Review: Applications of Bayesian Skyline Plots and Approximate Bayesian Computation for Human Demography

Bayesian methods have been adopted by anthropologists for their utility in resolving complex questions about human history based on genetic data. The main advantages of Bayesian methods include simple model comparison, presenting results as a summary of probability distributions, and the explicit inclusion of prior information into analyses. In the field of anthropological genetics, for example, implementing Bayesian skyline plots and approximate Bayesian computation is becoming ubiquitous as means to analyze genetic data for the purpose of demographic or historic inference. Correspondingly, there is a critical need to better understand the underlying assumptions, proper applications, and limitations of these two methods by the larger anthropological community. Here we present a review of Bayesian skyline plots and approximate Bayesian computation as applied to human demography, as well as provide examples of the application of these methods to anthropological research questions. We also review the two core components of Bayesian demographic analysis: the coalescent and Bayesian inference. Our goal is to describe their basic mechanics in attempt to demystify them

How Much DNA is Lost? Measuring DNA Loss of STR Length Fragments Targeted by the PowerPlex 16® System Using the Qiagen MinElute Purification Kit

The success in recovering genetic profiles from aged and degraded biological samples is diminished by fundamental aspects of DNA extraction, as well as its long-term preservation that are not well understood. While numerous studies have been conducted to determine whether one extraction method performed superior to others, nearly all of them were initiated with no knowledge of the actual starting DNA quantity in the samples prior to extraction, so they ultimately compared the outcome of all methods relative to the best. Using quantitative PCR (qPCR) to estimate the copy count of synthetic standards before (i.e., “copies in”) and after (i.e., “copies out”) purification by the Qiagen MinElute PCR Purification Kit, we documented DNA loss within a pool of 16 different sized fragments ranging from 106–409 base pairs (bps) in length, corresponding to those targeted by the Promega PowerPlex 16® System. Across all standards starting from 10^4 to 10^7 copies/μL, loss averaged between 21.75% to 60.56% (mean 39.03%), which is not congruent with Qiagen’s claim that 80% of 70 bp to 4 kb fragments are retained using this product (i.e., 20% loss). Our study also found no clear relationship between neither DNA strand length and retention, nor starting copy number and retention. This suggests that there is no molecule bias across the MinElute column membrane and highlights the need for manufacturers to clearly and accurately describe how their claims are made, and should also encourage researchers to document DNA retention efficiencies of their own methods and protocols. Understanding how and where to reduce loss of molecules during extraction and purification will serve to generate clearer and more accurate data, which will enhance the utility of ancient and low copy number DNA as a tool for closing forensic cases or in reconstructing the evolutionary history of humans and other organisms

The Earliest Farmers of Northwest China Exploited Grain-fed Pheasants not Chickens

Though chickens (Gallus gallus domesticus) are globally ubiquitous today, the timing, location, and manner of their domestication is contentious. Until recently, archaeologists placed the origin of the domestic chicken in northern China, perhaps as early as 8,000 years ago. Such evidence however complicates our understanding of how the chicken was domesticated because its wild progenitor – the red jungle fowl (Gallus gallus) – lives in tropical ecosystems and does not exist in northern China today or in the recent past. Increasingly, multiple lines of evidence suggest that many of the archaeological bird remains underlying this northern origins hypothesis have been misidentified. Here we analyze the mitochondrial DNA of some of the earliest purported chickens from the Dadiwan site in northern China and conclude that they are pheasants (Phasianus colchicus). Curiously, stable isotope values from the same birds reveal that their diet was heavy in agricultural products (namely millet), meaning that they lived adjacent to or among some of the earliest farming communities in East Asia. We suggest that the exploitation of these baited birds was an important adaptation for early farmers in China’s arid north, and that management practices like these likely played a role in the domestication of animals – including the chicken – in similar contexts throughout the region.The original isotopic analyses of these remains were conducted in collaboration with Seth Newsome (then at the Carnegie Institution of Washington) and Chen Fahu (Lanzhou University), with funding from the Wenner-Gren Foundation (awarded to L.B.). The University of Oklahoma provided funding for all molecular analyses (through B.M.K.). Open Access fees paid for in whole or in part by the University of Oklahoma LibrariesYe

