28 research outputs found
A nomenclature system for the tree of human Y-chromosomal binary haplogroups
This is the published version, also available here: http://dx.doi.org/10.1101/gr.217602.The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping system, with applications in evolutionary studies, forensics, medical genetics, and genealogical reconstruction. However, the emergence of several unrelated and nonsystematic nomenclatures for Y-chromosomal binary haplogroups is an increasing source of confusion. To resolve this issue, 245 markers were genotyped in a globally representative set of samples, 74 of which were males from the Y Chromosome Consortium cell line repository. A single most parsimonious phylogeny was constructed for the 153 binary haplogroups observed. A simple set of rules was developed to unambiguously label the different clades nested within this tree. This hierarchical nomenclature system supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered
Multiplex DNA Typing of Short-Tandem-Repeat Loci on the Y Chromosome
This is the published version. Copyright 1997 de Gruyter.To facilitate evolutionary and forensic studies of DNA
polymorphisms on the Y chromosome, we devised a
multiplex amplification procedure for short-tandemrepeat
(STR) loci. Four tetranucleotide STR loci
(DYS19, DYS390, DYS391, and DYS393) were simultaneously
amplified with FAM-labeled primers and
genotypes were determined with an automated DNA
sequencer. We typed 162 males from three U.S. populations
(African-Americans, European-Americans and
Hispanics) and found that the haplotype diversities
range from 0.920 to 0.969. This quadruplex system
provides a facile means of genotyping these Y chromosome
STRs, and should be useful in population
genetic and forensic applications
Family tree and or map-like approaches to Slavic languages?
The file consists of the presenters' raw notes and the PowerPoint presentation delivered at the "Slavic Languages: Time and Contingency” conference, UC Berkeley 12–13 Feb. 2010.Lexicostatistics is decades old, but newer techniques for computational approaches to historical linguistics have gained new attention with the rise of more sophisticated methods of data handling. Thus, for example, Gray and Atkinson (2003) claim to have established, using lexicostatistics and a Bayesian (MCMC) model, an authoritative Stammbaum for the Indo-European language family, including absolute chronologies of its branching. Others have argued that such methods, while valid for biology, cannot yield authoritative dates for language data (Atkinson 2009: 128).
The present paper examines a smaller subset of languages—Slavic—using new lexicostatistical methods in attempt to compare the computational results with received analyses that are closer to the present. We assume that examining a group of languages closer in time to the present, where the splits are more easily verifiable, allows testing of quantifiable methods. If a close fit can be found between a lexicostatistical approach and traditional analysis in Slavic, it should allow extension to greater time depths and larger families such as Indo-European.
The present paper applies several methods to two corpora, one the Slavic subset of Indo-European in Dyen, Kruskal and Black (1992) and the Slavic text-token set in Mańczak 2004.
References
Atkinson, Quentin D. 2009. Review of Language Classification by Numbers. By April McMahon and Robert McMahon. Oxford: Oxford University Press, 2005. Pp xvii, 265. Diachonica 26/1: 125–133.
Dyen, Isidore, Joseph B. Kruskal, and Paul Black. 1992. An Indoeuropean Classification: A Lexicostatistical Experiment. Philadelphia: American Philosophical Society.
Gray, Russell D. and Quentin D. Atkinson. 2003. Language-Tree Divergence Times Support the Anatolian Theory of Indo-European Origin. Nature 426: 435–439.
Mańczak, Witold. 2004. Przedhistoryczne migracje słowian i pochodzenie języka staro-cerkiewno-słowianskiego. Cracow: PAU
Genetic Evidence for Modifying Oceanic Boundaries Relative to Fiji
We present the most comprehensive genetic characterization to date of five Fijian island populations: Viti Levu, Vanua Levu, Kadavu, the Lau Islands, and Rotuma, including non-recombinant Y (NRY) chromosome and mitochondrial DNA (mtDNA) haplotypes and haplogroups. As a whole, Fijians are genetically intermediate between Melanesians and Polynesians, but the individual Fijian island populations exhibit significant genetic structure reflecting different settlement experiences in which the Rotumans and the Lau Islanders were more influenced by Polynesians, and the other Fijian island populations were more influenced by Melanesians. In particular, Rotuman and Lau Islander NRY chromosomal and mtDNA haplogroup frequencies and Rotuman mtDNA hypervariable segment 1 (HVS1) region haplotypes more closely resemble those of Polynesians, while genetic markers of the other populations more closely resemble those of the Near Oceanic Melanesians. Our findings provide genetic evidence supportive of modifying regional boundaries relative to Fiji, as has been suggested by others based on a variety of non-genetic evidence. Specifically, for the traditional Melanesia/Polynesia/Micronesia scheme, our findings support moving the Melanesia-Polynesia boundary so as to include Rotuma and the Lau Islands in Polynesia. For the newer Near/Remote Oceania scheme, our findings support keeping Rotuma and the Lau Islands in Remote Oceania and locating the other Fijian island populations in an intermediate or “Central Oceania” region to better reflect the great diversity of Oceania
A Polynesian Motif on the Y Chromosome: Population Structure in Remote Oceania
This is the publisher's version, also available electronically from http://digitalcommons.wayne.edu/humbiol/vol79/iss5/5/.The Polynesian motif, a mitochondrial DNA marker of ancestral Polynesian communities, has filled a critical role in reconstructions of remote Oceanic history. Although the motif provides an effective narrative for Polynesian females, no equivalent male history is available from paternal lineages. Here, we describe a Y-chromosome binary polymorphism with absolute Polynesian affinity. We illustrate its unique spatial and temporal connections to early Polynesian communities, and through an analysis of associated short tandem repeat variation, we describe the first clear genealogic structure within Polynesia. Unlike the eastern and western regions advocated by archeology, we identify a tripartite structure comprising interaction spheres in the west (Tonga and Samoa), center (Tahiti), and east (Rapanui/Easter Island). Such patterning, a product of early regional contact and subsequent isolation, signals the conflicting roles of mobility and seclusion in Polynesian prehistory
Hierarchical Patterns of Global Human Y-Chromosome Diversity
We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion out of Africa at the level of the total cladogram. Our new results support a general scenario in which, after an early out-of-Africa range expansion, global-scale patterns of NRY variation were mainly influenced by migrations out of Asia. Two other notable findings of the NCA were (1) Europe as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analyses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global levels. Finally, our results underscore the importance of subdivision of the human paternal gene pool and imply that caution should be exercised when using models and experimental strategies based on the assumption of panmixia
Genetic Evidence on the Origins of Indian Caste Populations
This is the published version, also available here: http://www.dx.doi.org/10.1101/gr.173301.The origins and affinities of the ∼1 billion people living on the subcontinent of India have long been contested.
