Online Journal of Anthropology

Antrocom

 

The Spanish conquest of the Americas was devastating for native peoples. Many native men died in conflicts with the invaders. Male Spanish colonists often came without their wives and took native women as partners. A new genetic analysis of Panamanian men by a team including a Smithsonian scientist shows this historical legacy: only 22 percent had Y-chromosomes of native origin, even though most Panamanians are of female indigenous ancestry.

 

Everyone has a pair of sex chromosomes that determine their gender. Females have two X-chromosomes, while males have one X and one Y, the latter inherited from their father. These chromosomes are found in each cell’s nucleus. Another genetic component called mitochondrial DNA (mtDNA) is found in cells outside the nucleus. Both males and females inherit their mtDNA from their mother alone. Over time, small mutations accumulate in both mtDNA and Y-chromosomes, allowing scientists to trace their history.

 

A team of geneticists from the University of Pavia including Antonio Torroni found that among the 408 Panamanian men whose genetics were analyzed, 60 percent had Y-chromosomes that originated in West Eurasia and North Africa (probably mostly from Europe). About 22 percent were of Native American origin, 6 percent from sub-Saharan Africa and 2 percent from South Asia (probably China or the Indian sub-continent). In contrast, a large majority of this group—including nearly all those with Native American, African and Asian Y-chromosomes—had mtDNA of indigenous origin. Among men with Eurasian Y-chromosomes, 13 percent had mtDNA from sub-Saharan Africa and only a very few had European mtDNA.

 

Although overall a majority of Panamanian men had Eurasian Y-chromosomes, the percentage differed regionally within Panama in accord with the pattern of Spanish colonization. After A.D. 1519, the Spanish settled most densely on the Pacific side of Panama, where a drier climate made agriculture and cattle raising more feasible. Those indigenous groups that survived the conquest took refuge mostly in the remote mountains and dense tropical forests of the Caribbean side.

 

In most provinces on Panama’s Pacific side, the prevalence of Eurasian Y-chromosomes varied from 62 to 72 percent. This was entirely different in Caribbean regions, where the proportion of native Y-chromosomes ranged from 66 to almost 88 percent. The highest level of sub-Saharan Y-chromosomes, 44 percent, was found in Darien Province on the Pacific side, where many escaped slaves found refuge during the colonial period.

 

Variation within native Y-chromosomes also illuminated the history of these groups within Panama. One type, found in western Panama, probably originated more than 10,000 years ago, indicating some indigenous populations have been living in this region continuously for a very long time. Another much more recently differentiated type was found in eastern Panama and may represent peoples who moved into the area from adjacent areas of what is now Colombian territory after the original population, known to the invading Spanish as the “people of the language of Cueva,” had virtually disappeared.

 

The Smithsonian Tropical Research Institute, headquartered in Panama City, Panama, is a part of the Smithsonian Institution. The Institute furthers the understanding of tropical nature and its importance to human welfare, trains students to conduct research in the tropics and promotes conservation by increasing public awareness of the beauty and importance of tropical ecosystems. Website: www.stri.si.edu. Promo video: https://www.youtube.com/watch?v=M9JDSIwBegk.

 

Grugni, V., V. Battaglia, U. A. Perego, A. Raveane, H. Lancioni, A. Olivieri, L. Ferretti, S. R. Woodward, J. M. Pascale, R. Cooke, N. Myres, J. Motta, A. Torroni, A. Achilli, and O. Semino. 2015. Exploring the Y Chromosomal Ancestry of Modern Panamanians. PLoS ONE doi:10(12):E0144223

 

(Text & Images’ Source: Smithsonian Tropical Research Institute)

 

 

 

 

 

 

Using several genetic analytical methods, an international research team has identified an interbreeding event between Neanderthals and modern humans that occurred about 100,000 years ago – tens of thousands of years earlier than previous scientific estimates. Dr. FU Qiaomei, a researcher at the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences, is part of the team that made this ground-breaking discovery, which was published February 17 in the journal Nature.

 

The authors have pieced together the first genetic evidence supporting the scenario that some modern humans may have left Africa in an early migration and admixed with archaic hominids in Eurasia before the ancestors of present-day non-Africans migrated out of Africa less than 65,000 years ago. The breakthrough involves a specific “Altai Neanderthal” (Figure 1), whose remains were found in a cave in the Altai Mountains in southern Siberia.

