Papers by Antonia Rodrigues
PLoS ONE, 2012
Bookmarks Related papers MentionsView impact
Journal of Archaeological Sciences Reports
Long-term use of herring by Alaska Natives is not well-documented over space or through time, yet... more Long-term use of herring by Alaska Natives is not well-documented over space or through time, yet this information can illuminate pre-industrial patterns of herring abundance and distribution. Such information is important to understand the sustained relationships Alaska Native fishers and egg collectors have had with herring. Understanding the genetics of pre-industrial herring may also inform management of the fish and fisheries to insure their survival into the future. In this paper, we attempt a contextualized account of the long-term history of Alaska Native herring fisheries, bringing together archaeological, ethnographic, and ethno-historical data. We tie these together as background for presenting the preliminary results of the NSF-funded project, The Archaeology of Herring: Reconstructing the Past to Redeem the Future (No. 1203868). We have now tested 84 herring bone samples from 17 archaeological sites in Alaska expanding beyond Speller et al. (2012), having tripled the earlier archaeological dataset. The oldest herring bones identified archaeologically in Alaska are dated to more than 10,000 cal BP. Early Holocene and Middle Holocene sites have also yielded herring bones, although most of the record dates to the last 2400 years. Preservation of genetic information is effectively complete for the last 2400 years, but achievable back to the terminal Pleistocene (68% success rate for samples between 10,500 and 2400 cal BP). This gives considerable confidence to the potential to expand the analyses and develop a richer pattern of biological variability. The resulting data show genetic continuity between archaeological and modern herring populations. The main technical challenge for the future is to extract adequate amounts of nuclear DNA from the ancient samples for identifying more informative DNA markers that can be used to more effectively reveal any population diversity and/or population size changes over time when compared to modern herring.
Bookmarks Related papers MentionsView impact
PloS One, 2018
Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments... more 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
Bookmarks Related papers MentionsView impact
Horses were a dominant component of North American Pleistocene land mammal communities and their ... more 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 Bayes-ian 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.
Bookmarks Related papers MentionsView impact
Domestic taurine cattle (Bos taurus) were introduced to China from Central Asia between 3600 and ... more Domestic taurine cattle (Bos taurus) were introduced to China from Central Asia between 3600 and 2000 cal BCE. Most of the earliest domestic cattle remains in China come from sacrificial or ritual contexts, especially in the form of oracle bones used in divination rituals. These oracle bones became closely tied to royal authority and are the source of the earliest written inscriptions in ancient China. In this article, we use ancient DNA to identify uninscribed bovine oracle bones from the Longshan period archaeological sites of Taosi and Zhoujiazhuang (late third millennium BCE). We found that in addition to making oracle bones out of domestic cattle scapulae, people also used aurochs (wild cattle: Bos primigenius) scapulae for oracle bone divination. Wild water buffalo (Bubalus mephistopheles) were also exploited at Zhoujiazhuang, but we did not identify water buffalo oracle bones in our analysis. We propose some morphological criteria that may be useful for distinguishing between these animals, but conclude that it is not always possible to identify bovine scapulae based on morphology alone. Our results indicate that wild and domestic bovines were sometimes present at the same sites and their bones were used in similar ways to make oracle bones. This raises the possibility that these species interbred and that people in ancient China may have experimented with managing indigenous Chinese wild bovines.
