Y-chromosome Short Tandem Repeat DYS458.2 Non-consensus Alleles Occur Independently in Both Binary Haplogroups J1-M267 and R1b3-M405

Cilj: Odrediti haploskupinsku osnovu “non-consensus” kratkih udvojenih sljedova (engl., short tandem repeat, STR) alela DYS458.2 na kromosomu Y i procijeniti njihov filogenetski podustroj i učestalost u reprezentativnim uzorcima sa Srednjega Istoka, Europe i Pakistana. Postupci: Molekularna karakterizacija povezanosti i konstrukcija haplotipova provedena je kombinacijom dvaju pristupa – analizom binarnog polimorfizma koji definira haploskupinu kromosoma Y i analizom do 37 lokusa STR, uključujući i DYS388. Za utvrđivanje povezanosti kromosoma Y koji sadrže slijed DYS458.2, rabljeno je sekvencioniranje DNA lokusa DYS458 i mrežna analiza udaljenosti od medijana. Rezultati Pokazali smo da je novi alel DYS458.2 nastao nezavisno na najmanje dvije osnove binarnih haploskupina, a možda i na trećoj. U svim haploskupinama kromosoma J1 koje su pregledane, uključivši i njegove poznate a malobrojne pod-haploskupine, nađen je fiksan dužinski uzorak parcijalnoga alela. U alternativnom M405 povezanom s R1b3 definiranoj pod-haploskupini nađene su i DYS458.0 i DYS458.2 alelne klase. Pojedinačni kromosom također se mogao svrstati u R1b3-M269*(xM405) klasu. Fizički smještaj djelomične nsercije/delecije u normalnom slijedu tetramera jasno se razlikovao u kontekstu svake haploskupine. Zaključak: Iako neobični aleli DYS458.2 pružaju korisne informacije, prilikom zaključivanja o haploskupinskoj osnovi i uobičajenom nasljeđivanju potrebne su dodatne informacije o drugim vezanim polimorfnim lokusima.Aim: To determine the human Y-chromosome haplogroup backgrounds of non-consensus DYS458.2 short tandem repeat alleles and evaluate their phylogenetic substructure and frequency in representative samples from the Middle East, Europe, and Pakistan. Methods: Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci, including DYS388 to construct haplotypes. DNA sequencing of the DYS458 locus and median-joining network analyses were used to evaluate Y-chromosome lineages displaying the DYS458.2 motif. Results: We showed that the DYS458.2 allelic innovation arose independently on at least two distinctive binary haplogroup backgrounds and possibly a third as well. The partial allele length pattern was fixed in all haplogroup J1 chromosomes examined, including its known rare sub-haplogroups. Within the alternative R1b3 associated M405 defined sub-haplogroup, both DYS458.0 and DYS458.2 allele classes occurred. A single chromosome also allocated to the R1b3-M269*(xM405) classification. The physical position of the partial insertion/deletion occurrence within the normal tetramer tract differed distinctly in each haplogroup context. Conclusions: While unusual DYS458.2 alleles are informative, additional information for other linked polymorphic loci is required when using such non-conforming alleles to infer haplogroup background and common ancestry

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

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

Spatial distribution of A2af and A2ad mtDNAs identified in general mixed populations.

<p>Exact values are listed in Table S3A.</p

The Mountain Meadows Massacre and "poisoned springs": scientific testing of the more recent, anthrax theory

It has been recorded that one of the possible causes that eventually escalated into the 1857 manslaughter at Mountain Meadows in Southern Utah was the poisoning of an open spring by the Fancher-Baker party as they crossed the Utah territory on their way from Arkansas to California. Historical accounts report that a number of cattle died, followed by human casualties from those that came in contact with the dead animals. Even after the Arkansas party departed, animals continued to perish and people were still afflicted by some unknown plague. Proctor Hancock Robison, a local 14-year-old boy, died shortly after skinning one of the "poisoned" cows. A careful review of the historical records, along with the more recent scientific literature, seems to exclude the likelihood of actual poisoning in favor of a more recent theory that would point to the bacterium Bacillus anthracis as the possible cause of human and animal deaths. In order to test this hypothesis, Proctor's remains were exhumed, identified through mitochondrial DNA analysis, and tested for the presence of anthrax spores. Although preliminary testing of remains and soil was negative, description of the clinical conditions that affected Proctor and other individuals does not completely rule out the hypothesis of death by anthrax

Frequency distribution (%) of major haplogroups in Panama.

<p>Frequency distribution (%) of major haplogroups in Panama.</p

Sources and haplogroup affiliation for the A2ad and A2af complete mtDNA sequences.

<p>Sources and haplogroup affiliation for the A2ad and A2af complete mtDNA sequences.</p

Network of A2af control-region haplotypes from Panama subdivided according to their geographic origin.

<p>The mutations on the connecting branches refer to the (revised) Cambridge reference sequence (rCRS) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038337#pone.0038337-Andrews1" target="_blank">[52]</a>. Markers of different clusters are in colors. Mutations are transitions unless the base change is explicitly indicated. Insertions, deletions and heteroplasmic mutations were excluded, with the notable exception of the 106–111 6 bp deletion. The size of each circle is proportional to the haplotype frequency and geographical origins are indicated by different colors. Coalescence ages of A2af and A2af1 are also reported using the control-region mutation rate reported by Soares <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038337#pone.0038337-Soares2" target="_blank">[50]</a>.</p

Distributions in Panama of the 1565 samples analyzed in this paper.

<p>Bars show both place of collection and terminal maternal ancestor (TMA) origin. This means the origin of the last known ancestor on the maternal side of the recorded pedigree.</p