Arrival of Paleo-Indians to the Southern Cone of South America: New Clues from Mitogenomes

With analyses of entire mitogenomes, studies of Native American mitochondrial DNA (mtDNA) variation have entered the final phase of phylogenetic refinement: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clues on the colonization processes of the different regions of the double continent. As for the Southern Cone of South America, this approach has recently allowed the identification of two local clades (D1g and D1j) whose age estimates agree with the dating of the earliest archaeological sites in South America, indicating that Paleo-Indians might have reached that region from Beringia in less than 2000 years. In this study, we sequenced 46 mitogenomes belonging to two additional clades, termed B2i2 (former B2l) and C1b13, which were recently identified on the basis of mtDNA control-region data and whose geographical distributions appear to be restricted to Chile and Argentina. We confirm that their mutational motifs most likely arose in the Southern Cone region. However, the age estimate for B2i2 and C1b13 (11–13,000 years) appears to be younger than those of other local clades. The difference could reflect the different evolutionary origins of the distinct South American-specific sub-haplogroups, with some being already present, at different times and locations, at the very front of the expansion wave in South America, and others originating later in situ, when the tribalization process had already begun. A delayed origin of a few thousand years in one of the locally derived populations, possibly in the central part of Chile, would have limited the geographical and ethnic diffusion of B2i2 and explain the present-day occurrence that appears to be mainly confined to the Tehuelche and Araucanian-speaking grou

A Sino-German λ\lambda6\ cm polarization survey of the Galactic plane. V. Large supernova remnants

Observations of large supernova remnants (SNRs) at high frequencies are rare, but provide valuable information about their physical properties. The total intensity and polarization properties of 16 large SNRs in the Galactic plane were investigated based on observations of the Urumqi $\lambda$6\ cm polarization survey of the Galactic plane with an angular resolution of 9\farcm5. We extracted total intensity and linear polarization maps of large SNRs from the Urumqi $\lambda$6\ cm survey, obtained their integrated flux densities, and derived the radio spectra in context with previously published flux densities at various frequencies. In particular, Effelsberg $\lambda$11\ cm and $\lambda$21\ cm survey data were used for calculating integrated flux densities. The $\lambda$6\ cm polarization data also delineate the magnetic field structures of the SNRs. We present the first total intensity maps at $\lambda$6\ cm for SNRs G106.3+2.7, G114.3+0.3, G116.5+1.1, G166.0+4.3 (VRO 42.05.01), G205.5+0.5 (Monoceros Nebula) and G206.9+2.3 (PKS 0646+06) and the first polarization measurements at $\lambda$6\ cm for SNRs G82.2+5.3 (W63), G106.3+2.7, G114.3+0.3, G116.5+1.1, G166.0+4.3 (VRO 42.05.01), G205.5+0.5 (Monoceros Nebula) and G206.9+2.3 (PKS 0646+06). Most of the newly derived integrated radio spectra are consistent with previous results. The new flux densities obtained from the Urumqi $\lambda$6\ cm, Effelsberg $\lambda$11\ cm and $\lambda$21\ cm surveys are crucial to determine the spectra of SNR G65.1+0.6, G69.0+2.7 (CTB 80), G93.7-0.2 and G114.3+0.3. We find that G192.8$-$1.1 (PKS 0607+17) consists of background sources, \ion{H}{II} regions and the extended diffuse emission of thermal nature, and conclude that G192.8$-$1.1 is not a SNR.Comment: 15 pages, 10 figures, accepted by A&\amp;A. Language improved. For the version with high resolution figures, please go to: http://zmtt.bao.ac.cn/6cm/paper/gxy_largeSNR.pd

The initial peopling of the Americas: a growing number of founding mitochondrial genomes from Beringia

