Nicotine extracted from ancient dental plaque for the first time

A team of scientists including researchers from Washington State University has shown for the first time that nicotine residue can be extracted from plaque, also known as "dental calculus," on the teeth of ancient tobacco users.

This is a 1945 picture of a Yokuts Native American woman smoking a pipe
[Credit: Clifford Relander]

Their research provides a new method for determining who was consuming tobacco in the ancient world and could help trace the use of tobacco and other intoxicating plants further back into prehistory.

"The ability to identify nicotine and other plant-based drugs in ancient dental plaque could help us answer longstanding questions about the consumption of intoxicants by ancient humans," said Shannon Tushingham, a WSU assistant professor of anthropology and co-author of a new study on the research in Journal of Archaeological Science Reports. "For example, it could help us determine whether all members of society used tobacco, or only adults, or only males or females."

A new source of information

Tracing the ancient spread of tobacco in the Americas has traditionally relied on the presence of pipes, charred tobacco seeds and the analysis of hair and fecal matter. However, these items are rare in the archeological record and are hard to link to particular individuals. As a result, tobacco use has been difficult to document archeologically.

On the other hand, dental plaque adheres to the surfaces of teeth and mineralizes over time, preserving a wide range of substances that are in the mouth. It is easy to link to particular individuals because it can be removed directly from teeth.

Nevertheless, dental plaque was largely ignored by archaeologists until recently.

However, using modern and highly sensitive instrumentation, scientists have found they can detect and characterize trace amounts of a wide variety of compounds, including proteins, bacterial DNA, starch grains and other plant fibers in dental plaque.

Because nicotine is detectable in the dental plaque of contemporary smokers, Tushingham and her collaborators wanted to find out if it also preserved in plaque taken from people who lived long ago.

She and David Gang, a professor in the WSU Institute of Biological Chemistry, Korey Brownstein, a graduate student in the WSU Molecular Plant Sciences Program, and Jelmer Eerkens, an anthropologist at the University of California, Davis, collaborated with members from the Ohlone tribe in San Francisco Bay to extract plaque from the teeth of eight individuals, buried between 6,000 and 300 years ago, and analyze it for nicotine.

Using ordinary dental picks, Eerkens and his team at UC Davis extracted the dental plaque from the ancient teeth and then sent it to Tushingham and Gang's labs at WSU for analysis. The WSU researchers used liquid chromatography-mass spectrometry to test the samples for nicotine and other plant-based drugs like caffeine and atropine, a muscle-relaxant.

Among the samples they analyzed, two tested positive for nicotine, demonstrating for the first time that the drug can survive in detectable amounts in ancient plaque. One of these individuals, an adult man, was also buried with a pipe. A surprise came from the molar of an older woman, which also tested positive for nicotine.

"While we can't make any broad conclusions with this single case, her age, sex, and use of tobacco is intriguing," Eerkens said. "She was probably past child-bearing age, and likely a grandmother. This supports recent research suggesting that younger adult women in traditional societies avoid plant toxins like nicotine to protect infants from harmful biochemicals, but that older women can consume these intoxicants as needed or desired."

While the researchers did not detect evidence of any other plant-based drugs in this particular study, they believe dental plaque could be used help trace the use and spread of other intoxicants as well.

"We think a wide variety of plant-based, intoxicating chemicals could be detected in ancient dental plaque," Brownstein said. "It really opens up a lot of interesting avenues of discovery."

Author: Will Ferguson | Source: Washington State University [February 27, 2018]

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Archaeologist uncovers hidden history of conquistadors in American South

Chris Rodning, the Paul and Debra Gibbons Professor in the Tulane School of Liberal Arts’ Department of Anthropology, unravels early entanglements between Native Americans and European explorers, revealing how their interactions shaped the history of the American South.

