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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.

Spanish colonial rule in Peru was marked by dramatic changes to indigenous mortuary customs, bodily practices, and morbidity profiles. However, that era of transformation was not solely shaped by Spanish policies; Native Andeans creatively negotiated with those newcomers, sculpting novel practices that sometimes integrated, and other times challenged, the Spanish agenda. Theoretical perspectives on the constrained agency of indigenous communities under colonial rule and the negotiated outcomes of those colonial encounters are explored through a case study of mummy burials from the cave site of Vinchos in highland Peru and comparisons to other colonial Andean populations. We conduct osteological and stable isotope analyses, molecular assessment of sex chromosomes, and ancient mitochondrial DNA (mtDNA) analysis of the Vinchos mummies and 3,314 other HVR1 sequences from South America (haplotype network analysis). Results show that there are four adults, one child, and one fetus/infant. mtDNA analysis shows three distinct mtDNA lineages. Principal coordinate analysis shows that the Vinchos individuals are near to modern and ancient populations from the Andes; haplotype network analysis shows that one individual shares a haplotype with several geographically dispersed groups in South America, while three individuals exhibit two unique haplotypes. The data show the ongoing practice of cranial modification, the continuation of native mortuary practices, and some continuities in diet and foodways. Despite Spanish colonial attempts to eradicate indigenous practices, these multiple data sets reveal the agential capacities of Native Andeans—though constrained by colonial structures—to continue specific cultural traditions and forge novel practices while subjects of the Spanish Crown. La colonizacion espanola en Peru llevo cambios dramaticos en las costumbres mortuorias indigenas, las practicas corporales y los perfiles de morbilidad. Sin embargo, este periodo de transformacion no fue creado unicamente por las politicas espanolas. Los nativos andinos negociaron creativamente con los espanoles, desarrollando practicas novedosas que a veces integraban, y otras veces desafiaban, la agenda espanola. Las perspectivas teoricas sobre la agencia restringida de las comunidades indigenas y los resultados negociados del gobierno colonial se exploran a traves de un estudio de caso de entierros de momias del sitio de la cueva de Vinchos en las tierras altas de Peru en comparacion con otros poblados andinos. Realizamos analisis de isotopos estables y osteologicos, evaluacion molecular de cromosomas sexuales, analisis de mtADN antiguo de las momias de Vinchos y otras 3,314 secuencias de HVRI de America del Sur (analisis de red de haplotipos). Los resultados muestran que hay cuatro adultos, un nino y un feto/infante. El analisis de mtADN muestra tres linajes de mtADN distintos. El analisis de coordenadas principales muestra que los individuos Vinchos estan cerca de las poblaciones modernas y antiguas de los Andes. El analisis de la red de haplotipos muestra que un individuo comparte un haplotipo con varios grupos geograficamente dispersos en America del Sur, mientras que tres individuos exhiben dos haplotipos unicos. Los datos muestran la practica continua de modificacion craneal, la continuacion de las practicas mortuorias nativas (al menos para algunos) y algunas continuidades en la dieta y los alimentos. A pesar de los intentos coloniales por erradicar las practicas indigenas, estos conjuntos de datos multiples revelan las capacidades agenciales de los andinos nativos, aunque estan limitados por las estructuras coloniales, para continuar con tradiciones culturales especificas y forjar practicas novedosas mientras son sujetos de la Corona espanola.

Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape ( n = 7; 700 CE Mexico) and historic dental calculus ( n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya ( n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians ( n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria ( Treponema denticola , Fusobacterium nucleatum and Eubacterium saphenum ) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers ( Eubacterium biforme, Phascolarctobacterium succinatutens ) and potentially disease-associated bacteria ( Escherichia , Brachyspira) . Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

The developmental transition to motherhood requires gene expression changes that alter the brain to drive the female to perform maternal behaviors. We broadly examined the global transcriptional response in the mouse maternal brain, by examining four brain regions: hypothalamus, hippocampus, neocortex, and cerebellum, in virgin females, two pregnancy time points, and three postpartum time points. We find that overall there are hundreds of differentially expressed genes, but each brain region and time point shows a unique molecular signature, with only 49 genes differentially expressed in all four regions. Interestingly, a set of “early-response genes” is repressed in all brain regions during pregnancy and postpartum stages. Several genes previously implicated in underlying postpartum depression change expression. This study serves as an atlas of gene expression changes in the maternal brain, with the results demonstrating that pregnancy, parturition, and postpartum maternal experience substantially impact diverse brain regions.