Brunson K, Zhao X, He N, Dai X, Rodrigues A and Yang D. New insights into the origins of oracle bone divination: Ancient DNA from Late Neolithic Chinese bovines. Journal of Archaeological Science 74: 35-44. http://dx.doi.org/10.1016/j.jas.2016.08.008
Bookmarks Related papers MentionsView impact
Long-term use of herring by Alaska Natives is not well-documented over space or through time, yet... more Long-term use of herring by Alaska Natives is not well-documented over space or through time, yet this information can illuminate pre-industrial patterns of herring abundance and distribution. Such information is important to understand the sustained relationships Alaska Native fishers and egg collectors have had with herring. Understanding the genetics of pre-industrial herring may also inform management of the fish and fisheries to insure their survival into the future. In this paper, we attempt a contextualized account of the long-term history of Alaska Native herring fisheries, bringing together archaeological, ethnographic, and ethnohistorical data. We tie these together as background for presenting the preliminary results of the NSF-funded project, The Archaeology of Herring: Reconstructing the Past to Redeem the Future (No. 1203868). We have now tested 84 herring bone samples from 17 archaeological sites in Alaska expanding beyond Speller et al. (2012), having tripled the earlier archaeological dataset. The oldest herring bones identified archaeologically in Alaska are dated to more than 10,000 cal BP. Early Holocene and Middle Holocene sites have also yielded herring bones, although most of the record dates to the last 2400 years. Preservation of genetic information is effectively complete for the last 2400 years, but achievable back to the terminal Pleistocene (68% success rate for samples between 10,500 and 2400 cal BP). This gives considerable confidence to the potential to expand the analyses and develop a richer pattern of biological variability. The resulting data show genetic continuity between archaeological and modern herring populations. The main technical challenge for the future is to extract adequate amounts of nuclear DNA from the ancient samples for identifying more informative DNA markers that can be used to more effectively reveal any population diversity and/or population size changes over time when compared to modern herring.
MORE INFO: Moss ML, Rodrigues AT, Speller CF and Yang DY. (2015). The historical ecology of Pacific herring: Tracing Alaska Native use of forage fish. Journal of Archaeological Science: Reports doi: 10.1016/j.jasrep.2015.10.005.
Bookmarks Related papers MentionsView impact
Whales have long been an important part of Pacific Northwest Coast human subsistence and lifeways... more Whales have long been an important part of Pacific Northwest Coast human subsistence and lifeways. Native peoples on the Oregon Coast were not known to hunt whales, but a humpback whale phalange with an embedded bone harpoon at the Par-Tee site (35CLT20) and ethnographic accounts raised the possibility of opportunistic whale hunting. We analyzed a suite of whale remains from Par-Tee and performed ancient DNA-based species identifications on 30 specimens. The assemblage includes gray whales (Eschrichtius robustus, 60.7% of the assemblage), humpbacks (Megaptera novaeangliae, 32.1%), minkes (Balaenoptera acutorostrata, 3.6%), and orcas (Orcinus orca, 3.6%). While the species composition is similar to those found in archaeological deposits from systematic whaling areas in Washington and Vancouver Island, bone modification patterns and element representation reveal important differences. Our analysis demonstrates that whales were likely a supplementary part of human subsistence at Par-Tee and, while opportunistic whale hunting likely occurred, it may have been secondary to scavenging and utilization of beached and/or drift whales.
MORE INFO: Wellman HP, Rick TC, Rodrigues AT and Yang DY. (2016). Evaluating ancient whale exploitation on the Northern Oregon Coast through ancient DNA and zooarchaeological analysis. The Journal of Island and Coastal Archaeology doi: 10.1080/15564894. 2016.1172382.
Bookmarks Related papers MentionsView impact
Salmon represented a critical resource for prehistoric foragers
along the North Pacific Rim, and ... more Salmon represented a critical resource for prehistoric foragers
along the North Pacific Rim, and continue to be economically and culturally important; however, the origins of salmon exploitation remain unresolved. Here we report 11,500-y-old salmon associated with a cooking hearth and human burials from the Upward Sun River Site, near the modern extreme edge of salmon habitat in central Alaska. This represents the earliest known human use of salmon in North America. Ancient DNA analyses establish the species as Oncorhynchus keta (chum salmon), and stable isotope analyses indicate anadromy, suggesting that salmon runs were established by at least the terminal Pleistocene. The early use of this resource has important implications for Paleoindian land use, economy, and expansions into northwest North America.
