Details of first historically recorded plague pandemic revealed by ancient genomes

An international team of researchers has analyzed human remains from 21 archaeological sites to learn more about the impact and evolution of the plague-causing bacterium Yersinia pestis during the first plague pandemic (541-750 AD). In a study published in Proceedings of the National Academy of Sciences, the researchers reconstructed 8 plague genomes from Britain, Germany, France and Spain and uncovered a previously unknown level of diversity in Y. pestis strains. Additionally, they found the first direct genetic evidence of the Justinianic Plague in the British Isles.

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Lunel-Viel (Languedoc-Southern France). Victim of the plague thrown into a demolition 
trench of a Gallo-Roman house; end of the 6th-early 7th century 
[Credit: CNRS - Claude Raynaud]

The Justinianic Plague began in 541 in the Eastern Roman Empire, ruled at the time by the Emperor Justinian I, and recurrent outbreaks ravaged Europe and the Mediterranean basin for approximately 200 years.

Contemporaneous records describe the extent of the pandemic, estimated to have wiped out up to 25% of the population of the Roman world at the time. Recent genetic studies revealed that the bacterium Yersinia pestis was the cause of the disease, but how it had spread and how the strains that appeared over the course of the pandemic were related to each other was previously unknown.

In the current study, an international team of researchers led by the Max Planck Institute for the Science of Human History analyzed human remains from 21 sites with multiple burials in Austria, Britain, Germany, France and Spain. They were able to reconstruct 8 new Y. pestis genomes, allowing them to compare these strains to previously published ancient and modern genomes.

Additionally, the team found the earliest genetic evidence of plague in Britain, from the Anglo-Saxon site of Edix Hill. By using a combination of archaeological dating and the position of this strain of Y. pestis in its evolutionary tree, the researchers concluded that the genome is likely related to an ambiguously described pestilence in the British Isles in 544 AD.

High diversity of Y. pestis strains during the First Pandemic

The researchers found that there was a previously unknown diversity of strains of Y. pestis circulating in Europe between the 6th and 8th centuries AD. The 8 new genomes came from Britain, France, Germany and Spain.

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Sampling of a tooth from a suspected plague burial 
[Credit: Evelyn Guevara]

"The retrieval of genomes that span a wide geographic and temporal scope gives us the opportunity to assess Y. pestis' microdiversity present in Europe during the First Pandemic," explains co-first author Marcel Keller, PhD student at the Max Planck Institute for the Science of Human History, now working at the University of Tartu.

The newly discovered genomes revealed that there were multiple, closely related strains of Y. pestis circulating during the 200 years of the First Pandemic, some possibly at the same times and in the same regions.

Despite the greatly increased number of genomes now available, the researchers were not able to clarify the onset of the Justinianic Plague.

"The lineage likely emerged in Central Asia several hundred years before the First Pandemic, but we interpret the current data as insufficient to resolve the origin of the Justinianic Plague as a human epidemic, before it was first reported in Egypt in 541 AD. However, the fact that all genomes belong to the same lineage is indicative of a persistence of plague in Europe or the Mediterranean basin over this time period, instead of multiple reintroductions."

Possible evidence of convergent evolution in strains from two independent historical pandemics

Another interesting finding of the study was that plague genomes appearing towards the end of the First Pandemic showed a big deletion in their genetic code that included two virulence factors. Plague genomes from the late stages of the Second Pandemic some 800-1000 years later show a similar deletion covering the same region of the genomes.

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Map and phylogenetic tree showing the newly published (yellow) and previously published (turquoise) genomes. 
Shaded areas and dots represent historically recorded outbreaks of the First Pandemic 
[Credit: Marcel Keller]

"This is a possible example of convergent evolution, meaning that these Y. pestis strains independently evolved similar characteristics. Such changes may reflect an adaptation to a distinct ecological niche in Western Eurasia where the plague was circulating during both pandemics," explains co-first author Maria Spyrou of the Max Planck Institute for the Science of Human History.

The current study offers new insights into the first historically documented plague pandemic, and provides additional clues alongside historical, archaeological, and palaeoepidemiological evidence, helping to answer outstanding questions.