In this study, we sought to document the efficiency of primer extension capture (PEC) as a method to enrich DNA eluates of targeted DNA molecules and remove nontarget molecules from pools containing both. Efficiency of the method was estimated by comparing number of "copies in" to "copies out" by quantitative polymerase chain reaction. PEC retention of DNA targets ranging 109-288 base pairs (bps) in length was 15.88-2.14% (i.e., loss of 84.12-97.86% of target molecules). Experimental modifications of the PEC method resulted in no significant improvements. However, the benefit of PEC was revealed in its ability to remove most nontarget DNA molecules (99.99%). We also discovered that many (56.69%) of the target molecules are "lost" prior to their immobilization on the streptavidin-coated beads. These estimates of methodological efficiency are directly comparable to previous ones observed following "fishing" for DNA, an alternative method for DNA enrichment.

This study sought to document the efficiency of DNA bait capture (i.e., "fishing") methods by two measures: (1) its ability to retain targeted DNA molecules, and (2) its ability to remove non-target DNA molecules from a pool containing both. DNA bait capture uses synthetic biotinylated DNA primers to bind target DNA, which are then immobilized onto streptavidin coated magnetic beads and drawn to a magnet. Bound DNA should, therefore, be isolated from non-target DNA and impurities (e.g., PCR inhibitors) and can be later eluted from the beads for downstream applications. Efficiencies were estimated by comparing the number of "copies in" to "copies out" with quantitative polymerase chain reaction (qPCR). Retention of target DNA molecules, ranging from 109 to 288 base pairs (bps) in length, averaged just 9.06–3.53% (i.e., loss of 90.94–96.47%) using the fishing protocol as originally described. Some improvement was achieved by employing a modified protocol (i.e., with a shortened hybridization time, use of twice the amount of M-270 streptavidin-coated beads, and modified bead washing), resulting in average retention of 31.41–12.08% of the same set of targeted molecules. Noted was the lack of efficacy in removing non-target DNA molecules as opposed to targeted molecules. It was also observed that most of the molecules (61.35–69.49%) are "lost" during the essential hybridization step of the fishing protocol, suggesting its suitability for high copy number samples only. While the bait capture method may be useful in the study of polymerase chain reaction (PCR) inhibited DNA samples as previously suggested, it is necessary to carefully weigh this possible advantage against the degree of expected DNA loss and the non-selectivity of the method for targeted over non-targeted DNA.

DNA from ancient sources is generally believed to be of low copy number, despite minimal attention towards direct measurement of DNA loss accumulated through the extraction process. We developed synthesized “standards” to measure the efficiency of some common DNA extraction methods for degraded skeletal samples, and used quantitative PCR to estimate a known quantity of DNA subjected to a given extraction method (i.e. “copies in”) versus quantity of DNA retained (i.e. “copies out”). All methods performed poorly in retaining short segments of DNA, giving low copy number results even when pre-extraction copy numbers exceeded those expected of ancient samples. These findings challenge low copy number expectations, suggesting that ancient specimens may contain far more preserved genetic material than previously recognized. Furthermore, they emphasize the importance of optimizing and/or developing specialized extraction methods for retrieving degraded DNA.