An image taken in June 2017 by a camera mounted on a drone displays the exposed remnants of Fort San Juan.
Excavations of this area of the site will be continued in June 2018 [Credit: Ryan Wallace]

“Native Americans’ responses to Spanish explorers and colonists form an important part of the story behind the history of European colonialism in North America,” said Rodning, who conducts archaeological research at Fort San Juan — the earliest known permanent European settlement in the interior United States, located near Morganton, North Carolina.

Since 2001, Rodning has collaborated with David Moore, an anthropology professor from Warren Wilson College, and Rob Beck, an associate professor of anthropology from the University of Michigan, to excavate the site.

“In 2013, we identified the archaeological footprint of the fort,” said Rodning, noting that the team has since focused on learning how the structure was built and where it was located in relation to a nearby Native American settlement called Joara.

In 1540, the conquistador Hernando de Soto traversed this part of western North Carolina.

“He threatened communities with violence, demanded food and sometimes attacked when they did not comply with his demands. He also pressed Native Americans into service as porters to carry supplies for his men,” said Rodning.

Hannah Hoover, a Tulane senior double majoring in anthropology and classical studies, digs dirt from excavation
squares at the Fort San Juan site and throws it up to sifters to screen the dirt in search of artifacts
[Credit: Christopher Rodning]

One generation after de Soto’s expedition, Spanish explorer Juan Pardo arrived with another group of soldiers and established Fort San Juan in 1566.

“When Pardo marched inland, the town of Joara was a much more powerful town than it had been 26 years previously,” said Rodning — possibly because of Joara’s previous interactions with de Soto.

At first, an alliance formed between Pardo and the people of Joara, but in 1568, warriors from Joara sacked the fort and burned the compound.

“Architectural materials and designs of burned houses at the site demonstrate evidence of the typical Native American style of architectural design and construction, but some wooden fragments also indicate that they were cut and shaped with metal tools. The significance of that is Native Americans didn’t have those types of metal tools,” said Rodning.

Rodning said that it’s likely that Native Americans gained access to these new tools from Spanish soldiers, or that Spanish soldiers participated in the construction and maintenance of houses where the men garrisoned at Fort San Juan lived.

Rodning said his team remains committed to the project in hopes of understanding how early moments and subsequent episodes of Spanish contact changed Native American communities in this region.

University Press of Florida published the group’s findings in a book called Fort San Juan and the Limits of Empire: Colonialism and Household Practice at the Berry Site in 2016.

Source: Tulane University [February 27, 2018]

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Fossil turtle species, 5.5 million years old, sheds light on invasive modern relatives

A University of Pennsylvania paleontologist has described a 5.5 million-year-old fossil species of turtle from eastern Tennessee. It represents a new species of the genus Trachemys, commonly known as sliders, which are frequently kept as pets today.

Trachemys haugrudi represents a new species of fossil turtle that lived in what is now eastern Tennessee
more than 5.5 million years ago [Credit: Mary P. Williams]

Steven Jasinski, author of the new study, is a doctoral student at the University of Pennsylvania and acting curator of paleontology and geology at the State Museum of Pennsylvania. He is completing his Ph.D. at Penn under Peter Dodson, a professor of paleontology in the Department of Earth and Environmental Science in the School of Arts and Sciences and a professor of anatomy in the School of Veterinary Medicine.

The study published in PeerJ Journal, investigated a fossil turtle found around the Miocene-Pliocene boundary in the Gray Fossil Site, an area rich with fossils in eastern Tennessee near East Tennessee State University, where Jasinski completed his master's degree. The site represents an ancient sinkhole surrounded by a forest from which dozens of fossil animal species have been characterized, including new species of red panda, Eurasian badger, kinosternid turtle, and colubrid snake.

Thorough examination of the dozens of turtle fossils from the site revealed important differences between this turtle and other known fossil and living species. Jasinski named the fossil turtle Trachemys haugrudi, after Shawn Haugrud, the lab and field manager and lead preparer at the Gray Fossil Site.

"Shawn has spent an incredible number of hours working on these specimens," Jasinski said. "He cleaned and prepared the fossils and was able to essentially glue this turtle back to life, giving me numerous nearly complete turtle shells to use in this research. Without all that time and effort, I wouldn't have been able to determine nearly as much about this turtle as I did.

