The Role of Canids in Ritual and Domestic Contexts: New Ancient DNA Insights from Complex Hunter-Gatherer Sites in Prehistoric Central California

This study explores the interrelationship between the genus Canis and hunter–gatherers through a case study of prehistoric Native Americans in the San Francisco Bay-Sacramento Delta area. A distinctive aspect of the region\u27s prehistoric record is the interment of canids, variously classified as coyotes, dogs, and wolves. Since these species are difficult to distinguish based solely on morphology, ancient DNA analysis was employed to distinguish species. The DNA study results, the first on canids from archaeological sites in California, are entirely represented by domesticated dogs (including both interments and disarticulated samples from midden deposits). These results, buttressed by stable isotope analyses, provide new insight into the complex interrelationship between humans and canids in both ritual and prosaic contexts, and reveal a more prominent role for dogs than previously envisioned

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p 10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10−392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group

Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation

Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The “southerly refugia model” has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star-like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice-free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range-wide patterns and identifies unique genetic units that can likely be used to inform conservation of at-risk populations at the northern periphery.Peer reviewe

Towards high–throughput analyses of fecal samples from wildlife

Towards high–throughput analyses of fecal samples from wildlife. High–throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor–intensive steps. We evaluate alternative protocols which could allow higher throughput for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods are tested here on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extraction from a fecal fragment. In addition, there is a lot of room for improvement in the DNA extraction step. Optimization of protocols can lead to very much more efficient, cheaper and higher throughput noninvasive monitoring. Selection of appropriate markers is still of paramount importance to increase genotyping success..Hacia análisis genéticos de alto rendimiento de muestras fecales de fauna silvestre. La secuenciación de alto rendimiento ofrece nuevas posibilidades en ecología molecular y biología de la conservación. Sin embargo, el potencial de esta técnica no ha sido totalmente explotado para estudios no invasivos, a partir de muestras fecales, de fauna en libertad. La secuenciación de alto rendimiento permite la secuenciación de fragmentos de ADN cortos y podría permitir el genotipado simultáneo de un gran número de muestras y marcadores a un bajo coste. La aplicación de estas técnicas a muestras fecales de fauna silvestre ha sido obstaculizada por la gran cantidad de trabajo requerido en varios pasos, desde la recolección de muestras hasta la secuenciación. Aquí evaluamos protocolos alternativos que podrían permitir un mayor rendimiento en dos de estos pasos: muestreo de campo y extracción de ADN. En este trabajo comparamos dos métodos distintos de conservación de las muestras obtenidas en el campo y siete métodos de extracción de ADN para heces de lobos (Canis lupus). Observamos una gran variación en el éxito de genotipado según los protocolos que se sigan. El método de muestreo de campo basado en frotado superficial de los excrementos dio resultados peores que la recolección de un fragmento del excremento. Por otro lado, los protocolos para la extracción de ADN mostraban resultados muy variables y ofrecen mucho margen de optimización y mejora. La optimización de protocolos puede llevar a un monitoreo no invasivo mucho más eficiente, económico y con mayor rendimiento. La selección de marcadores apropiados sigue siendo de importancia vital para incrementar el éxito de genotipado.Peer reviewe

Translational Diffusion in Mixtures of Imidazolium ILs with Polar Aprotic Molecular Solvents

Self-​diffusion coeffs. of cations and solvent mols. were detd. with 1H NMR in mixts. of 1-​n-​butyl-​3-​methylimidazolium (Bmim+) tetrafluoroborate (BF4-​)​, hexafluorophosphate (PF6-​)​, trifluoromethanesulfonate (TfO-​)​, and bis(trifluoromethylsulfonyl)​imide (TFSI-​) with acetonitrile (AN)​, γ-​butyrolactone (γ-​BL)​, and propylene carbonate (PC) over the entire compn. range at 300 K. The relative diffusivities of solvent mols. to cations as a function of concn. were found to depend on the solvent but not on the anion (i.e., IL)​. In all cases the values exhibit a plateau at low IL content (xIL < 0.2) and then increase steeply (AN)​, moderately (γ-​BL)​, or negligibly (PC) at higher IL concns. This behavior was related to the different solvation patterns in the employed solvents. In BmimPF6-​based systems, anionic diffusivities were followed via 31P nuclei and found to be higher than the corresponding cation values in IL-​poor systems and lower in the IL-​rich region. The inversion point of relative ionic diffusivities was found around equimolar compn. and does not depend on the solvent. At this point, a distinct change in the ion-​diffusion mechanism appears to take place