This study evaluated techniques that can potentially decrease time, cost, and labor in eliminating, circumventing, and/or inactivating as many polymerase chain reaction (PCR) inhibitors as possible while preserving DNA yield. In order to further explore the role of PCR inhibitors in ancient DNA (aDNA) studies, 140 DNA extractions were conducted on 112 Pacific salmonid vertebrae recovered from two archaeological sites located at Dionisio Point on Galiano Island, in southwestern British Columbia, Canada. These DNA extracts and their dilutions at 1:10 and 1:50 were screened for the presence of a 189 base pair (bp) portion of the 12S mitochondrial gene that is used for species identification of Pacific salmonids and other fish. These extracts and their dilutions were also screened for the presence of PCR inhibitors that can cause negative results for amplification of salmonid mtDNA. Repeat silica extraction was conducted on the full concentration extracts until: (1) they either produced a positive result in the salmonid mtDNA reaction, or (2) were deemed to be free of inhibition, but failed to amplify in the salmonid mtDNA reaction. In the latter case, the samples were concluded to not contain sufficient salmonid mtDNA to permit PCR amplification. In obtaining positive salmonid species identification, repeat silica purified extracts (81/133 successes) statistically outperformed dilutions at 1:10 (55/140, p ¼0.0018), 1:50 (63/140, p ¼0.0312), as well as across all dilutions combined (118/280, p ¼0.0025). We also explored the efficacy of EGTA as a decalcifying agent as compared to EDTA, which is commonly employed in aDNA studies. The only extracts that amplified at full concentration (6/140, 4.3%) were those in which EGTA decalcification was used. However, when diluted there was no statistical difference in the success of obtaining positive species identification from bone decalcified with EGTA or EDTA (1:10 and 1:50 dilutions, p ¼0.7891 and p > 0.9999 respectively). From the results of this study, we recommend that aDNA researchers employ greater flexibility in their methodologies as well as be cognizant of the role that PCR inhibitors may play in their investigations.

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 a relationship between clan membership and genetic variation of matrilines and patrilines. To further understand this association, in this study mitochondrial DNA sequences from the Tlingit (n = 154) were examined. By comparing mitochondrial DNA with moiety membership information, the authors 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. This study additionally illustrates the relevance of data derived from Tlingit oral traditions to test hypotheses about population history on the Northwest Coast.

Studies of low copy number (LCN) and degraded DNA are prone to contamination from exogenous DNA sources that in some cases out-compete endogenous DNA in PCR amplification, thus leading to false positives and/or aberrant results. Particularly problematic is contamination that is inadvertently deposited on the surfaces of bones through direct handling. Whereas some previous studies have shown that contamination removal is possible by subjecting samples to sodium hypochlorite prior to DNA extraction, others caution that such treatment can destroy a majority of the molecules endogenous to the sample. To further explore this topic, we experimentally contaminated ancient northern fur seal ( Callorhinus ursinus ) ribs with human DNA and treated them with sodium hypochlorite to remove that contamination. Our findings are consistent with previous studies that found sodium hypochlorite to be highly efficient (∼81–99%) at contamination removal; however, there emerged no treatment capable of removing 100% of the contamination across all of the experiments. Moreover, the ability to estimate the degree of damage to endogenous northern fur seal molecules was compromised due to the inherent variability of preserved mtDNA across the bones, and the presence of co-extracted PCR inhibitors.

A recent study of mitochondrial DNA variation in Native American populations from the American Southwest detected signatures of a population expansion of subhaplogroup B2a, dated to 2,105 years before present (99.5% confidence interval, 1,273–3,773 YBP), following the introduction and intensification of maize agriculture in the region. Only one Yuman group and no Athapaskan speakers were analyzed in previous studies. Here we report mtDNA haplogroup and hypervariable region (HVR I, and II) sequence data from 263 extant Yuman speakers, representing the major branches of the Yuman language family, in addition to the Western Apache (Athapaskan) to further investigate the demographic context and geographic extent of this expansion. Data presented indicate that the expansion of B2a is only slightly older [2,410 YBP (99.5% CI: 1,458–4,320 YBP)] than previously estimated and not significantly. Despite large confidence intervals there are implications for the origin and expansion of the Yuman language family. Cultural transformations due to the inundation and draining of Lake Cahuilla may explain in part the frequencies of this lineage among the Kumeyaay and other Yuman and Takic groups in Southern California. This may have been the result of group fissions and fusions followed by migration and interaction that included expanded trade networks and intermarriage among Yuman speakers. In addition, a series of in-situ genetic bottlenecks is proposed to have occurred among the Western Apache leading to increasing homogeneity within haplogroup A, culminating in an admixture event with the Yavapai. Am J Phys Anthropol 150:618–631, 2013. © 2013 Wiley Periodicals, Inc.