This is owing, in part, to the many different waves of immigrants that have influenced the genetic structure of
India. In the most recent of these waves, Indo-European-speaking people from West Eurasia entered India from
the Northwest and diffused throughout the subcontinent. They purportedly admixed with or displaced
indigenous Dravidic-speaking populations. Subsequently they may have established the Hindu caste system and
placed themselves primarily in castes of higher rank. To explore the impact of West Eurasians on contemporary
Indian caste populations, we compared mtDNA (400 bp of hypervariable region 1 and 14 restriction site
polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short tandem repeats) variation in ∼265
males from eight castes of different rank to ∼750 Africans, Asians, Europeans, and other Indians. For maternally
inherited mtDNA, each caste is most similar to Asians. However, 20%–30% of Indian mtDNA haplotypes
belong to West Eurasian haplogroups, and the frequency of these haplotypes is proportional to caste rank, the
highest frequency of West Eurasian haplotypes being found in the upper castes. In contrast, for paternally
inherited Y-chromosome variation each caste is more similar to Europeans than to Asians. Moreover, the
affinity to Europeans is proportionate to caste rank, the upper castes being most similar to Europeans,
particularly East Europeans. These findings are consistent with greater West Eurasian male admixture with castes
of higher rank. Nevertheless, the mitochondrial genome and the Y chromosome each represents only a single
haploid locus and is more susceptible to large stochastic variation, bottlenecks, and selective sweeps. Thus, to
increase the power of our analysis, we assayed 40 independent, biparentally inherited autosomal loci (1 LINE-1
and 39 Alu elements) in all of the caste and continental populations (∼600 individuals). Analysis of these data
demonstrated that the upper castes have a higher affinity to Europeans than to Asians, and the upper castes are
significantly more similar to Europeans than are the lower castes. Collectively, all five datasets show a trend
toward upper castes being more similar to Europeans, whereas lower castes are more similar to Asians. We
conclude that Indian castes are most likely to be of proto-Asian origin with West Eurasian admixture resulting
in rank-related and sex-specific differences in the genetic affinities of castes to Asians and Europeans
Resolving catastrophic error bursts from cosmic rays in large arrays of superconducting qubits
Scalable quantum computing can become a reality with error correction,
provided coherent qubits can be constructed in large arrays. The key premise is
that physical errors can remain both small and sufficiently uncorrelated as
devices scale, so that logical error rates can be exponentially suppressed.
However, energetic impacts from cosmic rays and latent radioactivity violate
both of these assumptions. An impinging particle ionizes the substrate,
radiating high energy phonons that induce a burst of quasiparticles, destroying
qubit coherence throughout the device. High-energy radiation has been
identified as a source of error in pilot superconducting quantum devices, but
lacking a measurement technique able to resolve a single event in detail, the
effect on large scale algorithms and error correction in particular remains an
open question. Elucidating the physics involved requires operating large
numbers of qubits at the same rapid timescales as in error correction, exposing
the event's evolution in time and spread in space. Here, we directly observe
high-energy rays impacting a large-scale quantum processor. We introduce a
rapid space and time-multiplexed measurement method and identify large bursts
of quasiparticles that simultaneously and severely limit the energy coherence
of all qubits, causing chip-wide failure. We track the events from their
initial localised impact to high error rates across the chip. Our results
provide direct insights into the scale and dynamics of these damaging error
bursts in large-scale devices, and highlight the necessity of mitigation to
enable quantum computing to scale
The Druze: A Population Genetic Refugium of the Near East
BACKGROUND: Phylogenetic mitochondrial DNA haplogroups are highly partitioned across global geographic regions. A unique exception is the X haplogroup, which has a widespread global distribution without major regions of distinct localization. PRINCIPAL FINDINGS: We have examined mitochondrial DNA sequence variation together with Y-chromosome-based haplogroup structure among the Druze, a religious minority with a unique socio-demographic history residing in the Near East. We observed a striking overall pattern of heterogeneous parental origins, consistent with Druze oral tradition, together with both a high frequency and a high diversity of the mitochondrial DNA (mtDNA) X haplogroup within a confined regional subpopulation. Furthermore demographic modeling indicated low migration rates with nearby populations. CONCLUSIONS: These findings were enabled through the use of a paternal kindred based sampling approach, and suggest that the Galilee Druze represent a population isolate, and that the combination of a high frequency and diversity of the mtDNA X haplogroup signifies a phylogenetic refugium, providing a sample snapshot of the genetic landscape of the Near East prior to the modern age