Bookmarks Related papers MentionsView impact
Canadian Journal of Zoology
North American elk (Cervus elaphus L., 1758) are an important component of Canada’s natural ecosy... more North American elk (Cervus elaphus L., 1758) are an important component of Canada’s natural ecosystems. Overhunting and habitat decline in the 19th century led to the near eradication of Rocky Mountain elk (Cervus elaphus nelsoni Bailey, 1935) and Manitoban elk (Cervus elaphus manitobensis Millais, 1915) within Alberta. Though elk populations have been restored within provincial and national parks, it is unknown to what degree historic population declines affected overall genetic diversity and population structuring of the two subspecies. This study targeted 551 bp of mitochondrial D-loop DNA from 50 elk remains recovered from 16 archaeological sites (2260 BCE (before common era) to 1920 CE (common era)) to examine the former genetic diversity and population structure of Alberta’s historic elk populations. Comparisons of ancient and modern haplotype and nucleotide diversity suggest that historic population declines reduced the mitochondrial diversity of Manitoban elk, while translocation of animals from Yellowstone National Park in the early 20th century served to maintain the diversity of Rocky Mountain populations. Gene flow between the two subspecies was significantly higher in the past than today, suggesting that the two subspecies previously formed a continuous population. These data on precontact genetic diversity and gene flow in Alberta elk provide essential baseline data integral for elk management and conservation in the province.
Bookmarks Related papers MentionsView impact
American Journal of Physical Anthropology
Hypoplastic pits on human deciduous canine teeth are attributed to nutritionally induced thinning... more Hypoplastic pits on human deciduous canine teeth are attributed to nutritionally induced thinning of the crypt wall prior to eruption, exposing ameloblasts to unspecified physical trauma through the fenestration. Traditionally known as localized hypoplasia of the primary canine (LHPC), this little-understood condition is reported in fields ranging from public health to bioarchaeology. We propose the defect be termed a ‘crypt fenestration hypoplastic enamel defect’ (CFED) to reflect that an analogous lesion is created postnatally on maxillary molars of pigs. Pigs are accepted as a suitable proxy for many studies in human biology. We compare fenestration defects and CFEDs between 50 Sick Pen pigs, who died naturally, and 20 Controls. Observations were made of the presence, number and size of fenestrations in molar crypts. CFEDs were counted on erupted deciduous last molars and permanent first molars. Signs of being underweight and cranio-dental infection at death were recorded. Sick pen pigs show significantly more fenestrations at death and CFEDs acquired before death. These conditions co-occur with infection and poor growth. The deep fibers of temporalis muscle lie adjacent to the crypt wall of maxillary molars. We propose that contraction of this muscle during suckling and chewing creates large compressive forces against fenestrated bony surfaces sufficient to have physiological consequences for physically unprotected ameloblasts. While we conclude that a pig model is appropriate to study fenestration-induced enamel defects, this naturalistic experiment leaves unresolved whether osteopenia in pigs, and by extension in human infants, is due to disease and/or malnutrition.
Bookmarks Related papers MentionsView impact
Quaternary Sciences
This research aims to use an ancient DNA approach to genetically characterize ancient horse remai... more This research aims to use an ancient DNA approach to genetically characterize ancient horse remains(400~120 BC)from Shirenzigou site in Barkol County,Xinjiang,China. Excavated in 2006~2007,Shirenzigou site(43° 31'12.8''~43° 34'28.9''N,93° 13' 44.8''~93° 16'49.1''E) is 5km long from north to south and 3.5km long from east to west,with an area of 8.75km2. DNA was successfully extracted from five ancient horse samples in dedicated ancient DNA labs following vigorous protocols for maximal contamination prevention. Both mitochondrial DNA(mtDNA)and single nucleotide polymorphic(SNP)markers for coat colors were targeted for PCR amplification. The results show a high success rate(100%)of DNA recovery due to the superior DNA preservation conditions in the region. The mtDNA reveals three haplotypes belonging to three haplogroups(A,B and E)while the amplified SNP markers indicate three different coat colors(chestnut,bay and palomino). While the sample size is relatively small,it is clear that the analyzed remains have a high genetic diversity as demonstrated by both the mtDNA and SNP results. The relatively recent antiquity of the horse remains and the nature of the archaeological contexts strongly indicate that these skeletal remains represent domesticated horses instead of wild horses. Although this study cannot provide any direct evidence as to how these remains are linked to older horse remains in Central China,it is clear that the remains analyzed did not originate from Central China. These results are consistent with the hypothesis that Chinese domesticated horses were imported via Xinjiang of Northwest China. The high genetic diversity of the analyzed horse remains in this study can be adequately explained by the fact that this geographic region represents an easy exchange area for horses traded in from other regions. One extremely rare coat color of palomino(light golden color)was detected in this study,marking the first time it has been reported in ancient horses. It is worth noting that the horse skeleton with the palomino coat was buried together with a human skeleton,while two other chestnut colored horse skeletons(a common coat color)were buried in sacrificial pits(animals only). While more studies are needed to fully understand this burial practice,it is clear that horses must have played extremely important roles in human life then. This study demonstrates the unique contribution that ancient DNA analysis can make,when combined with archaeology,to our understanding of human-animal interactions in the past. Ancient DNA in this study reveals not only a high genetic diversity of ancient horse populations but also a rare coat color that is found to be associated with special cultural implications in the region.