"This study shows the potential of palaeogenomic research for understanding historical and modern pandemics by comparing genomes across millennia," explains senior author Johannes Krause of the Max Planck Institute for the Science of Human History.

"With more extensive sampling of possible plague burials, we hope to contribute to the understanding of Y. pestis' microevolution and its impact on humans during the course of past and present pandemics."

Source: Max Planck Institute for the Science of Human History [June 05, 2019]

Read more at https://archaeologynewsnetwork.blogspot.com/2019/06/details-of-first-historically-recorded.html#iEqEqXwQmQUeHKKc.99

DNA from 31,000-year-old milk teeth leads to discovery of new group of ancient Siberians

Two children's milk teeth buried deep in a remote archaeological site in north eastern Siberia have revealed a previously unknown group of people lived there during the last Ice Age.

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Alla Mashezerskaya maps the artefacts in the area where two 31,000-year-old 
milk teeth were found [Credit: Elena Pavlova]

The finding was part of a wider study which also discovered 10,000 year-old human remains in another site in Siberia are genetically related to Native Americans - the first time such close genetic links have been discovered outside of the US.

The international team of scientists, led by Professor Eske Willerslev who holds positions at St John's College, University of Cambridge, and is director of The Lundbeck Foundation Centre for GeoGenetics at the University of Copenhagen, have named the new people group the 'Ancient North Siberians' and described their existence as 'a significant part of human history'.

The DNA was recovered from the only human remains discovered from the era - two tiny milk teeth - that were found in a large archaeological site found in Russia near the Yana River. The site, known as Yana Rhinoceros Horn Site (RHS), was found in 2001 and features more than 2,500 artefacts of animal bones and ivory along with stone tools and evidence of human habitation.

The discovery is published as part of a wider study in Nature and shows the Ancient North Siberians endured extreme conditions in the region 31,000 years ago and survived by hunting woolly mammoths, woolly rhinoceroses, and bison.

Professor Willerslev said: "These people were a significant part of human history, they diversified almost at the same time as the ancestors of modern day Asians and Europeans and it's likely that at one point they occupied large regions of the northern hemisphere."

Dr Martin Sikora, of The Lundbeck Foundation Centre for GeoGenetics and first author of the study, added: "They adapted to extreme environments very quickly, and were highly mobile. These findings have changed a lot of what we thought we knew about the population history of north eastern Siberia but also what we know about the history of human migration as a whole."

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The two 31,000-year-old milk teeth found at the Yana Rhinoceros Horn Site in Russia 
which led to the discovery of a new group of ancient Siberians 
[Credit: Russian Academy of Sciences]

Researchers estimate that the population numbers at the site would have been around 40 people with a wider population of around 500. Genetic analysis of the milk teeth revealed the two individuals sequenced showed no evidence of inbreeding which was occurring in the declining Neanderthal populations at the time.

The complex population dynamics during this period and genetic comparisons to other people groups, both ancient and recent, are documented as part of the wider study which analysed 34 samples of human genomes found in ancient archaeological sites across northern Siberia and central Russia.

Professor Laurent Excoffier from the University of Bern, Switzerland, said: "Remarkably, the Ancient North Siberians people are more closely related to Europeans than Asians and seem to have migrated all the way from Western Eurasia soon after the divergence between Europeans and Asians."

Scientists found the Ancient North Siberians generated the mosaic genetic make-up of contemporary people who inhabit a vast area across northern Eurasia and the Americas - providing the 'missing link' of understanding the genetics of Native American ancestry.

It is widely accepted that humans first made their way to the Americas from Siberia into Alaska via a land bridge spanning the Bering Strait which was submerged at the end of the last Ice Age. The researchers were able to pinpoint some of these ancestors as Asian people groups who mixed with the Ancient North Siberians.

Professor David Meltzer, Southern Methodist University, Dallas, one of the paper's authors, explained: "We gained important insight into population isolation and admixture that took place during the depths of the Last Glacial Maximum - the coldest and harshest time of the Ice Age - and ultimately the ancestry of the peoples who would emerge from that time as the ancestors of the indigenous people of the Americas."

