern South America harbors moregenetic variation than has been recognized. We find no evidencethat there is increased identity by descent in the East relativeto the total for South America. By contrast, we discovered thatpopulations in the Western region, as a group, harbor more identityby descent than has been previously recognized, despite thefact that average identity by descent within groups is lower.In this light, there is no need to postulate separate foundingpopulations for the East and the West because the variabilityin the East could serve as a source for the Western gene pools.     

American beginnings. the prehistory and palaeoecology of Beringia

Edited by Frederick Hadleigh West. Chicago: The University of Chicago Press. 1996. xxi + 576 pp. $75.00 (cloth).     

Recent colonization and radiation of North American Lycaeides (Plebejus) inferred from mtDNA

North American Lycaeides populations exhibit remarkable variation in ecological, morphological, and behavioral characters, as well as an established history of introgressive hybridization. We examined mitochondrial DNA variation from 55 Eurasian and North American Lycaeides populations using molecular phylogenetics and coalescent-based methods in order to clarify the evolutionary and demographic history of this polytypic group. Specifically we addressed the following questions: (1) Do mitochondrial alleles sampled from North America form a monophyletic group, which would be expected if North American Lycaeides were descended from a single Eurasian ancestor? (2) When did Lycaeides colonize North America? and (3) What is the demographic history of North American Lycaeides since their colonization? Bayesian maximum likelihood methods identified three major mitochondrial lineages for Lycaeides; each lineage contained haplotypes sampled from both Eurasia and North America. This suggests a complex colonization history for Lycaeides, which likely involved multiple founding lineages. Coalescent-based analyses placed the colonization of North America by Eurasian Lycaeides sometime during or after the late Pliocene. This was followed by a sudden increase in population size of more than an order of magnitude for the North American population of Lycaeides approximately 100,000-150,000 years before the present. These mitochondrial data, in conjunction with data from previous ecological, morphological, and behavioral studies, suggest that the diversity observed in Lycaeides in North America is the result of a recent evolutionary radiation, which may have been facilitated, in part, by hybridization.     

mtDNA diversity in Chukchi and Siberian Eskimos: implications for the genetic history of Ancient Beringia and the peopling of the New World.

The mtDNAs of 145 individuals representing the aboriginal populations of Chukotka-the Chukchi and Siberian Eskimos-were subjected to RFLP analysis and control-region sequencing. This analysis showed that the core of the genetic makeup of the Chukchi and Siberian Eskimos consisted of three (A, C, and D) of the four primary mtDNA haplotype groups (haplogroups) (A-D) observed in Native Americans, with haplogroup A being the most prevalent in both Chukotkan populations. Two unique haplotypes belonging to haplogroup G (formerly called "other" mtDNAs) were also observed in a few Chukchi, and these have apparently been acquired through gene flow from adjacent Kamchatka, where haplogroup G is prevalent in the Koryak and Itel'men. In addition, a 16111C-->T transition appears to delineate an "American" enclave of haplogroup A mtDNAs in northeastern Siberia, whereas the 16192C-->T transition demarcates a "northern Pacific Rim" cluster within this haplogroup. Furthermore, the sequence-divergence estimates for haplogroups A, C, and D of Siberian and Native American populations indicate that the earliest inhabitants of Beringia possessed a limited number of founding mtDNA haplotypes and that the first humans expanded into the New World approximately 34,000 years before present (YBP). Subsequent migration 16,000-13,000 YBP apparently brought a restricted number of haplogroup B haplotypes to the Americas. For millennia, Beringia may have been the repository of the respective founding sequences that selectively penetrated into northern North America from western Alaska.     

A reevaluation of the genus Malassezia by means of genome comparison

Results of a study of the genus Malassezia on the basis of genome characters confirm that two species should be maintained, M. furfur and M. pachydermatis. The two forms associated with skin disease, frequently referred to as Pityrosporum orbiculare and P. ovale, were found to be synonymous, the name M. furfur having priority. Malassezia pachydermatis, hitherto regarded as a strictly zoophilic species, may also be found on humans.     