 

The individual shows signs of gene flow from modern humans. In comparison, the two Neanderthals from European caves who were also sequenced for this study, as well as a Denisovan, all appeared to lack specific DNA derived from modern humans.

 

Some of their findings reveal that alleles in the windows of the Altai Neanderthal genome with low divergence from Africans have higher divergence from the Denisovan than Denisovan windows with low divergence from Africans. The latter windows in the Altai Neanderthal genome have higher heterozygosity than in the Denisovan genome.

 

Research also found that a demographic model that estimates gene flow from these early modern humans into the ancestors of the Altai Neanderthal to be about 1.0–7.1%. Although the exact source is unclear, the authors suspect that it may have come from a deep population that either split off from the ancestors of present-day Africans or from one of the early African lineages. The study finds that complex computer simulations also support the data.

 

The team was able to further calculate that early modern human introgression into the Altai Neanderthal lineage occurred 100,000–230,000 years ago, based on the amount of shared haplotypes (50 kilobases or longer in length) between modern humans and the Altai Neanderthal. This introgression is much earlier than previously reported gene flow from Neanderthals into modern humans outside Africa (47,000–65,000 years ago).

 

Possibly, there was an extended lag between when this group branched off from the modern human family tree, roughly 200,000 years ago, and when its members left their genetic mark in the Altai Neanderthal, about 100,000 years ago, before the group became extinct.

 

This research was partly supported by the Special Foundation of the President of the Chinese Academy of Sciences.

 

 

Dorsal view of the Denisova Neandertal toe bone. (Image by Bence Viola)

 

(Text & Images’ Source: article by Chen Na, Chinese Academy of Sciences)

 

 

 

 

 

 

Long ago, in a field far away…

 

Impressions of cockroach egg cases from 4,300 year old Japanese potsherds (broken pottery fragments) have been found in southern Japan. X-ray, computed tomography (CT) and scanning electron microscopy were used to image the impressions and reveal aspects about ancient Japanese life in this latest archeological survey from Kumamoto University.

 

These are impressions you are looking for.

 

To archeologists, ancient earthenware is almost always packed full of treasure. This may seem logical since the pots may have held water, food or other historically valuable items. This time, however, the “treasure” was found not in the pot, but inside the pottery itself.

 

“Countless vacant holes on the surface of potsherds had been all but ignored until about 25 years ago,” said Professor Hiroki Obata, researcher of archeology from Kumamoto University, Japan. “Since then, however, the meaning and importance of these holes has become well understood. They can be the impression of seeds, nuts, insects or shells.”

 

From the cavities left by soybeans or adzuki beans which were mixed in the pottery during creation, it is possible to more correctly estimate the beginning of cultivation in the district. Impressions are an important key to understanding the lifestyle of those who lived in a particular area during a particular period. Furthermore, with a quantitative survey of the impressions, it is possible to extrapolate the range of the propagation and cultivation of the plants.

 

Professor Obata’s group examined impressions on the surface and from the inside of the potsherds from the Odake shell mound site in Toyama Prefecture, which contains artifacts from the early Jomon Period of Japan (5,300 – 3,500 BC). Using X-ray, CT and scanning electron microscopy they found more than 500 impressions, even though only 66 could be visually confirmed, of Egoma Perilla frutescens var. frutescens) seed related imprints on the surface. The impressions within the potsherds were unique to the period making them easily distinguishable from potsherds that had been created at another time.

 
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Stalagmites reveal huge shift in ancient Madagascar’s plant life, unrelated to climate change.

 

There’s no question that our species has had a dramatic impact on the planet’s physical environment, particularly over the last few centuries, with the rise of modern industry, transportation, and infrastructure. But as new research shows, humans have been transforming the landscape, with lasting impacts, since long before the start of the Industrial Era.

 

Scientists from MIT and the University of Massachusetts at Amherst have found that a widespread and permanent loss of forests in Madagascar that occurred 1,000 years ago was due not to climate change or any natural disaster, but to human settlers who set fire to the forests to make way for grazing cattle.