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A fragment of a decorative ivory hair ornament or head band discovered 
at the excavation site near the Yana River [Credit: Elena Pavlova]

This discovery was based on the DNA analysis of a 10,000 year-old male remains found at a site near the Kolyma River in Siberia. The individual derives his ancestry from a mixture of Ancient North Siberian DNA and East Asian DNA, which is very similar to that found in Native Americans. It is the first time human remains this closely related to the Native American populations have been discovered outside of the US.

Professor Willerslev added: "The remains are genetically very close to the ancestors of Paleo-Siberian speakers and close to the ancestors of Native Americans. It is an important piece in the puzzle of understanding the ancestry of Native Americans as you can see the Kolyma signature in the Native Americans and Paleo-Siberians. This individual is the missing link of Native American ancestry."

Source: University of Cambridge [June 05, 2019]

Read more at https://archaeologynewsnetwork.blogspot.com/2019/06/dna-from-31000-year-old-milk-teeth.html#p2CDfflWEY7KQ0BJ.99

Signs of ancient Neolithic settlement unearthed in Scotland

Carnoustie is continuing to reveal the story of its ancient past in the latest excavation works linked to a major residential and business development.

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Early Neolithic pit during excavation showing pottery finds
[Credit: © ARO]

A team of archaeologists has been involved in earthworks at fields neighbouring Pitskelly Farm, where more than 200 new homes and a business park are planned.

The site is close to land where an internationally significant treasure trove was unearthed in 2016, and experts involved with the current project say the farmland has also shown signs of settlement from as far back as the late Neolithic period of thousands of years ago.

The project, visible to A92 motorists at Upper Victoria, follows approval in principle for the ambitious scheme as part of land allocation made in the 2016 Angus Local Development Plan.

Lindsay Dunbar of Midlothian-based consultant AOC Archaeology Group, said: “As excavations over the last few years at Carnoustie, specifically at David Moyes Road a kilometre or so from our site have shown, there is potential for truly amazing archaeology to be uncovered.

“Here at Upper Victoria we have found more evidence of the long-lived and continual occupation of this part of the Angus coastline with the remains from the late Neolithic through to the post-Medieval period.”

Site findings will be recorded, recovered and handed over to Aberdeenshire Council Archaeological Service who act as archaeological curators for Angus Council.

The 2016 finds from the nearby site included a gold-adorned Bronze Age sword.

Carnoustie company D J Laing Homes Ltd will establish the business park while the housing is to be a joint venture project between town firm and Persimmon Homes.

The outcome of  consultancy projects including archaeological excavations, will support a detailed planning application due to come forward in late summer.

D J Laing Homes managing director Karen Nicoll said: “This project has been in the pipeline for the past six years so we are delighted that the consultancy studies are now nearing completion and will support the current planning conditions and enable full planning approval for over 200 houses and a new business park to come forward.

“It represents a substantial commitment by D J Laing Homes to both Carnoustie and Angus.”

Project managers Voigt Architects added: “This major development will provide new mainstream and much needed affordable housing in south Angus but of equal importance will be the delivery of a new business/industrial development area with direct access to the A92 road network, increasing opportunity for existing businesses within the town and also attracting new inward investment to Carnoustie and Angus.”

This research was undertaken by Cameron Archaeology and  is freely available to download from the ARO website – Archaeology Reports Online.

Author: Graham Brown | Source: The Courier [June 05, 2019]

Collapse and resilience of Levant communities during the Early Bronze Age

The system of centralised, urbanised settlements established in agriculturally productive valleys and plans broke down in the southern Levant around 2,500-1,950 BC, during the Early Bronze (EB) Age IV, noted an American archaeologist.

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Tell Umayri outside of Amman with what is left on the site's surface, 
winter 2019 [Credit: Amy Karoll]

“Previous theories imply that this breakdown coincided with a major climatological event: a widespread drought that occurred around 2,200 BC across the ancient Near East. According to this theory, a series of crises in the Near East occurred over a century, first affecting semi-arid regions along agricultural margins in northern Mesopotamia and moved towards the eastern margins of the Levant,” explained Amy Karoll, adding that settlements along river systems were less affected due to access to water that was not dependent on rainfall.

