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Item Open Access Biogeographic Study of Human Gut-Associated CrAssphage Suggests Impacts From Industrialization and Recent Expansion(2020-01-15) Honap, Tanvi P.; Sankaranarayanan, Krithivasan; Schnorr, Stephanie L.; Ozga, Andrew T.; Warinner, Christina; Lewis Jr., Cecil M.CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of an expansion event within crAssphage. Using a Bayesian dating approach, we estimate that this expansion has occurred fairly recently. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle and the absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.Item Open Access The Earliest Farmers of Northwest China Exploited Grain-fed Pheasants not Chickens(2020-02-13) Barton, Loukas; Bingham, Brittany; Sankaranarayanan, Krithivasan; Monroe, Cara; Thomas, Ariane; Kemp, Brian M.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.Item Open Access Ancient DNA Analysis and Stable Isotope Ecology of Sea Turtles (Cheloniidae) from the Gold Rush-era (1850s) Eastern Pacific Ocean(2018-05-30) Kemp, Brian; Pagès Barceló, Laura; Seminoff, Jeffrey; Turner Tomaszewicz, Calandra; Labonte, Marie; Jones, Emily Lena; Stolyka, Michael; Bruner, Kale; Pastron, Allen; Conrad, CylerHistorical and archaeological evidence documents the importation of sea turtles from the eastern Pacific Ocean (Baja California) to California during the Gold Rush (1848–1855) and through the end of 19th century, but it is unknown whether these 19th century sea turtles foraged in similar ways to their modern counterparts. To identify the species of two Gold Rush-era sea turtle specimens recovered from archaeological deposits in San Francisco, California, we first analyze ancient DNA (aDNA). We then analyze carbon (δ13Ccol), nitrogen (δ15N), and hydrogen (δD) stable isotopes of bone collagen and carbon (δ13Cap) and oxygen (δ18Oap) stable isotopes of bone apatite to test if eastern Pacific sea turtle diets have changed over the past 160 years. Ancient DNA confirms that both archaeological specimens are green sea turtles (Chelonia mydas). The stable isotope values from the 19th-century specimens are statistically indistinguishable from the modern comparatives in both δ13Ccoland δ15N, suggesting that green sea turtle dietary intake has remained relatively unchanged since the 1850s. However, the values are unclear for δD and δ18Oapand require additional research.Item Open Access Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha(2018-01-10) Johnson, Bobbi M.; Kemp, Brian M.; Thorgaard, Gary; University of Oklahoma Libraries Open Access FundThe Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed “the four H’s”: habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have divergent demographic histories.Item Open Access Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification(2015-11-13) Warriner, Christina; Lewis, Cecil; Mann, Allison; Sankaranarayanan, Krithivasan; Ozga, AndrewTo date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.