 

The researchers came to this conclusion after determining the composition of two stalagmites from a cave in northwestern Madagascar. Stalagmites form from water that percolates from the surface, through the soil, and into a cave. These finely layered pillars can be preserved for thousands of years, and their composition serves as a historical record of the environment above ground.

 

From their analysis, the team found that around 1,000 years ago, both stalagmites’ calcium carbonate composition shifted suddenly and completely, from carbon isotope ratios typical of trees and shrubs, to those more consistent with grassland, within just 100 years.

 

Was this landscape transformation triggered by climate change? The team’s results suggest otherwise. Around the same period, they found that oxygen isotope levels remained unchanged in both stalagmites, indicating that rainfall rates — and climate in general — remained relatively stable.

 

“We went in expecting to just tell a climate change story, and were surprised to see a huge carbon isotope change in both stalagmites,” says David McGee, the Kerr-McGee Career Development Assistant Professor in the Department of Earth, Atmospheric and Planetary Sciences at MIT. “Both the speed at which this shift occurred and the fact that there’s no real climate signal suggest human involvement.”

 

The team’s results are published this week in the journal Quaternary Science Reviews.
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Prehistoric Village Links Old and New Stone Age

 

Newly-excavated village in the Jordan Valley sheds light on the historical shift from foraging to agriculture, say Hebrew University of Jerusalem archaeologists

 

Archaeologists from The Hebrew University of Jerusalem revealed in Israel a prehistoric village, dated around 12,000 years ago, in excavations in the fertile Jordan Valley.

 

The site, named NEG II, is located in Nahal (wadi) Ein-Gev, at the middle of the perennial stream that flows west to the Sea of Galilee.

 

A series of excavations on site revealed an abundance of findings, including human burial remains, flint tools, art manifestations, faunal assemblage, ground stone and bone tools. The excavated area revealed an extensive habitation with deep cultural deposits (2.5 to 3 meters deep) and the site is estimated as covering roughly 1200 m2

 

Surprisingly, the village differs markedly from others of its period in Israel. The findings encapsulate cultural characteristics typical of both the Old Stone Age — known as the Paleolithic period, and the New Stone Age — known as the Neolithic period.

 

“Although attributes of the lithic tool kit found at NEG II places the site chronologically in the Paleolithic period, other characteristics – such as its artistic tradition, size, thickness of archaeological deposits and investment in architecture – are more typical of early agricultural communities in the Neolithic period,” said Dr. Leore Grosman, from the Institute of Archaeology at The Hebrew University of Jerusalem, who led the excavations.

 
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Virtual museum brings thousands of digital specimens to your desktop, in 3-D

 

Newest member of the human family tree, now in 3-D

 

3-D scan of the fossilized skull of Homo naledi, an ancient human whose remains were discovered in a South African cave. The creature is one of more than 500 extinct species whose fossil scans are available for anyone to download at http://MorphoSource.org. Reconstruction by Peter Schmid and Ashley Kruger, University of the Witwatersrand.

 

Duke assistant professor Doug Boyer’s office is more than 8,000 miles away from the vault at the University of Witwatersrand in Johannesburg, South Africa, where the fossil remains of a newly discovered human ancestor, Homo naledi, rest under lock and key.

 

But with a few clicks of his computer’s mouse, he can have models of any one of hundreds of naledi bone fragments delivered to his desk in a matter of minutes.

 

Paleontologists like Boyer frequently travel halfway around the world to examine such unique and fragile specimens. That is, assuming their curators will even allow such access.

 

But the Homo naledi specimens are a different story. They, and hundreds of other species, are now available in a free online database of digital scans that anyone can download and print in 3-D.

 

MorphoSource, which Boyer launched at Duke in 2013, is the largest and most open digital fossil repository of its kind.

 

“We’re essentially taking bones out of museum catacombs and putting them online,” Boyer said.

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A new study of humans on Sanak Island, Alaska and their historical relationships with local species suggests that despite being super-generalist predators, the food gathering behaviors of the local Aleut people were stabilizing for the ecosystem.

 

The findings, presented in a paper published today in Nature Scientific Reports, provide novel insights into how human roles and behavior impact complex ecological networks and offer new quantitative tools for studying sustainability.