They Walked Together Paisley Cave in Oregon provides some of the earliest evidence for humans in North America. Jenkins et al. (p. 223 ) provide a wide variety of additional evidence of early human occupation of this site, including a series of radiocarbon ages extending back to nearly 12,500 radiocarbon years ago (about 14,500 calendar years ago). The find includes examples of projectile points representative of the Western Stemmed Tradition dating to about 11,100 radiocarbon years ago. The Western Stemmed Tradition has been thought to have evolved after the dominant Clovis technology, but the find suggests that the two cultures overlapped in time.

The Farming/Language Dispersal Hypothesis posits that prehistoric population expansions, precipitated by the innovation or early adop-tion of agriculture, played an important role in the uneven distribution of language families recorded across the world. In this case, the most widely spread language families today came to be distributed at the expense of those that have more restricted distributions. In the Americas, Uto-Aztecan is one such language family that may have been spread across Mesoamerica and the American Southwest by ancient farmers. We evaluated this hypothesis with a large-scale study of mitochondrial DNA (mtDNA) and Y-chromosomal DNA vari-ation in indigenous populations from these regions. Partial correlation coefficients, determined with Mantel tests, show that Y-chromosome variation in indigenous populations from the American Southwest and Mesoamerica correlates significantly with linguistic distances ( r = 0.33–0.384; P < 0.02), whereas mtDNA diversity correlates significantly with only geographic distance ( r = 0.619; P = 0.002). The lack of correlation between mtDNA and Y-chromosome diversity is consistent with differing population histories of males and females in these regions. Although unlikely, if groups of Uto-Aztecan speakers were responsible for the northward spread of agriculture and their languages from Mesoamerica to the Southwest, this migration was possibly biased to males. However, a recent in situ population expansion within the American Southwest (2,105 years before present; 99.5% confidence interval = 1,273–3,773 YBP), one that probably followed the introduction and intensification of maize agriculture in the region, may have blurred ancient mtDNA patterns, which might otherwise have revealed a closer genetic relationship between females in the Southwest and Mesoamerica.

Although the cultural and nutritive importance of the turkey ( Meleagris gallopavo ) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC–AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey ( Meleagris gallopavo gallopavo ) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices.

Background:Oxidative stress largely contributes to early brain injury after subarachnoid hemorrhage (SAH). One of the major sources of reactive oxygen species is NADPH oxidase, upregulated after SAH. We hypothesized that NADPH oxidase-induced oxidative stress plays a major causative role in early brain injury after SAH.Methods:Using gp91phox knockout (ko) and wild-type (wt) mice, we studied early brain injury in the endovascular perforation model of SAH. Mortality rate, cerebral edema, oxidative stress, and superoxide production were measured at 24 h after SAH. Neurological evaluation was done at 23 h after SAH surgery.Results:Genotyping confirmed the existence of a nonfunctional gp91phox gene in the ko mice. CBF measurements did not show differences in SAH-induced acute ischemia between ko and wt mice. SAH caused a significant increase of water content in the ipsilateral hemisphere as well as an increase of Malondialdehyde (MDA) levels and superoxide production. There were no significant differences in post-SAH mortality rate, brain water content and the intensity of the oxidative stress between knockout and wild type groups of mice.Conclusions:Our results suggest that gp91phox is not critically important to the early brain injury after SAH. An adaptive compensatory mechanism for free radical production in knockout mice is discussed.

Polymerase chain reaction (PCR) inhibitors are often co-extracted with ancient DNA (aDNA) and when present make the analysis of aDNA difficult, if not impossible. In this study we review previous research on PCR inhibitors and techniques that address their co-extraction with DNA from sub-optimal samples. Additionally, we introduce a simple extraction technique, ‘‘repeat silica extraction,’’ that effectively removed PCR inhibitors from extracts of 7000e8000-year-old human skeletal remains from the Windover archaeological site in Florida and 700e2000-yearold human coprolites excavated from Fish Slough Cave in southern California. A series of tests on these same samples demonstrates that N-phenacylthiazolium bromide is largely ineffective, despite previously reported success using this compound as part of the DNA extraction process. We also describe a method for demonstrating the presence as well as successful removal of PCR inhibitors by use of a ‘‘positive aDNA control,’’ a test necessary to conclude that negative PCR amplification is the result of the absence of preserved DNA. 2006 Elsevier Ltd. All rights reserved.