Genetic diversity present within the near-complete mtDNA genome of 17 breeds of indigenous Chinese pigs

The genetic diversity present within the near-complete mitochondrial genome (15,982 bp) was determined from 17 indigenous Chinese pig breeds and 3 European breeds. Animals were selected from 17 Chinese breeds that reflect the large phenotypic diversity of Chinese pigs and represent each of the six breed types, which are grouped based on morphological characteristics. Analysis of nucleotide diversity confirmed a high level of divergence between animals of European versus Asian origin; however, much more limited variation was observed between the 17 indigenous Chinese breeds. Each had a unique haplotype, but the lowest pairwise sequence divergence was only 0.01 +/- 0.01%, observed between the Tongcheng and Yushan Black. Comparison of control region sequence diversity revealed the 17 Chinese breeds contain a lower average pairwise distance (0.61 +/- 0.19%) than a group of European commercial breeds (0.91 +/- 0.21%). The dendrogram constructed from the near-complete mtDNA sequences showed the Chinese sequences loosely clustering into two groups. Although some correspondence with geographic origin was present, notable differences between the dendrogram and the traditional pig breed grouping system were observed.     

Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas

Through extended survey of mitochondrial DNA (mtDNA) diversity in the Nganasan, Yukaghir, Chuvantsi, Chukchi, Siberian Eskimos, and Commander Aleuts, we filled important gaps in previously unidentified internal sequence variation within haplogroups A, C, and D, three of five (A-D and X) canonical mtDNA lineages that defined Pleistocenic extension from the Old to the New World. Overall, 515 mtDNA samples were analyzed via high-resolution SNP analysis and then complete sequencing of the 84 mtDNAs. A comparison of the data thus obtained with published complete sequences has resulted in the most parsimonious phylogenetic structure of mtDNA evolution in Siberia-Beringia. Our data suggest that although the latest inhabitants of Beringia are well genetically reflected in the Chukchi-, Eskimo-Aleut-, and Na-Dene-speaking Indians, the direct ancestors of the Paleosiberian-speaking Yukaghir are primarily drawn from the southern belt of Siberia when environmental conditions changed, permitting recolonization the high arctic since early Postglacial. This study further confirms that (1) Alaska seems to be the ancestral homeland of haplogroup A2 originating in situ approximately 16.0 thousand years ago (kya), (2) an additional founding lineage for Native American D, termed here D10, arose approximately 17.0 kya in what is now the Russian Far East and eventually spread northward along the North Pacific Rim. The maintenance of two refugial sources, in the Altai-Sayan and mid-lower Amur, during the last glacial maximum appears to be at odds with the interpretation of limited founding mtDNA lineages populating the Americas as a single migration.     

Cranial morphology of the early tertiary Phenacolemur and its bearing on primate phylogeny

An early Eocene skull of the paromomyid Phenacolemur, a plesiadapoid primate, is described with particular emphasis on the ear region. The auditory bulla is composed of the petrosal and of a large ectotympanic plate which is outside of the bulla. The preserved morphology of the middle ear is distinctly more primitive than that of the older Plesiadapis. It cannot be determined with certainty whether Phenacolemur had the carotid circulation enclosed in bony tubes or not. The auditory bulla of early primates and relevant living ones is discussed and it is suggested that an extrabullar ectotympanic, as seen in all non-lemuriform fossil and extant primates, was probably the primitive ordinal condition, rather than the intrabullar ring-like ectotympanic in the Lemuriformes. Aspects of the carotid circulation are discussed as they pertain to the relationship of early Tertiary primates, living Tarsiiformes, Lemuriformes and Lorisiformes.     

mtDNA history of the Cayapa Amerinds of Ecuador: detection of additional founding lineages for the Native American populations.

mtDNA variation in the Cayapa, an Ecuadorian Amerindian tribe belonging to the Chibcha-Paezan linguistic branch, was analyzed by use of hypervariable control regions I and II along with two linked regions undergoing insertion/deletion mutations. Three major maternal lineage clusters fit into the A, B, and C founding groups first described by Schurr and colleagues in 1990, whereas a fourth lineage, apparently unique to the Cayapa, has ambiguous affinity to known clusters. The time of divergence from a common maternal ancestor of the four lineage groups is of sufficient age that it indicates an origin in Asia and supports the hypothesis that the degree of variability carried by the Asian ancestral populations into the New World was rather high. Spatial autocorrelation analysis points out (a) statistically significant nonrandom distributions of the founding lineages in the Americas, because of north-south population movements that have occurred since the first Asian migrants spread through Beringia into the Americas, and (b) an unusual pattern associated with the D lineage cluster. The values of haplotype and nucleotide diversity that are displayed by the Cayapa appear to differ from those observed in other Chibchan populations but match those calculated for South American groups belonging to various linguistic stocks. These data, together with the results of phylogenetic analysis performed with the Amerinds of Central and South America, highlight the difficulty in the identification of clear coevolutionary patterns between linguistic and genetic relationships in particular human populations.     