 

With a team of ecologists and archeologists, SFI’s Vice President for Science Jennifer Dunne wanted to understand the niche humans filled in Sanak’s marine ecosystems by compiling and analyzing local food web data. “It’s the first highly detailed ecological network data to include humans, which allows us to ask questions about how they compare in their roles to other predators,” says Dunne. “Unlike most ecological studies that ignore humans or consider them as external actors, our analysis includes them as an integral part of the ecosystem.”

 

For roughly 7,000 years, the Sanak Aleuts hunted marine mammals and fishes in the nearby open water and gathered shellfish and algae closer to shore. Dunne and her colleagues put together a precise picture of the local marine food webs by studying the bones and shells left behind in middens, or trash heaps, through oral histories gathered from Aleut elders, and with ecological data.

 

Through analysis of the network structure of the food webs, they discovered that in both the intertidal and nearshore food webs, humans fed on approximately a quarter of the species present, far more than other predators in the systems. This varied diet, ranging from primary producers like algae to top carnivores like sea lions, puts humans in a niche similar to other super-generalist predators like Pacific cod.

 

And like other generalists, the Aleuts prey-switched. As a favored prey species became difficult to find due to population decreases or unfavorable environmental conditions, the Aleuts chose alternative food sources. In food webs where predators prey-switch, dwindling prey populations can bounce back and extinctions are rare. “It’s a very stabilizing behavior for the system,” says Dunne.

 

In addition, while simple technologies like fish hooks, spears, and kayaks helped the Aleut hunt some of their prey more strongly than expected for non-human predators, Dunne’s analysis of the dynamics of model food webs suggests that as long as such strong hunting was limited to a few prey species, it would cause few extinctions.

 

Modern fisheries can put a very different pressure on food webs, she notes. Advanced technology allows for highly intensive fishing, and in many cases as a resource becomes scarce, its value goes up. In these cases, such as with Bluefin tuna that are highly prized for sushi, “increased rarity increases economic value, leading to increased harvesting pressure at just the wrong time,” says Dunne. “You’re not only driving those populations to extinction, you’re also introducing a destabilizing dynamic into the system.”

 

Read the paper in Nature Scientific Reports (February 17, 2016)

 

(Text & Images’ Source: Santa Fe Institute)

 

 

 

 

 

 

First genetic evidence of modern human DNA in a Neanderthal individual

 

Cold Spring Harbor, NY – Using several different methods of DNA analysis, an international research team has found what they consider to be strong evidence of an interbreeding event between Neanderthals and modern humans that occurred tens of thousands of years earlier than any other such event previously documented.

 

Today in Nature the team publishes evidence of interbreeding that occurred an estimated 100,000 years ago. More specifically the scientists provide the first genetic evidence of a scenario in which early modern humans left the African continent and mixed with archaic (now-extinct) members of the human family prior to the migration “out of Africa” of the ancestors of present-day non-Africans, less than 65,000 years ago.

 

siepel feb2016

 

Scenario of interbreeding between modern humans and Neanderthals: Neanderthal DNA in present-day humans outside Africa originates from interbreeding that occurred 47,000 – 65,000 years ago (green arrow). Modern human DNA in Neanderthals is likely a consequence of earlier contact between the two groups roughly 100,000 years ago (red arrow). © Ilan Gronau

 

“It’s been known for several years, following the first sequencing of the Neanderthal genome in 2010, that Neanderthals and humans must have interbred,” says Professor Adam Siepel, a co-team leader and Cold Spring Harbor Laboratory (CSHL) quantitative biologist.  “But the data so far refers to an event dating to around 47,000-65,000 years ago, around the time that human populations emigrated from Africa. The event we found appears considerably older than that event.”

 

In addition to Siepel, who is Chair of CSHL’s Simons Center for Quantitative Biology, the team included several members of the Max Plank Institute for Evolutionary Anthropology, including Martin Kuhlwilm, Svante Pääbo, Matthias Meyer and co-team leader Sergi Castellano. Kuhlwilm was co-first author of the new paper with Ilan Gronau, a former member of Siepel’s Lab who is now at the Herzliya Interdisciplinary Center, Israel. Melissa Hubisz, a Ph.D. student with Siepel at Cornell University, also made major contributions to the work.  The full international research team included 15 additional co-authors.