© 2017 Kemp et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The 13thcentury Puebloan depopulation of the Four Corners region of the US Southwest is an iconic episode in world prehistory. Studies of its causes, as well as its consequences, have a bearing not only on archaeological method and theory, but also social responses to climate change, the sociology of social movements, and contemporary patterns of cultural diversity. Previous research has debated the demographic scale, destinations, and impacts of Four Corners migrants. Much of this uncertainty stems from the substantial differences in material culture between the Four Corners vs. hypothesized destination areas. Comparable biological evidence has been difficult to obtain due to the complete departure of farmers from the Four Corners in the 13thcentury CE and restrictions on sampling human remains. As an alternative, patterns of genetic variation among domesticated species were used to address the role of migration in this collapse. We collected mitochondrial haplotypic data from dog (Canis lupus familiaris) and turkey (Meleagris gallopavo) remains from archaeological sites in the most densely-populated portion of the Four Corners region, and the most commonly proposed destination area for that population under migration scenarios. Results are consistent with a large-scale migration of humans, accompanied by their domestic turkeys, during the 13thcentury CE. These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations.

Objectives There is a paucity of studies on psychosocial disorders in clinic populations in Jamaica. Therefore, we sought to determine the prevalence and correlates of symptoms of depression and anxiety in a clinic population in western Jamaica. Methods A total of 338 participants from four outpatient clinics of : A total of 338 participants from four outpatient clinics of the Western Regional Health Authority (WRHA) were screened for symptoms of depression and anxiety using questions from the Beck Depression Inventory-II and the Beck Anxiety Inventory. The Chi-square test was used to examine differences in symptoms of anxiety and depression by gender. Multivariate linear and logistic regression were used to examine the associations between symptoms and sociodemographic variables with significance set at p Results Approximately 30% of participants had moderate or severe depression symptoms while 18.6% had moderate or severe anxiety symptoms. Participants aged 30-39 years were more likely than older participants to have moderate or severe anxiety symptoms (odds ratio [OR]: 2.0, 95% confidence interval [CI]: 1.39, 5.56). Women reported a statistically significant higher prevalence of anxiety symptoms (10.0% vs 7.1%, p = 0.003). There was also a statistically significant difference between anxiety means by gender. Furthermore, income was found to be a significant predictor of anxiety for women only (p = 0.0113). Married persons were more likely than those who had never married to have moderate or severe anxiety symptoms (OR: 2.57, 95% CI: 1.14, 5.76). Conclusions Our findings suggest that the prevalence of depression may be higher than global estimates in similar outpatient settings. Screening and intervention efforts may need to focus on younger persons, women, and married persons.

To evaluate the prevalence of parent-reported attention-deficit/hyperactivity disorder (ADHD) in two clinics in Alabama serving children with vision impairment.The medical records of children 4-17 years of age attending the Alabama School for the Blind (ASB) during the 2010-2011 school year or seen at the University of Alabama at Birmingham (UAB) Center for Low Vision Rehabilitation between 2006 and 2010 were retrospectively reviewed. Sociodemographics, ocular characteristics, and parental report of ADHD diagnosis were obtained. The prevalence of ADHD was compared to national and state figures for age-similar children regardless of comorbidities. The prevalence of ADHD, sociodemographic, and ocular characteristics was also compared between clinical sites.A total of 264 children participated in the study (95 from ASB and 169 from UAB). The prevalence of ADHD among children with visual acuity better than hand motion (n = 245) was 22.9%, which is higher than reported state (14.3%) and national prevalence (9.5%) for children in this age range. The prevalence was similar at ASB (22.4%) and UAB (23.1%). Those with ADHD were similar to those without ADHD with respect to age, sex, and race. Children with ADHD were significantly less likely to have nystagmus and more likely to have better visual acuity (P0.05). The prevalence of ADHD among the 19 participants with total or near total vision loss (all from ASB) was 10.5%.Our analyses suggest that children with vision impairment may be more likely to be diagnosed with ADHD than children in the general population.