Pan-American mitochondrial DNA (mtDNA) haplogroup C1 has been recently subdivided into three branches, two of which (C1b and C1c) are characterized by ages and geographical distributions that are indicative of an early arrival from Beringia with Paleo-Indians. In contrast, the estimated ages of C1d—the third subset of C1—looked too young to fit the above scenario. To define the origin of this enigmatic C1 branch, we completely sequenced 63 C1d mitochondrial genomes from a wide range of geographically diverse, mixed, and indigenous American populations. The revised phylogeny not only brings the age of C1d within the range of that of its two sister clades, but reveals that there were two C1d founder genomes for Paleo-Indians. Thus, the recognized maternal founding lineages of Native Americans are at least 15, indicating that the overall number of Beringian or Asian founder mitochondrial genomes will probably increase extensively when all Native American haplogroups reach the same level of phylogenetic and genomic resolution as obtained here for C1d.Fil: Perego, Ugo A.. Soreson Molecular Genealogy Foundation; Estados Unidos. Università di Pavia. Dipartimento di Genetica e Microbiologia; ItaliaFil: Angerhofer, Norman. Soreson Molecular Genealogy Foundation; Estados UnidosFil: Pala, Maria. Università di Pavia. Dipartimento di Genetica e Microbiologia; ItaliaFil: Olivieri, Anna. Università di Pavia. Dipartimento di Genetica e Microbiologia; ItaliaFil: Lancioni, Hovirag. Universita Di Perugia; ItaliaFil: Kashani, Baharak Hooshiar. Università di Pavia. Dipartimento di Genetica e Microbiologia; ItaliaFil: Carossa, Valeria. Università di Pavia. Dipartimento di Genetica e Microbiologia; ItaliaFil: Ekins, Jayne E.. Soreson Molecular Genealogy Foundation; Estados UnidosFil: Gómez Carballa, Alberto. Universidad de Santiago de Compostela; EspañaFil: Huber, Gabriela. Universidad de Innsbruck; AustriaFil: Zimmermann, Bettina. Universidad de Innsbruck; AustriaFil: Corach, Daniel. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Servicio de Huellas Digitales Genéticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Babudri, Nora. Universita Di Perugia; ItaliaFil: Panara, Fausto. Universita Di Perugia; ItaliaFil: Myres, Natalie M.. Soreson Molecular Genealogy Foundation; Estados UnidosFil: Parson, Walther. Universidad de Innsbruck; AustriaFil: Semino, Ornella. Università di Pavia. Dipartimento di Genetica e Microbiologia; ItaliaFil: Salas, Antonio. Universidad de Santiago de Compostela; EspañaFil: Woodward, Scott R.. Soreson Molecular Genealogy Foundation; Estados UnidosFil: Achilli, Alessandro. Università di Pavia. Dipartimento di Genetica e Microbiologia; Italia. Universita Di Perugia; ItaliaFil: Torroni, Antonio. Università di Pavia. Dipartimento di Genetica e Microbiologia; Itali

Mitochondrial DNA signals of late glacial recolonization of Europe from near Eastern refugia

Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ?19–12 thousand years (ka) ago.<br/

Decrypting the Mitochondrial Gene Pool of Modern Panamanians

The Isthmus of Panama–the narrow neck of land connecting the northern and southern American landmasses–was an obligatory corridor for the Paleo-Indians as they moved into South America. Archaeological evidence suggests an unbroken link between modern natives and their Paleo-Indian ancestors in some areas of Panama, even if the surviving indigenous groups account for only 12.3% of the total population. To evaluate if modern Panamanians have retained a larger fraction of the native pre-Columbian gene pool in their maternally-inherited mitochondrial genome, DNA samples and historical records were collected from more than 1500 volunteer participants living in the nine provinces and four indigenous territories of the Republic. Due to recent gene-flow, we detected ∼14% African mitochondrial lineages, confirming the demographic impact of the Atlantic slave trade and subsequent African immigration into Panama from Caribbean islands, and a small European (∼2%) component, indicating only a minor influence of colonialism on the maternal side. The majority (∼83%) of Panamanian mtDNAs clustered into native pan-American lineages, mostly represented by haplogroup A2 (51%). These findings reveal an overwhelming native maternal legacy in today's Panama, which is in contrast with the overall concept of personal identity shared by many Panamanians. Moreover, the A2 sub-clades A2ad and A2af (with the previously named 6 bp Huetar deletion), when analyzed at the maximum level of resolution (26 entire mitochondrial genomes), confirm the major role of the Pacific coastal path in the peopling of North, Central and South America, and testify to the antiquity of native mitochondrial genomes in Panama

Models for Stochastic Texture Generation

technical reportThis work explores current models of textures for image synthesis and analysis, with an emphasis on generation of stochastic textures. Digital signal processing techniques are applied to create a general and robust model for the generation of stochastic textures. Martingale sequences are analyzed, and it is determined that the best way to develop martingale sequences is through the use of convolution. Methods of convolution with white noise are discussed. A number of ways to obtain the point spread function or texture filter for a target texture are developed. Important ways include the use of preexisting texture samples and the construction of ensemble averages. The theoretical framework behind the robustness of these methods is developed. Stochastic textures which have been generated with these methods are then used in the rendering process to give greater realism to objects in computer-generated images

Using Y−Chromosome Haplotypes to Improve Inferred Ancestral Origins in European Populations

International audienc

The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q

<div><p>Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.</p></div

Observed Frequencies of Haplogroup Q and of its Sub-Lineages.

a<p>Marker described here for the first time.</p>b<p>Grouping due to sample size <10 in single populations. <u>C</u>entral <u>American Isthmus</u>: El Salvador, Guatemala and Honduras; <u>N</u>orthern <u>S</u>outh<u> America</u>: Colombia, Ecuador, Venezuela; <u>S</u>outhern <u>S</u>outh <u>America</u>: Argentina and Paraguay; <u>The Caribbeans</u>: Barbados, Bermuda, Cuba, Dominican Rep., French Guiana, Grenada, Haiti, Jamaica, Martinique.</p><p>The following mutations were surveyed in all potential carrier samples but they were not observed: NTW01, M323, L401 and M19. M199 was only typed in a subset of samples.</p><p>In parentheses, % frequencies.</p