 

 

“One very interesting thing about our finding is that it shows a signal of breeding in the ‘opposite’ direction from that already known,” Siepel notes. “That is, we show human DNA in a Neanderthal genome, rather than Neanderthal DNA in human genomes.”

 

This finding, the result of several kinds of advanced computer modeling algorithms comparing complete genomes of hundreds of contemporary humans with complete and partial genomes of four archaic humans, has implications for our knowledge of human migration patterns.

 
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BINGHAMTON, NY – Analysis of artifacts found on the shores of Rapa Nui, Chile (Easter Island) originally thought to be used as spear points reveal that these objects were likely general purpose tools instead, providing evidence contrary to the widely held belief that the ancient civilization was destroyed by warfare.

 

According to Carl Lipo, professor of anthropology at Binghamton University and lead on the study, the traditional story for Rapa Nui holds that the people, before Europeans arrived, ran out of resources and, as a result, engaged in massive in-fighting, which led to their collapse. One of the pieces of evidence used to support this theory is the thousands of obsidian, triangular objects found on the surface, known as mata’a. Because of their large numbers and because they’re made of sharp glass, many believe the mata’a to be the weapons of war that the ancient inhabitants of the island used for interpersonal violence

 

Lipo and his team analyzed the shape variability of a photo set of 400-plus mata’a collected from the island using a technique known as morphometrics, which allowed them to characterize the shapes in a quantitative manner. Based on the wide variability in shape of the mata’a and their difference from other traditional weapons, the team determined that the mata’a were not used in warfare after all, as they would have made poor weapons.

 

“We found that when you look at the shape of these things, they just don’t look like weapons at all,” said Lipo. “When you can compare them to European weapons or weapons found anywhere around the world when there are actually objects used for warfare, they’re very systematic in their shape. They have to do their job really well. Not doing well is risking death.”

 

“You can always use something as a spear. Anything that you have can be a weapon. But under the conditions of warfare, weapons are going to have performance characteristics. And they’re going to be very carefully fashioned for that purpose because it matters…You would cut somebody {with a mata’a], but they certainly wouldn’t be lethal in any way.”

 

According to Lipo, this evidence strongly supports the idea that the ancient civilization never experienced this oft-theorized combat and warfare, and that the belief that the mata’a were weapons used in the collapse of the civilization is really a late European interpretation of the record, not an actual archeological event.

 
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University of Oklahoma anthropologists are studying the ancient and modern human microbiome and the role it plays in human health and disease. By applying genomic and proteomic sequencing technologies to ancient human microbiomes, such as coprolites and dental calculus, as well as to contemporary microbiomes in traditional and industrialized societies, OU researchers are advancing the understanding of the evolutionary history of our microbial self and its impact on human health today.

 

Christina Warinner, professor in the Department of Anthropology, OU College of Arts and Sciences, will present, “The Evolution and Ecology of Our Microbial Self,” during the American Association for the Advancement of Science panel on Evolutionary Biology Impacts on Medicine and Public Health, at 1:30 pm, Sunday, Feb. 14, in the Marriott Marshall Ballroom West, Washington, DC. Warinner will discuss how major events, such as the invention of agriculture and the advent of industrialization, have affected the human microbiome.

 

“We don’t have a complete picture of the microbiome,” Warinner said. “OU research indicates human behavior over the past 2000 years has impacted the gut microbiome. Microbial communities have become disturbed, but before we can improve our health, we have to understand our ancestral microbiome. We cannot make targeted or informed interventions until we know that. Ancient samples allow us to directly measure changes in the human microbiome at specific times and places in the past.”

 

Warinner and colleague, Cecil M. Lewis, Jr., co-direct OU’s Laboratories of Molecular Anthropology and Microbiome Research and the research focused on reconstructing the ancestral human oral and gut microbiome, addressing questions concerning how the relationship between humans and microbes has changed through time and how our microbiomes influence health and disease in diverse populations, both today and in the past. Warinner and Lewis are leaders in the field of paleogenomics, and the OU laboratories house the largest ancient DNA laboratory in the United States.

 
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