"Shawn also didn't do this work alone, as numerous other people including volunteers worked on these fossils and got them prepared so that I could complete my research. They really did all the hard work, and I was then able to determine why it was new and what its implications are" he said.

Turtles are best known for their shells, and indeed it is this feature of their anatomy that is commonly found as fossils. Yet the fossil shells are typically found in broken pieces. Often gaps or holes remain, or only single small pieces are found, and the whole must be inferred from other information, including other fossil and living creatures.

Though initially found in pieces, Gray Fossil Site preparator Shawn Haugrud was able to glue the shell of this species
back together, enabling Penn's Steven Jasinski to complete an analysis of the turle. Jasinski named the species
 in Haugrud's honor [Credit: University of Pennsylvania]

"It is extremely rare to get more complete fossils," Jasinski said, "but Trachemys haugrudi, commonly called Haugrud's slider turtle, provides me with dozens of shells, and several are nearly complete."

Haugrud's slider turtle was a fairly small turtle, not more than approximately 10 inches (25 cm) in total shell length, smaller than the modern-day red-eared slider turtle, Trachemys scripta elegans. Red-eared slider turtles are commonly purchased as pets, though they can grow large, and some owners release them into the wild. As a result, though native to the southeastern United States, red-eared sliders have become one of the most invasive animal species in the world today, found on every continent except Antarctica.

"People tend to see all turtles as similar and release them into whatever pond or river is close by when they no longer want to care for them," Jasinski said. "Once released, however, they often outcompete native species. It is a problem that scientists are still dealing with."

As part of the study, Jasinski sought to determine where Trachemys haugrudi was positioned in the evolution of similar turtles both within the genus and in related genera. He performed a phylogenetic analysis, a method that compares shapes and features of different species to determine how similar or dissimilar and therefore how closely related they may be. He found Haugrud's to be most closely related to a group of fossil Trachemys turtles from Florida and next most closely related to a distinct group of fossil Trachemys from the midwestern U.S. Together, these fossil Trachemys form a closely related group situated within other still-living species of Trachemys.

Today, distinct, closely-related groups of Trachemys species dwell in Mexico, Central and South America, and the Caribbean. Jasinski's investigation, along with other information from previous studies, indicates that one group evolved in Mexico and Central and South America and evolved into different species within this geographic area, and another group evolved separately in the Caribbean.

Species from the U.S., including the red-eared slider turtle, are found near the base of their "branch" of the Trachemys family tree; their fossil ancestors are still waiting to be discovered. The fossil Trachemys species in Jasinski's analysis are on a distinct part of the Trachemys tree, and current understanding suggests that they did not give rise to the modern species living today.

Trachemys haugrudi is the latest in a rich array of fossils, including species of red panda, badger, and snake, that have
been identified from the Gray Fossil Site, located in eastern Tennesse [Credit: University of Pennsylvania]

The findings imply that there was once much greater diversity in Trachemys turtles than exists today. It seems that many of the ancient slider species died out without leaving any direct descendents, perhaps because they lacked the ability to adapt to different environments.

"While Trachemys turtle species are considered plastic, implying they can adapt to and live in many environments, this adaptive lifestyle may be a relatively newer characteristic of these turtles," Jasinski said. "More fossils are needed to better understand if this aspect of their evolution is a recent addition."

To get a handle on invasive turtles, understanding more about their ancient relatives could only be helpful, Jasinski said.

"Trachemys haugrudi helps provide more information on Trachemys and begins to offer us insights into the evolution of an animal that has become a problematic invader in many areas of the world," he said. "Understanding how something evolved into its present form may help us understand why an animal is so adaptive and good at invading new areas and outcompeting native species. If we can see that Trachemys today are especially adaptive because evolution has allowed them to become more generalized through time, we can use that information to determine where they may invade, what species they may outcompete and what we can do to counteract those invasions or help native species compete against them."