Genetic Diversity and Relationships of Tlingit Moieties

The Tlingit from Southeast Alaska belong to the Northwest Coast cultural tradition, which is defined by regionally shared sociocultural practices. A distinctive feature of Tlingit social organization is the matrilineal exogamous marriage system among clans from two opposite moieties: the Raven/Crow and Eagle/Wolf. Clan and moiety membership are determined by matrilineal descent, and previous genetic studies of Northwest Coast populations have shown that there is a relationship between clan membership and genetic variation of matrilines and patrilines. To further understand this association, mitochondrial DNA (mtDNA) sequences from the Tlingit (n=154) are examined. By comparing mtDNA with moiety membership information, we explore the impact of marriage traditions among the Tlingit with their observable genetic variation. At the genetic level, the results support cultural persistence of Tlingit maternal moiety identity despite the negative impacts of European colonization. Our study additionally illustrates the relevance of data derived from Tlingit oral traditions to test hypotheses about population history on the Northwest Coast

Origins of an Unmarked Georgia Cemetery Using Ancient DNA Analysis

Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we utilize ancient DNA extraction methods to investigate the origins of Avondale Burial Place through the use of well-preserved skeletal fragments from 20 individuals buried in the cemetery. Through examination of hypervariable region I in the mitochondrial genome (HVR1, mtDNA), we determine haplotypes for all 20 of these individuals. A total of 18 of the 20 individuals belong to the L or U haplogroups, suggesting that Avondale Burial Place was most likely used primarily as a resting place for African Americans. After the surrounding Bibb County community expressed interest in investigating potential ancestral relationships to those within the cemetery, a total of eight potential descendants provided saliva in order to obtain mtDNA HVR1 information. This phase of the study revealed that two different individuals from Avondale Burial Place matched two individuals with oral history ties to the cemetery. Using the online tool EMPOP, we calculated the likelihood of these exact matches occurring by chance alone

The HIV-1 late domain-2 S40A polymorphism in antiretroviral (or ART)-exposed individuals influences protease inhibitor susceptibility.

BackgroundThe p6 region of the HIV-1 structural precursor polyprotein, Gag, contains two motifs, P7TAP11 and L35YPLXSL41, designated as late (L) domain-1 and -2, respectively. These motifs bind the ESCRT-I factor Tsg101 and the ESCRT adaptor Alix, respectively, and are critical for efficient budding of virus particles from the plasma membrane. L domain-2 is thought to be functionally redundant to PTAP. To identify possible other functions of L domain-2, we examined this motif in dominant viruses that emerged in a group of 14 women who had detectable levels of HIV-1 in both plasma and genital tract despite a history of current or previous antiretroviral therapy.ResultsRemarkably, variants possessing mutations or rare polymorphisms in the highly conserved L domain-2 were identified in seven of these women. A mutation in a conserved residue (S40A) that does not reduce Gag interaction with Alix and therefore did not reduce budding efficiency was further investigated. This mutation causes a simultaneous change in the Pol reading frame but exhibits little deficiency in Gag processing and virion maturation. Whether introduced into the HIV-1 NL4-3 strain genome or a model protease (PR) precursor, S40A reduced production of mature PR. This same mutation also led to high level detection of two extended forms of PR that were fairly stable compared to the WT in the presence of IDV at various concentrations; one of the extended forms was effective in trans processing even at micromolar IDV.ConclusionsOur results indicate that L domain-2, considered redundant in vitro, can undergo mutations in vivo that significantly alter PR function. These may contribute fitness benefits in both the absence and presence of PR inhibitor