Bookmarks Related papers MentionsView impact
Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystem... more 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.
Bookmarks Related papers MentionsView impact
Posters by Antonia Rodrigues
Bookmarks Related papers MentionsView impact
Poster presented at the 67th Northwest Anthropological Conference, Western Washington University, Bellingham, WA, Mar 2014
Bookmarks Related papers MentionsView impact
Uploads
Papers by Antonia Rodrigues
Brunson K, Zhao X, He N, Dai X, Rodrigues A and Yang D. New insights into the origins of oracle bone divination: Ancient DNA from Late Neolithic Chinese bovines. Journal of Archaeological Science 74: 35-44. http://dx.doi.org/10.1016/j.jas.2016.08.008
MORE INFO: Moss ML, Rodrigues AT, Speller CF and Yang DY. (2015). The historical ecology of Pacific herring: Tracing Alaska Native use of forage fish. Journal of Archaeological Science: Reports doi: 10.1016/j.jasrep.2015.10.005.
MORE INFO: Wellman HP, Rick TC, Rodrigues AT and Yang DY. (2016). Evaluating ancient whale exploitation on the Northern Oregon Coast through ancient DNA and zooarchaeological analysis. The Journal of Island and Coastal Archaeology doi: 10.1080/15564894. 2016.1172382.
along the North Pacific Rim, and continue to be economically and culturally important; however, the origins of salmon exploitation remain unresolved. Here we report 11,500-y-old salmon associated with a cooking hearth and human burials from the Upward Sun River Site, near the modern extreme edge of salmon habitat in central Alaska. This represents the earliest known human use of salmon in North America. Ancient DNA analyses establish the species as Oncorhynchus keta (chum salmon), and stable isotope analyses indicate anadromy, suggesting that salmon runs were established by at least the terminal Pleistocene. The early use of this resource has important implications for Paleoindian land use, economy, and expansions into northwest North America.
Posters by Antonia Rodrigues
Brunson K, Zhao X, He N, Dai X, Rodrigues A and Yang D. New insights into the origins of oracle bone divination: Ancient DNA from Late Neolithic Chinese bovines. Journal of Archaeological Science 74: 35-44. http://dx.doi.org/10.1016/j.jas.2016.08.008
MORE INFO: Moss ML, Rodrigues AT, Speller CF and Yang DY. (2015). The historical ecology of Pacific herring: Tracing Alaska Native use of forage fish. Journal of Archaeological Science: Reports doi: 10.1016/j.jasrep.2015.10.005.
MORE INFO: Wellman HP, Rick TC, Rodrigues AT and Yang DY. (2016). Evaluating ancient whale exploitation on the Northern Oregon Coast through ancient DNA and zooarchaeological analysis. The Journal of Island and Coastal Archaeology doi: 10.1080/15564894. 2016.1172382.
along the North Pacific Rim, and continue to be economically and culturally important; however, the origins of salmon exploitation remain unresolved. Here we report 11,500-y-old salmon associated with a cooking hearth and human burials from the Upward Sun River Site, near the modern extreme edge of salmon habitat in central Alaska. This represents the earliest known human use of salmon in North America. Ancient DNA analyses establish the species as Oncorhynchus keta (chum salmon), and stable isotope analyses indicate anadromy, suggesting that salmon runs were established by at least the terminal Pleistocene. The early use of this resource has important implications for Paleoindian land use, economy, and expansions into northwest North America.