Jasinski is undertaking further study into the fossil species of not only Trachemys but other turtles within the family Emydidae, which includes Trachemys. He hopes that further data and fossils will help shed light on other turtle species and provide a clearer understanding of the evolution of this group of mainly New World turtles.

Author: Katherine Unger Baillie | Source: University of Pennsylvania [February 26, 2018]

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Extinct lakes of the American desert west

The vestiges of lakes long extinct dot the landscape of the American desert west. These fossilized landforms provide clues of how dynamic climate has been over the past few million years.

Erosional Pleistocene shorelines in Surprise Valley, California, USA [Credit: Anne Egger]

Identification of ancient lake shoreline features began with early explorers of the continent. The first detailed studies were conducted by pioneering American geologists such as G.K. Gilbert and I.C. Russell in the late 1800s, who studied Lake Bonneville, now the remnant Great Salt Lake in Utah, and Lake Lahonton, located in northwestern Nevada.

Through this long history of studying fossil shorelines and lake sediments, we know that these lakes existed during two periods with distinct environmental conditions during the geologically recent past. The first was during ice age maxima, such as the last ice age, 14 to 30 thousand years ago, when global temperatures were 4 to 6 degrees colder and continental ice sheets expanded into the continental United States.

The second time period was about three million years ago during the middle of the Pliocene epoch--a global climate characterized by warmer temperatures and atmospheric CO2 levels roughly equivalent to today's values, which has led many scientists to view the Pliocene as a potential analogue for future climate change.

These observations lead to an important question, says the study's lead author, Daniel Ibarra, "Why are there lake systems under both colder and warmer climates, but not today?" Of particular interest, he says, is the presence of lakes under warmer conditions, which, under a "wet gets wetter, dry gets drier" paradigm, goes against projections of future warming.

Shorelines of Lake Bonneville along the Oquirrh Mountains, Utah, USA. (H.H. Nichols [artist] and G.K. Gilbert,
in Gilbert, 1884) [Credit: H.H. Nichols [artist] and G.K. Gilbert, in Gilbert, 1884. Public domain]

To answer this question, Ibarra and colleagues looked at the competing influences of temperature and precipitation, and how they combine to allow for the existence of lakes under these dual climate states.

The authors compiled evidence for, and created models of, lakes during both colder and warmer than modern periods of the Pliocene-Pleistocene (the last 5 million years). During colder glacial periods, they found that increased precipitation and decreased evaporation combined to form large lakes that occupied the inward draining basins in the western United States, particularly in northern Nevada and Utah.

Increased precipitation also drove the formation of lakes, particularly in southern Nevada and southern California during the warmer middle Pliocene, outpacing higher temperatures and evaporation rates during that time. This increase in precipitation during the middle Pliocene and dominantly southwestern distribution of lake deposits is similar to the pattern of precipitation during modern El Niño years, corroborating previous hypotheses for mean "El Niño-like" conditions during the mid-Pliocene.

The team's interdisciplinary approach explains the conditions driving lake systems in mid-latitude regions today and over the geologic past. Further, notes Ibarra, "This work illustrates the importance of understanding how the El Niño Southern Oscillation drives precipitation patterns in arid regions, which is important for future water resources planning for the western United States."

The study appears in the Geological Society of America Bulletin.

Source: Geological Society of America [February 22, 2018]

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More light shines on Pleistocene extinction event with possible discovery of new genus of horse

Referred to as ‘perplexing’, a group of North American Pleistocene horses have been identified, until now, as different species. Now mitochondrial and partial nuclear genomic studies support the idea that there was only one species, which belongs to a new genus.