Rapid Oscillations in Cataclysmic Variables. XVI. DW Cancri

We report photometry and spectroscopy of the novalike variable DW Cancri. The spectra show the usual broad H and He emission lines, with an excitation and continuum slope characteristic of a moderately high accretion rate. A radial-velocity search yields strong detections at two periods, 86.1015(3) min and 38.58377(6) min. We interpret these as respectively the orbital period P_orb of the binary, and the spin period P_spin of a magnetic white dwarf. The light curve also shows the spin period, plus an additional strong signal at 69.9133(10) min, which coincides with the difference frequency 1/P_spin-1/P_orb. These periods are stable over the 1 year baseline of measurement. This triply-periodic structure mimics the behavior of several well-credentialed members of the "DQ Herculis" (intermediate polar) class of cataclysmic variables. DQ Her membership is also suggested by the mysteriously strong sideband signal (at nu_spin-nu_orb), attesting to a strong pulsed flux at X-ray/EUV/UV wavelengths. DW Cnc is a new member of this class, and would be an excellent target for extended observation at these wavelengths.Comment: PDF, 28 pages, 6 tables, 9 figures; accepted, in press, to appear June 2004, PASP; more info at http://cba.phys.columbia.edu

Coherent states for compact Lie groups and their large-N limits

The first two parts of this article surveys results related to the heat-kernel coherent states for a compact Lie group K. I begin by reviewing the definition of the coherent states, their resolution of the identity, and the associated Segal-Bargmann transform. I then describe related results including connections to geometric quantization and (1+1)-dimensional Yang--Mills theory, the associated coherent states on spheres, and applications to quantum gravity. The third part of this article summarizes recent work of mine with Driver and Kemp on the large-N limit of the Segal--Bargmann transform for the unitary group U(N). A key result is the identification of the leading-order large-N behavior of the Laplacian on "trace polynomials."Comment: Submitted to the proceeding of the CIRM conference, "Coherent states and their applications: A contemporary panorama.

Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning

As sequencing costs decrease and availability of high fidelity long-read sequencing increases, generating experiment specific de novo genome assemblies becomes feasible. In many crop species, obtaining the genome of a hybrid or heterozygous individual is necessary for systems that do not tolerate inbreeding or for investigating important biological questions, such as hybrid vigor. However, most genome assembly methods that have been used in plants result in a merged single sequence representation that is not a true biologically accurate representation of either haplotype within a diploid individual. The resulting genome assembly is often fragmented and exhibits a mosaic of the two haplotypes, referred to as haplotype-switching. Important haplotype level information, such as causal mutations and structural variation is therefore lost causing difficulties in interpreting downstream analyses. To overcome this challenge, we have applied a method developed for animal genome assembly called trio-binning to an intra-specific hybrid of chili pepper (Capsicum annuum L. cv. HDA149 x Capsicum annuum L. cv. HDA330). We tested all currently available softwares for performing trio-binning, combined with multiple scaffolding technologies including Bionano to determine the optimal method of producing the best haplotype-resolved assembly. Ultimately, we produced highly contiguous biologically true haplotype-resolved genome assemblies for each parent, with scaffold N50s of 266.0 Mb and 281.3 Mb, with 99.6% and 99.8% positioned into chromosomes respectively. The assemblies captured 3.10 Gb and 3.12 Gb of the estimated 3.5 Gb chili pepper genome size. These assemblies represent the complete genome structure of the intraspecific hybrid, as well as the two parental genomes, and show measurable improvements over the currently available reference genomes. Our manuscript provides a valuable guide on how to apply trio-binning to other plant genomes

In the Shadow of the Transiting Disk: Imaging epsilon Aurigae in Eclipse

Eclipses of the single-line spectroscopic binary star, epsilon Aurigae, provide an opportunity to study the poorly-defined companion. We used the MIRC beam combiner on the CHARA array to create interferometric images during eclipse ingress. Our results demonstrate that the eclipsing body is a dark disk that is opaque and tilted, and therefore exclude alternative models for the system. These data constrain the geometry and masses of the components, providing evidence that the F-star is not a massive supergiant star.Comment: As submitted to Nature. Published in Nature April 8, 2010