Since this environmentally deterministic theory was first proposed, she continued, a new data has called into question the timing of the EB IV decline. As such, “collapse” may no longer be a valid model to analyse this period, Karoll said, and, instead, she proposed investigating “alternative explanations that situate people as active agents in a resilient socioeconomic system”.

“The changes in economic and political systems were conscious choices, shaped and limited by outside factors,” the scholar underlined, noting that rather than a sudden collapse of society due to catastrophic climatic change, disrupting agricultural production, it appears that the EB IV transition was the logical consequence of people actively responding to their steadily changing environment.

Karoll, who is a PhD candidate at the University of California Los Angeles in Near Eastern Languages and Cultures, has studied sites of the Jordan Valley.

According to her, the main site is Khirbet Iskander, located on the central Transjordanian Plateau, some 24km south of Madaba and right off the King’s Highway.

“The EB IV occupation is particularly important at the site: Khirbet Iskander was a fortified, sedentary town during the EB IV, one of very few. Another is Bab edh-Dhra, located near the Dead Sea on the Karak Plateau,” she noted, adding that she also looked at Tell Al Hammam and Tell Iktanu in the Jordan Valley, Khirbet Al Batrawy, northeast of Amman, and Tell Al Umayri on the road to the airport.

Trade connections between sites in east and west banks had been well known as Tell Al Hammam on the eastern side and Jericho on the western side had very close trade connections during the EB IV, Karoll claimed.

“Previous ideas of a purely nomadic society, first proposed in the mid-20th century, have been shown to be a fallacy,” the researcher said. She pointed out that agriculture is either integrated into seasonal rounds of pastoral groups or trade is required to provide these goods.

Furthermore, societies incorporated both modes of economy, Karoll said, adding that her study will not address urban agriculturalists and pastoral nomads as a dichotomy, but rather attempt to situate these concepts along a spectrum, where each is reliant upon the other.

Variations within pastoral systems, especially as they change over time during the late third millennium BC, will be addressed in order to identify the impact pastoral nomads had on economic, social and political regimes of this period, she stressed.

Her future plans regarding a dissertation research is to use this research as a means to study collapse and resilience in the entirety of the southern Levant.

“The EB IV is not the only period of ‘collapse’ and change in the Levant. These changes occur at every major period transition, from the Middle to the Late Bronze Age, from the Late Bronze Age to the Iron Age, etc,” Karoll underscored.

Author: Saeb Rawashdeh | Source: The Jordan Times [June 05, 2019]
Read more at https://archaeologynewsnetwork.blogspot.com/2019/06/collapse-and-resilience-of-levant.html#wUrpwGzQcrkh2Pk5.99

1,000-Year-Old Sarcophagus Opened In Mainz

1,000-Year-Old Sarcophagus Opened In Mainz

After months of preparations, an international team of researchers were able to open a 1,000-year-old sarcophagus at the St. Johannis (St. John's) church in the German city of Mainz on Tuesday.

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Raising the sarcophagus lid [Credit: Andreas Arnold/AFP/Getty Images]

Using a pulley system, the team lifted the 700 kilogram (1,540 pound) lid off the grave and took a peek inside at remains that likely haven't been seen in a millennium.

"We all got to feel a little bit like Indiana Jones," Mainz Dean Andreas Klodt said at a press conference.

Researchers found male human remains, although it is still uncertain who is buried inside.

The body was likely covered in quicklime shortly before the sarcophagus lid was put on in order to speed up the decay of the body — but that also makes identifying the remains difficult.

"Not even teeth could be found," Swiss archaeologist Guido Faccani said.

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Researcher measures contents of sarcophagus [Credit: Andreas Arnold/AFP/Getty Images]

Historians and church officials alike hope that the remains in the grave can help solve some of the historic mysteries surrounding the St. Johannis church, which is one of the oldest in the city.