This illustration depicts a family of New World stilt-legged horses (Haringtonhippus francisci) in Yukon,
Canada, during the last Ice Age [Credit: Jorge Blanco]

Meet ‘Haringtonhippus’, possibly a new genus of horse covering the extinct New World stilt-legged (NWSL) equids which, until now, have been thought of as multiple species. Prior to this study, these thin-limbed, lightly-built horses were believed to be related to the Asiatic wild ass or onager, or simply a separate species within the genus Equus, which includes all living horses, asses, and zebras. The fossil record shows how the ancestors of these animals evolved from dog-sized, three-toed browsers to larger, one-toed grazers over a period of about 55 million years. Along the way many species became extinct.

The current mitochondrial DNA (mtDNA) -based phylogenetic model suggests that the stilt-legged morphology arose independently in the New and Old Worlds. The thought is that the two may have converged in the face of the need to adapt to arid climates and habitats. But the researchers, supported in part by the EU through the PEGASUS project, point out that this is based on two questionable sources: an unreliable data type and mitochondrial genome sequences that are incomplete or otherwise problematic.

As they explain in their recently published paper ‘A new genus of horse from Pleistocene North America’, they used their phylogenetic framework and comparisons between specimens identified by palaeogenomics and/or morphology, to try to determine the taxonomy of middle-late Pleistocene NWSL equids.

A confused picture

The fossil record of the horse family is robust but more recently, from around 2.5 million years ago, things get a bit confused. This is the Pleistocene and it is not clear how horses of this period relate to each other. The downside of this abundant fossil record, say the researchers, is that many dubious fossil equid taxa have been erected, a problem especially acute within Pleistocene Equus of North America.

They have been classed into two groups, stout-legged and stilt-legged horses, both of which became extinct in North America towards the end of the period. Based on their anatomy, many scientists suggested that stilt-legged horses were most closely related to modern-day asses living in Asia. But other studies using ancient DNA placed the stilt-legged horses closer to the stout-legged horses.

A more nuanced understanding of evolution and extinction during this period

There appears to be a discrepancy between the rates of extirpation between NWSL equids south and north of the continental ice sheets. This implies that their populations responded variably to demographic pressures in different parts of their range, which is consistent with results from some other megafauna, report the researchers. To test this hypothesis, the team analyses 26 full mitochondrial genomes and 17 partial nuclear genomes from late Pleistocene NWSL equids.

‘This revealed that individuals from both eastern Beringia and southern North America form a single well-supported clade that falls outside the diversity of Equus and diverged from the lineage leading to Equus during the latest Miocene or early Pliocene,’ they explain. This, they claim, warrants the recognition of NWSL equids as a distinct genus, which they name ‘Haringtonhippus’.

Their results suggest that populations of stilt-legged Haringtonhippus and stout-legged caballine Equus were sympatric both north and south of the continental ice sheets, through the late Pleistocene and became extinct at roughly the same time. The near synchronous extinction of both horse groups across their entire range in North America suggests that similar causal mechanisms may have led each to their demise.

Rampant convergence, how to see through it?

Tracing morphology can be complex: this case underlines a recurrent problem in systematic biology, which is how best to discriminate authentic relationships within groups, such as Neogene equids, that were prone to what the researches refer to as ‘rampant convergence’. The solution they present in their paper utilised both palaeogenomic and morphometric information to reframe the position of Haringtonhippus, which, they assert, now clearly emerges as the closest known outgroup to all living Equus.

Proteins may persist significantly longer than ancient DNA and collagen proteomics may come to play a key role in characterising affinities. ‘A reciprocally informative approach like the one taken here holds much promise for lessening the amount of systematic noise, due to oversplitting, that hampers our understanding of the evolutionary biology of other major late Pleistocene megafaunal groups such as bison and mammoths,’ they say.

The 5,500 year long history of horse domestication and management, which transformed the natural evolutionary trajectory of wild horses into the more than 625 domestic breeds living today, is difficult to reconstruct from archaeology, history and modern genetics alone. PEGASUS (The makeup of the modern horse: a history of the biological changes introduced by human management) set out to build on the latest advances in the analysis of ancient DNA molecules to gather new genomic, epigenomic and metagenomic information from ancient horses.

Source: CORDIS [February 13, 2018]

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