Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations

Background: The ability to accurately identify bird species is crucial for wildlife law enforcement and bird-strikeinvestigations. However, such identifications may be challenging when only partial or damaged feathers areavailable for analysis.Results: By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that itwas feasible to obtain accurate mitochondrial (mt)DNA-based species identification with as few as two featherbarbs. This minimally destructive DNA approach was successfully used and tested on a variety of bird species,including North American wild turkey (Meleagris gallopavo), Canada goose (Branta canadensis), blue heron (Ardeaherodias) and pygmy owl (Glaucidium californicum). The mtDNA was successfully obtained from ‘fresh’ feathers,historic museum specimens and archaeological samples, demonstrating the sensitivity and versatility of thistechnique.Conclusions: By applying appropriate contamination controls, sufficient quantities of mtDNA can be reliablyrecovered and analyzed from feather barbs. This previously overlooked substrate provides new opportunities foraccurate DNA species identification when minimal feather samples are available for forensic analysis

Ancient mtDNA Analysis of Early 16th Century Caribbean Cattle Provides Insight into Founding Populations of New World Creole Cattle Breeds

The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15th to early 16th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus) breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the ‘African’ haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of “African-derived American” haplotypes (AA/T1c1a1) in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle

Ancient DNA Analysis of Indigenous Rockfish Use On the Pacific Coast: Implications for Marine Conservation Areas and Fisheries Management

Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory

An Efficient and Reliable DNA-based Sex Identification Method for Archaeological Pacific Salmonid (Oncorhynchus spp.) Remains

Pacific salmonid (Oncorhynchus spp.) remains are routinely recovered from archaeological sites in northwestern North America but typically lack sexually dimorphic features, precluding the sex identification of these remains through morphological approaches. Consequently, little is known about the deep history of the sex-selective salmonid fishing strategies practiced by some of the region\u27s Indigenous peoples. Here, we present a DNA-based method for the sex identification of archaeological Pacific salmonid remains that integrates two PCR assays that each co-amplify fragments of the sexually dimorphic on the Y chromosome (sdY) gene and an internal positive control (Clock1a or D-loop). The first assay coamplifies a 95 bp fragment of sdY and a 108 bp fragment of the autosomal Clock1a gene, whereas the second assay co-amplifies the same sdY fragment and a 249 bp fragment of the mitochondrial D-loop region. This method\u27s reliability, sensitivity, and efficiency, were evaluated by applying it to 72 modern Pacific salmonids from five species and 75 archaeological remains from six Pacific salmonids. The sex identities assigned to each of the modern samples were concordant with their known phenotypic sex, highlighting the method\u27s reliability. Applications of the method to dilutions of modern DNA samples indicate it can correctly identify the sex of samples with as little as ~39 pg of total genomic DNA. The successful sex identification of 70 of the 75 (93%) archaeological samples further demonstrates the method\u27s sensitivity. The method\u27s reliance on two co-amplifications that preferentially amplify sdY helps validate the sex identities assigned to samples and reduce erroneous identifications caused by allelic dropout and contamination. Furthermore, by sequencing the D-loop fragment used as a positive control, species-level and sex identifications can be simultaneously assigned to samples. Overall, our results indicate the DNA-based method reported in this study is a sensitive and reliable sex identification method for ancient salmonid remains

High Potential for Using DNA from Ancient Herring Bones to Inform Modern Fisheries Management and Conservation

Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much needed foundation for wider scale studies on temporal genetic variation in herring, with important implications for herring fisheries management, Aboriginal title rights and herring conservation

Stable Isotope and Dental Caries Data Reveal Abrupt Changes in Subsistence Economy in Ancient China in Response to Global Climate Change