The body is believed to belong to Erkanbald, the Archbishop of Mainz who died in 1021. Should this be true, it would make the St. Johannis church the first cathedral in Mainz, which was once a powerful territory in the former Holy Roman Empire.

Besides the human remains, researchers also uncovered pieces of fabric and cloth shoes, as well as the remains of what appeared to be a bishop's hat.

The sarcophagus' location in the central nave of the church and the fact that it was pointed towards the altar also indicate the person buried inside was a church official.

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Researchers document contents of sarcophagus [Credit: Andreas Arnold/AFP/Getty Images]

"It's still possible that it's him," Faccani said.

The team of archaeologists, anthropologists and textile experts will now examine the remains using carbon dating and DNA samples from tissue and bone samples.

They will need to work quickly, however, as the remains and specimens inside the grave are now exposed to the fresh air for the first time in what is likely 1,000 years and could change due to the oxygen exposure.

The sarcophagus will be open to the public over the weekend and is due to be closed again in the coming weeks.

Source: Deutsche Welle [June 05, 2019]
Read more at https://archaeologynewsnetwork.blogspot.com/2019/06/1000-year-old-sarcophagus-opened-in.html#fJWJK6RalPpACxi3.99

World's protected areas safeguard only a fraction of wildlife

A new analysis published in the journal Frontiers in Ecology and the Environment shows that the world's protected areas (PAs) are experiencing major shortfalls in staffing and resources and are therefore failing on a massive scale to safeguard wildlife.

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A new analysis shows that the world's protected areas are experiencing major shortfalls in staffing 
and resources and are therefore failing on a massive scale to safeguard wildlife 
[Credit: Julie Larsen Maher/WCS]

The analysis looked at more than 2,100 protected areas around the world and found that less than a quarter report having adequate resources in terms of staffing and budget. The authors then looked at nearly 12,000 species of terrestrial amphibians, birds, and mammals whose ranges include protected areas and found only 4-9 percent are represented within the borders of the adequately resourced PAs.

"This analysis shows that most protected areas are poorly funded and therefore failing to protect wildlife on a scale sufficient to stave off the global decline in biodiversity," said Dr. James Watson of WCS and the University of Queensland, and one of the study's co-authors. "Nations need to do much more to ensure that protected areas fulfill their role as a major tool to mitigate the growing biodiversity crisis."

The authors acknowledge that countries are on target to fulfill a global commitment of setting aside 17 percent of terrestrial areas and 10 percent of the marine realm as PAs by 2020 (known as Aichi Target 11 of the Convention on Biological Diversity). However, the findings show that protected areas are grossly under-funded, and that simply measuring the amount of area protected is insufficient in conserving biodiversity.

The authors recommend the use of a restricted set of simple, robust indicators that capture the essence of effective PA resourcing and management. These indicators should be used for reporting toward international targets, prioritizing conservation actions, and achieving new PA standards, such as the IUCN's Green List.

Said Watson: "While continued expansion of the world's protected areas is necessary, a shift in emphasis from quality over quantity is critical to effectively respond to the current biodiversity crisis. If metrics of management effectiveness are not included in measurements of progress toward target 11 before 2020, we risk mistakenly reporting success in achieving Target 11, and sending a false message that sufficient resources are being committed to biodiversity protection."

Protected areas provide the core of the last remaining strongholds for nature on planet Earth. If our efforts to hold on to these last intact natural areas remains inadequate, life as we know it will be threatened. Emphasis needs to be placed on building capacity, increasing and sustaining financial resources, scaling up conservation interventions, and improving overall effectiveness.

Source: Wildlife Conservation Society [June 05, 2019]

Read more at https://archaeologynewsnetwork.blogspot.com/2019/06/worlds-protected-areas-safeguard-only.html#jLwT7eEoy5EMzfia.99

Chimpanzees in the wild reduced to 'forest ghettos'


Urban expansion and hunting have pushed chimpanzees, humanity's closest relative in the animal kingdom, into shrinking islets of wildness, top experts said Tuesday after a three-day meeting in Germany.