On the position of Archigetes and its bearing on the early evolution of the tapeworms

The tapeworm Archigetes sieboldi Leuckart, 1878 (Platyhelminthes: Cestoda: Caryophyllidea) has been cited as a likely representative of the "protocestode" condition, owing to its lack of segmentation and ability to attain sexual maturity in the invertebrate host (aquatic oligochaetes). The idea has been variously amplified or rejected in the literature, although the actual phylogenetic position of the species has not been investigated until now. New collections of Archigetes sp. from both its vertebrate and invertebrate hosts provided the opportunity to estimate its phylogenetic position with the use of molecular systematics, while prompting new analyses aimed at assessing the early diversification of the Cestoda. Additional collections representing the Amphilinidea, Caryophyllidea, and Gyrocotylidea were combined with published gene sequences to construct data sets of complete 18S (110 taxa) and partial (D1-D3) 28S (107 taxa) rDNA sequences, including 8 neodermatan outgroup taxa. Estimates resulting from Bayesian inference, maximum likelihood, and maximum parsimony analyses of the separate and combined data sets supported a derived position of the genus within the Caryophyllidea, and thus reject the idea that Archigetes sp. may exemplify a "primitive" condition. Topological constraint analyses rejected the hypothesis that Archigetes represents the most basal lineage of the Eucestoda, but did not rule out that it could represent the earliest branching taxon of the Caryophyllidea. In all analyses, the Eucestoda were monophyletic and supported basal positions of the nonsegmented Caryophyllidea and Spathebothriidea relative to other major lineages of the Eucestoda, implying that segmentation is a derived feature of the common ancestor of the di- and tetrafossate eucestodes. However, constraint analyses could not provide unequivocal evidence as to the precise branching patterns of the cestodarian, spathebothriidean, and caryophyllidean lineages. Phylogenetic analyses favor the interpretation that sexual maturity of Archigetes sp. in the invertebrate host, and similar examples in members of the Spathebothriidea, are the result of progenesis and have little if any bearing on understanding the protocestode condition.     

Lower Miocene stratigraphy along the Panama Canal and its bearing on the Central American Peninsula

Before the formation of the Central American Isthmus, there was a Central American Peninsula. Here we show that southern Central America existed as a peninsula as early as 19 Ma, based on new lithostratigraphic, biostratigraphic and strontium chemostratigraphic analyses of the formations exposed along the Gaillard Cut of the Panama Canal. Land mammals found in the Miocene Cucaracha Formation have similar body sizes to conspecific taxa in North America, indicating that there existed a terrestrial connection with North America that allowed gene flow between populations during this time. How long did this peninsula last? The answer hinges on the outcome of a stratigraphic dispute: To wit, is the terrestrial Cucaracha Formation older or younger than the marine La Boca Formation? Previous stratigraphic studies of the Panama Canal Basin have suggested that the Cucaracha Formation lies stratigraphically between the shallow-marine Culebra Formation and the shallow-to-upper-bathyal La Boca Formation, the latter containing the Emperador Limestone. If the La Boca Formation is younger than the Cucaracha Formation, as many think, then the peninsula was short-lived (1–2 m.y.), having been submerged in part by the transgression represented by the overlying La Boca Formation. On the other hand, our data support the view that the La Boca Formation is older than the Cucaracha Formation. Strontium dating shows that the La Boca Formation is older (23.07 to 20.62 Ma) than both the Culebra (19.83–19.12 Ma) and Cucaracha (Hemingfordian to Barstovian North American Land Mammal Ages; 19–14 Ma) formations. The Emperador Limestone is also older (21.24–20.99 Ma) than the Culebra and Cucaracha formations. What has been called the “La Boca Formation” (with the Emperador Limestone), is re-interpreted here as being the lower part of the Culebra Formation. Our new data sets demonstrate that the main axis of the volcanic arc in southern Central America more than likely existed as a peninsula connected to northern Central America and North America for much of the Miocene, which has profound implications for our understanding of the tectonic, climatic, oceanographic and biogeographic history related to the formation of the Isthmus of Panama.     