Prior to the introduction of wheat and barley from Central Asia during the Neolithic period, northern Chinese agricultural groups subsisted heavily on millet. Despite being the focus of many decades of intensive interest and research, the exact route(s), date(s), and mechanisms of the spread and adoption of wheat and barley into the existing well-established millet-based diet in northern China are still debated. As the majority of the important introduced crops are C3plants, while the indigenous millet is C4, archaeologists can effectively identify the consumption of any introduced crops using stable carbon isotope analysis. Here we examine published stable isotope and dental caries data of human skeletal remains from 77 archaeological sites across northern and northwestern China. These sites date between 9000 to 1750 BP, encompassing the period from the beginning of agriculture to wheat’s emergence as a staple crop in northern China. The aim of this study is to evaluate the implications of the spread and adoption of these crops in ancient China. Detailed analysis of human bone collagen δ13C values reveals an almost concurrent shift from a C4-based to a mixed C3/ C4– based subsistence economy across all regions at around 4500–4000 BP. This coincided with a global climatic event, Holocene Event 3 at 4200 BP, suggesting that the sudden change in subsistence economy across northern and northwestern China was likely related to climate change. Moreover, the substantially increased prevalence of dental caries from pre–to post–4000 BP indicates an increase in the consumption of cariogenic cereals during the later period. The results from this study have significant implications for understanding how the adoption of a staple crop can be indicative of large-scale environmental and socio-political changes in a region

Osteoarthritis, Labour Division, and Occupational Specialization of the Late Shang China - Insights from Yinxu (ca. 1250 - 1046 B.C.)

This research investigates the prevalence of human osteoarthritis at Yinxu, the last capital of the Late Shang dynasty (ca. 1250–1046 B.C.), to gain insights about lifeways of early urban populations in ancient China. A total of 167 skeletal remains from two sites (Xiaomintun and Xin’anzhuang) were analyzed to examine osteoarthritis at eight appendicular joints and through three spinal osseous indicators. High osteoarthritis frequencies were found in the remains with males showing significantly higher osteoarthritis on the upper body (compared to that of the females). This distinctive pattern becomes more obvious for males from Xiaomintun. Furthermore, Xiaomintun people showed significantly higher osteoarthritis in both sexes than those from Xin’anzhuang. Higher upper body osteoarthritis is speculated to be caused by repetitive lifting and carrying heavy-weight objects, disproportionately adding more stress and thus more osseous changes to the upper than the lower body. Such lifting-carrying could be derived from intensified physical activities in general and specialized occupations in particular. Higher osteoarthritis in males may reveal a gendered division of labour, with higher osteoarthritis in Xiaomintun strongly indicating an occupational difference between the two sites. The latter speculation can be supported by the recovery of substantially more bronze-casting artifacts in Xiaomintun. It is also intriguing that relatively higher osteoarthritis was noticed in Xiaomintun females, which seems to suggest that those women might have also participated in bronze-casting activities as a “family business.” Such a family-involved occupation, if it existed, may have contributed to establishment of occupation-oriented neighborhoods as proposed by many Shang archaeologists

Increase Productivity of Machinig Center at Machine-shop by Using Multiple Machine at Small Seriality

Import 23/07/2015Diplomová práce se zaměřuje na problém, kterým je zvýšení produktivity na středisku obrobna s využitím více strojových obsluh při malé sériovosti. Hlavní cíl zvyšování produktivity spočívá v tom, zda je možné zavést dvou strojovou obsluhu na CNC strojích typu SP 30 CNC č. 1, č. 2. V rámci druhotného cíle zvyšování produktivity na středisku obrobna a zájmu firmy byly z projektového hlediska navrhnuty a umístěny nové CNC stroje, sklad přípravků a materiálu, skříňky a kovové bedny k jednotlivým strojům, skříňky na osobní věci a navrhnout jídelní kout.This master thesis focuses on the problem of increasing machine shop productivity by using multimachine operation in small series production. More specifically, the primary thesis aim is to analyze options and feasibility of implementing multimachine operation of two CNC lathes SP 30 CNC to increase productivity. The secondary aim of machine shop productivity increasing in the interest of the company includes design of new CNC machines and their layout, a material and jigs warehouse, cabinets and metal crates for each of workplaces, personal lockers and a dining area.345 - Katedra mechanické technologievelmi dobř

Differentiating Salmonid Migratory Ecotypes Through Stable Isotope Analysis of Collagen: Archaeological and Ecological Applications

The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ13C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare

Cheek Tooth Morphology and Ancient Mitochondrial DNA of Late Pleistocene Horses from the Western Interior of North America: Implications for the Taxonomy of North American Late Pleistocene Equus

Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus) and a non-caballine (E. conversidens) species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis) was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study