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All four sub-species of the African chimpanzee are threatened with extinction, with at least one - the western 
chimpanzee - declining in number by more than 80 percent over three generations 
[Credit: Rob Elliott/AFP]

All four sub-species of the African primate are threatened with extinction, with at least one -- the western chimpanzee -- declining in number by more than 80 percent over three generations.

Forty chimp experts from around the world -- with a combined 300 years of field experience -- issued a collective appeal to save the only animal whose DNA overlaps with humans by 98 percent.

"Over the decades that we have been working with wild chimpanzee communities, we have all seen our study groups become isolated," they said in a statement. "Chimpanzees are being reduced into living in forest ghettos."

The main threat to chimps and other large mammals is habitat loss. Africa still has large tracts of undisturbed savannah and forest, but these areas are shrinking rapidly due growing cities, mining, deforestation, and industrial agriculture.

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All four sub-species of the African primate are threatened with extinction, with at least one - the western 
chimpanzee - declining in number by more than 80 percent over the last three generations 
[Credit: STR/AFP]

The continent's human population of more than 1.2 billion is expected to double by mid-century, and could top four billion by the end of the century.

Chimps number in the thousands for three of the sub-species, and about 250,000 for the eastern chimpanzee, found mainly in the Democratic Republic of Congo. Western chimpanzees have already been wiped out in Burkina Faso, Benin, Gambia, and possibly Togo.

"Forty years ago, we drove 100 kilometres (60 miles) on a mud road to reach the park boundaries while encountering chimpanzees and elephants," said Christopher Boesch, a professor at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, referring to the Tai National Park in Ivory Coast. "Nowadays, you have to reach the park boundaries to see the first patch of forest."

Last common ancestor

Human encroachment and the hunting of chimpanzees for "bush meat" has also altered the social life and behaviour of the animals, said Crickette Sanz, an associate professor at Washington University in Missouri who has worked for decades in the Republic of Congo's Goualougo Triangle.

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The last common ancestor of humans and chimpanzees lived about seven million years ago 
[Credit: Guillaume Souvant/AFP]

"When we first arrived in the Ndoki forest, the chimpanzees would often approach us with curiosity," she recalled.

Now they hide.

"It is wise that they have changed their behaviour -- their survival depends on it," Sanz added.

Compared to chimpanzees in pristine forests, those in areas disrupted by humans also showed a decrease in the diversity of learned behaviour, according to a recent study.

Scientists studying nearly 150 chimpanzee communities across 17 countries identified 31 actions -- including cracking nuts, extracting termites or ants with tools, collected honey, throwing stones as a form of communication -- that were done differently from one group to the next.

The more humans had carved up the environment -- building roads, clear-cutting trees, setting up palm oil plantation -- the more uniform these actions became.

image: https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsGQ3_r8tpFHkxvhZmW9EEgxh4LiJkOr2tjcB7pKmX7G3B8R-D3YYwlcg_LbOC_xGFMmA5zGPXqKS8Nl54vi2YnK_eQy6YnSvoil13GQhfpBLk0xsJQbdo16MzekzPDTISMlcPiw/s640/chimp-04.jpg

"We did not evolve from bonobos or chimpanzees but we share with them a common ancestry," said Martin Surbeck, 
a primatologist at the Max Planck Institute for Evolutionary Anthropology, also in Leipzig 
[Credit: STR/AFP]

The last common ancestor of humans and chimpanzees lived about seven million years ago.

"We did not evolve from bonobos or chimpanzees but we share with them a common ancestry," said Martin Surbeck, a primatologist at the Max Planck Institute for Evolutionary Anthropology, also in Leipzig.

The famed anthropologist Irven DeVore once marvelled at humanity's indifference to our closest primate cousins.

"If we, in our travels in space, should encounter a creature that shared 98 percent of our genetic makeup, think of the money we would spend to study this species," he said.

"Such creatures exist on Earth and we are allowing them to become extinct."

Author: Marlowe Hood | Source: AFP [June 05, 2019]
Read more at https://archaeologynewsnetwork.blogspot.com/2019/06/chimpanzees-in-wild-reduced-to-forest.html#tw25vpmWWPhZ0UVU.99