The terminal web. A reevaluation of its structure and function

The apical cytoplasm of epithelial cells of the small and large intestines has been examined by freeze-etch techniques as well as conventional and high voltage electron microscopy of sectioned material to gain a better understanding of the fine structural organization of the terminal web region. In the small intestine the terminal web exhibits a distinct stratification caused by the association of different sets of filaments with the three members of the junctional complex. Individual filaments of this network are closely associated with the sealing elements of the tight junctions, the surface of the core microfilament bundles, and the intermicrovillar plasma membrane. This region of the terminal web is the apical zone. The adherens zone appears as a band of interwoven filaments of two different diameters extending across the cytoplasm at the level of the intermediate junction. Within this region of the terminal web, individual 60-70 A actin-like filaments separate from the bundles of core microfilaments to interact with one another and with filaments of similar diameter from the zonula adherens. 100 A tonofilaments also contribute to the adherens zone, presumably stabilizing the orientation of the actin-like filaments. The basal zone which underlies the adherens zone consists of closely interwoven bundles of tonofilaments that are anchored to and interconnect the spot desmosomes. Within the large intestine the cytoplasmic microfilaments form a looser and less clearly stratified network which nevertheless retains the same basic organization found in the small intestine. Transmembrane linkers appear to originate within the cytoplasmic plaques of the spot desmosomes, pass through the plasma membranes, and meet in a staggered configuration in the intercellular space; these linkers may thus mediate the actual mechanical coupling between the cytoskeletal networks of tonofilament bundles of adjacent cells. This integrated system of cytoplasmic filaments and intercellular junctions endows the apical cytoplasm with both the flexibility and the stability necessary for the normal functioning of the epithelium.     

中国黄牛mtDNA D-loop遗传多样性及起源

黄牛自古以来就是我国一个重要的畜种,其经济、文化价值很高。我国是世界上黄牛品种资源最丰富的国家之一。据《中国牛品种志》介绍,把一些地区同种异名的黄牛品种合并以后,尚有28个地方黄牛品种,按照其地理分布区域分为北方黄牛、中原黄牛和南方黄牛三大类型(邱怀,1986)。如果把中国地方黄牛品种分得更细,则有49个固有品种(常洪,1995)。关于中国黄牛的起源,历来有不同的观点。一般认为,中国黄牛是多元起源的,但究竟起源于哪几个牛种,观点不一(陈宏等,1993;于汝梁等,1993;Yu et al.,1999;陈幼春,1990)。主要的观点有:(1)中国黄牛主要起源于…     

Complete mtDNA genome of Otus sunia (Aves,Strigidae) and the relaxation of selective constrains on Strigiformes mtDNA following evolution

Most of owls are nocturnal raptor and usually use their soft and fluffy feathers to flight silently to catch prey while other diurnal raptors prefer fierce attack and swift flight. For energy cost of these different hunting strategies can be greatly different, we speculate that mitochondrial gene of owls may undergo a different evolution pattern following raptors evolution. To test our hypothesis, we sequenced the mtDNA genome of Otus sunia and calculated the ratio of nonsynonymous to synonymous nucleotide substitutions (ω, Ka/Ks, dN/dS) of raptors. The mtDNA genome of O. sunia was 17,609 bp in length, containing 13 PCGs, 2 ribosomal RNAs, 22 transfer RNAs and a control region. Secondly structure of tRNAs and rRNAs were predicted and conserved sequence blocks (CSBs) on control region were identified. The Bayesian inference tree and maximum likelihood tree based on 13 PCGs and 2 rRNAs suggested the owls were related to other raptors. Finally, calculation of ω-values of each owls and other raptors mtDNA PCGs indicated that owls accumulated more nonsynonymous nucleotide substitutions relative to synonymous substitutions compared to other raptors. For mtDNA PCGs associated with energy metabolism, this finding may reveal the degeneration of flight abilities of owls.     

Rapid deployment of the five founding Amerind mtDNA haplogroups via coastal and riverine colonization

Numerous studies of variation in mtDNA in Amerindian populations established that four haplogroups are present throughout both North and South America. These four haplogroups (A, B, C, and D) and perhaps a fifth (X) in North America are postulated to be present in the initial founding migration to the Americas. Furthermore, studies of ancient mtDNA in North America suggested long-term regional continuity of the frequencies of these founding haplogroups. Present-day tribal groups possess high frequencies of private mtDNA haplotypes (variants within the major haplogroups), consistent with early establishment of local isolation of regional populations. Clearly these patterns have implications for the mode of colonization of the hemisphere. Recently, the earlier consensus among archaeologists for an initial colonization by Clovis hunters arriving through an ice-free corridor and expanding in a "blitzkrieg " wave was shown to be inconsistent with extensive genetic variability in Native Americans; a coastal migration route avoids this problem. The present paper demonstrates through a computer simulation model how colonization along coasts and rivers could have rapidly spread the founding lineages widely through North America.