While recent forensic research has focused on determining which skeletal elements are superior in their preservation of DNA over the long term, little focus has been placed on measuring intra-element variation. Moreover, there is a general belief that dense (cortical) bone material will contain better-preserved DNA than does spongy (cancellous) bone. To address these ideas, quantitative PCR was used to estimate the degree of mitochondrial DNA (mtDNA) preservation variance across sections of 19 northern fur seal ribs ( Callorhinus ursinus ) that date to ∼3000 years before present. Further, we developed a measure called the “density index” that was used to gauge the relative densities of the rib sections studied here to determine if density was an appropriate predictor of preservation. The average preservation among the samples was significantly different (ANOVA, p = 1.9 × 10 −9 ) with only 15% of the total variance observed within samples. However, 12 of the 19 specimens (∼63.2%) exhibited at least an order of magnitude difference in mtDNA preservation across the whole. Regression of the amount of mtDNA extracted per gram of bone material against the density index of the bone from which it was extracted demonstrates no relationship between these variables ( R 2 = 0.03, p = 0.28).

DNA from ancient and forensic specimens is often co-extracted with unknown amounts of unknown PCR inhibitors, which can lead to underestimated DNA concentrations, allelic drop-out, and/or false-negative results. It is not surprising, in this case, that numerous methods have been developed to remove PCR inhibitors or subdue their effects. One simple and cost effective approach could be the adoption of a polymerase that overcomes or is less affected by PCR inhibitors. In this study, nine different polymerases were evaluated for their efficacy against PCR inhibitors co-extracted with DNA from 63 ancient salmon vertebrae. These samples were excavated from two archeological sites located at the Dionisio Point locality on the northern end of Galiano Island in coastal southwestern British Columbia, Canada and date to 700-1000 and 1300-1500 years before present. Previously, DNA extracts from samples studied from this locality were determined to be largely inhibited to PCR amplification. In the present study, Omni Klentaq LA (DNA Polymerase Technology, Inc.) outperformed the other 8 polymerases in two measures: (1) its success in genetic species identification of these vertebrae, and (2) its ability to amplify an ancient DNA positive control when spiked with a volume of potentially inhibited extract from the vertebrae.

A recent study of mitochondrial DNA variation in Native American populations from the American Southwest detected signatures of a population expansion of subhaplogroup B2a, dated to 2,105 years before present (99.5% confidence interval, 1,273-3,773 YBP), following the introduction and intensification of maize agriculture in the region. Only one Yuman group and no Athapaskan speakers were analyzed in previous studies. Here we report mtDNA haplogroup and hypervariable region (HVR I, and II) sequence data from 263 extant Yuman speakers, representing the major branches of the Yuman language family, in addition to the Western Apache (Athapaskan) to further investigate the demographic context and geographic extent of this expansion. Data presented indicate that the expansion of B2a is only slightly older [2,410 YBP (99.5% CI: 1,458-4,320 YBP)] than previously estimated and not significantly. Despite large confidence intervals there are implications for the origin and expansion of the Yuman language family. Cultural transformations due to the inundation and draining of Lake Cahuilla may explain in part the frequencies of this lineage among the Kumeyaay and other Yuman and Takic groups in Southern California. This may have been the result of group fissions and fusions followed by migration and interaction that included expanded trade networks and intermarriage among Yuman speakers. In addition, a series of in-situ genetic bottlenecks is proposed to have occurred among the Western Apache leading to increasing homogeneity within haplogroup A, culminating in an admixture event with the Yavapai.

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 was 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 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 to 409 bp in length, corresponding to those targeted by the PowerPlex 16 System (Promega, Madison, WI). Across all standards from 10(4) to 10(7) copies/μL, loss averaged between 21.75% and 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 either between DNA strand length and retention or between 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 on what their claims are based, 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.