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

1D Potts, Yang-Lee Edges and Chaos

It is known that the (exact) renormalization transformations for the one-dimensional Ising model in field can be cast in the form of a logistic map f(x) = 4 x (1 - x) with x a function of the Ising couplings. Remarkably, the line bounding the region of chaotic behaviour in x is precisely that defining the Yang-Lee edge singularity in the Ising model. In this paper we show that the one dimensional q-state Potts model for q greater than or equal to 1 also displays such behaviour. A suitable combination of Potts couplings can again be used to define an x satisfying f(x) = 4 x (1 -x). The Yang-Lee zeroes no longer lie on the unit circle in the complex z = exp (h) plane, but their locus is still reproduced by the boundary of the chaotic region in the logistic map.Comment: 6 pages, no figure

New Limits on the Low-frequency Radio Transient Sky Using 31 hr of All-sky Data with the OVRO-LWA

We present the results of the first transient survey from the Owens Valley Radio Observatory Long Wavelength Array (OVRO–LWA) using 31 hr of data, in which we place the most constraining limits on the instantaneous transient surface density at timescales of 13 s to a few minutes and at frequencies below 100 MHz. The OVRO–LWA is a dipole array that images the entire viewable hemisphere with 58 MHz of bandwidth from 27 to 84 MHz at 13 s cadence. No transients are detected above a 6.5σ flux density limit of 10.5 Jy, implying an upper limit to the transient surface density of 2.5 × 10⁻⁸ deg⁻² at the shortest timescales probed, which is orders of magnitude deeper than has been achieved at sub-100 MHz frequencies and comparable flux densities to date. The nondetection of transients in the OVRO–LWA survey, particularly at minutes-long timescales, allows us to place further constraints on the rate of the potential population of transients uncovered by Stewart et al. From their transient rate, we expect a detection of 8.4^(+31.8)_(-8.0) events, and the probability of our null detection is 1.9^(+644)_(-1.9) x 10⁻³, ruling out a transient rate >1.4 × 10⁻⁴ days⁻¹ deg⁻² with 95% confidence at a flux density limit of 18.1 Jy, under the assumption of a flat spectrum and wide bandwidth. We discuss the implications of our nondetection for this population and further constraints that can be made on the source spectral index, intrinsic emission bandwidth, and resulting luminosity distribution

The 21 cm Power Spectrum from the Cosmic Dawn: First Results from the OVRO-LWA

The 21 cm transition of neutral hydrogen is opening an observational window into the Cosmic Dawn of the universe—the epoch of first star formation. We use 28 hr of data from the Owens Valley Radio Observatory Long Wavelength Array to place upper limits on the spatial power spectrum of 21 cm emission at z ≈ 18.4 (Δ_(21) ≾ 10^4 mK), and within the absorption feature reported by the EDGES experiment. In the process we demonstrate the first application of the double Karhunen–Loève transform for foreground filtering, and diagnose the systematic errors that are currently limiting the measurement. We also provide an updated model for the angular power spectrum of low-frequency foreground emission measured from the northern hemisphere, which can be used to refine sensitivity forecasts for next-generation experiments

To Clone or Not To Clone: Method Analysis for Retrieving Consensus Sequences In Ancient DNA Samples

The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from “modern” DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be “gold standards” in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones