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With Ancient Human DNA, Africa’s Deep History Is Coming to Light

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Ancient DNA can reveal much about the genetic history of Africa because it predate major events like slavery and colonialism, which upended African populations and territories. (Credit: Zita/shutterstock)

In 2010, extraordinary circumstances allowed geneticists to reconstruct the first full genome of an ancient human: the DNA came from a hairball, frozen 4,000 years in Greenland soil. Since then, methods have improved so much in cost and efficiency that individual papers now report genomic data from hundreds of dead people (here, here, here). Ancient DNA (aDNA) has now been published from well over 2,000 human ancestors, stretching as far back as 430,000 years ago.

But around 70 percent of those sequences are from Eurasia, where cold temperatures favor DNA preservation and considerable archaeological research has occurred. For researchers interested in the genetic history of Europe and Asia, there are plenty of excavated skeletons, sitting in museums and other collections, and there’s a good chance those bones hold appreciable DNA.

The situation is different in Africa — the place where Homo sapiens originated some 300,000 years ago and has continued diversifying ever since. Despite Africa’s prominence in the human story, so far only 30 ancient genomes between 300 and 15,000 years old have been published from the continent.

Part of the reason is methodological and environmental: Hot, humid conditions destroy DNA in human remains, long before geneticists attempt to extract it. However, in 2015 scientists showed that aDNA preservation can be 100-fold higher in the petrous — dense bone surrounding the inner ear — than other skeletal parts. In 2018, researchers used this bone to recover the oldest African genomes yet, from 15,000-year-old skeletons excavated from a cave in Morocco.

It’s unlikely geneticists will capture much older African DNA than that. So, the petrous find is a “game changer,” not a miracle maker. But bones between 5,000 and 15,000 years old — surrounding the start of the Holocene, our current geologic epoch — can reveal much about the genetic history of Africa. That’s because they predate major events that upended African populations and territories. These include the slave trade and colonialism. Earlier still, there were major migrations within Africa linked to the spread of herders and farmers, starting around 5,000 years ago.

“What we see is this huge amount of noise from the past 5,000 years,” says Elizabeth Sawchuk, an archaeologist who works in East Africa.

DNA from Holocene remains would allow researchers to peer beyond this noise, to glimpse the genetic map of Africa prior to agriculture and historical migrations. And now, it’s technologically possible.

Yet there’s reason to pause, as ancient DNA studies receive criticism. Archaeologists and historians accuse geneticists of making sweeping claims based solely on DNA data, without considering the centuries of evidence and scholarship accumulated by other fields. Ethical concerns have also been raised about taking skeletal samples out of Africa and into Western laboratories for the destructive process of genetic sequencing. Moreover, the results may fuel ancestry claims over territories or cultural heritage, and therefore affect living people who did not consent to the research.

In this context, some scientists are proceeding with caution, and a number of African aDNA projects are underway. One of the largest is led by Sawchuk, archaeologist Mary Prendergast and geneticist David Reich, who runs the aDNA laboratory at Harvard Medical School.

Discover talked to Sawchuk, a post-doctoral researcher at Stony Brook University, about the potential risks and rewards of African aDNA.

Why is African aDNA important?

It’s where our species evolved, where we’ve been the longest. And as a consequence, Africa has the highest genetic diversity of anywhere else on the planet. It potentially is going to tell us the most about our species, but it’s an area that we know the least about.

Why is that?

Largely because of underfunded research. Africa is very expensive to go to. The continent is humongous. Areas are inaccessible for geographical, environmental and political reasons. As a result there are fewer skeletons and archaeological sites identified for this huge area and huge period of time. [Also aDNA] preservation is bad because high heat, humidity and water destroy the organic content of bones. Getting aDNA out of this continent was regarded to be something we would all love to do, but nobody could do.

Now that it’s technologically feasible, why should researchers be cautious?

Human remains are the only direct link we have to the past. We have far fewer skeletons in Africa than other parts of the world, so every skeleton is incredibly precious. That puts a really big burden on these genetics projects in terms of how much material they’re sampling, how many sites they’re sampling, if they’re sampling all of the sites.

There’s a fundamental tension: You don’t know which skeletons and sites will have aDNA preserved, so you just have to try them all. But if we try them all now, in 5 years, 10 years, 15 years, 50 years, the science might be completely different, and we may have limited ourselves in the future. So it’s a tight line to walk.

What are some concerns of present-day Africans?

Across a continent as big of Africa, [countries] with individual, imposed colonial histories have very different ways of approaching their own national heritage. Transporting material outside of Africa to a clean room — so we can minimize contamination and maximize the chance of getting a sequence — that kind of parallels a lot of the colonial justifications for removing artifacts out of their countries of origin to better funded European or American institutions. So there needs to be a lot of sensitivity about how human remains are approached, sampled, processed, and eventually returned.

How has your project been responsive to these concerns and other criticisms of aDNA research?

It’s taken a lot longer compared to other genetic projects to start — to get the permissions, to really get everybody on board, and to do this right. It just takes time, face-time. People who can go there, propose this research, bring on African collaborators in a senior role, and then do this project going forward together.

Many of the criticisms of other DNA projects are that it’s DNA first, Anthropology second. This was really an Anthropology first project. It’s driven by questions that myself and many other anthropologists have been asking for decades, but integrating this new line of evidence, DNA.

It’s absolutely really exciting that we might have this new line of evidence, but DNA will not be the magic key to all of these answers. It’s not to the exclusion of decades and hundreds of years of pottery studies, ancient tool studies, landscape archaeology, ethnographies. These are all just pieces of a puzzle that we need to put together. This is always going to have to be an interdisciplinary effort, where we work with other types of scientists and we work with local communities.

This is so exciting. We just have to make sure that we do it right, right now.

What have you found so far?

We’ve sampled from institutions in Tanzania and Zambia and Kenya. This will be one of the largest African DNA studies to date when it comes out. It’s blown my mind. I hope it will blow many other peoples’ minds.

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Ecology

Yukon and Northern BC First Nations tackle climate change using Indigenous knowledge and science

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YUKON, June 18, 2021 /CNW/ – The Government of Canada is working together in partnership with Indigenous and Northern communities in finding solutions to adapt to the impacts of climate change in the North.

Today, Minister of Northern Affairs, Daniel Vandal, along with Parliamentary Secretary to the Minister of Economic Development and Official Languages (Canadian Northern Economic Development Agency), Larry Bagnell, highlighted progress on three unique, Indigenous-led projects that are helping communities in Yukon and Northern British Columbia adapt to the challenges posed by climate change.

The Minister and Parliamentary Secretary met virtually with Carcross/Tagish First Nation (C/TFN) to learn about their community-led climate change monitoring program. C/TFN has partnered with Tsay Keh Dene Nation (TKDN) and Chu Cho Environmental of Prince George, British Columbia, to build a community-led monitoring project that examines environmental data and Indigenous knowledge to create a holistic picture of how the climate is changing across C/TFN and TKDN traditional territories. The project combines tracking of current and historical climate trends with knowledge shared by Elders while also providing opportunities for youth mentorship and climate change awareness.

The Taku River Tlingit First Nation (TRTFN) is also leading a unique project to assess the impacts of climate change within their traditional territory. Climate change is causing many of the culturally significant ice patches to melt, exposing organic artifacts to oxygen and leading to rapid deterioration. The TRTFN ice patch mapping project will involve performing archaeological assessments to prevent the degradation of artifacts. Research will be guided by traditional knowledge, Elders and oral histories, when available, and heavily involve community, Elders, youth and Knowledge Keepers.

The Pelly Crossing Selkirk Development Corporation is leading the Selkirk Wind Resource Assessment project through the installation of a Sonic Detection and Ranging (SODAR) system. The initiative includes a feasibility study leading up to the construction of a renewable energy facility, including wind, solar and battery energy storage. Expanding clean energy within the region will have direct benefits for communities, including reduced reliance on diesel, job creation and revenue generation for Selkirk First Nation. 

These projects are delivering important environmental, social and economic benefits that lead to healthier, more sustainable and resilient communities across Yukon and Northern British Columbia. They also build community clean energy capacity and help to avoid the impacts of climate change.

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Ecology

Atlantic Provinces Ready For Aquaculture Growth

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Aquaculture is an important economic driver for rural, coastal and Indigenous communities, and Atlantic Canada is well positioned to increase aquaculture production as global demand for sustainably sourced seafood grows.

That is why the ministers responsible for aquaculture in the Atlantic provinces have agreed to the ongoing development and management of their industries based on common principles. A new memorandum of understanding has been signed by the four ministers, which extends the previous agreement signed in 2008.

“In a time when food security is especially important, it is good to see our aquaculture industry has grown steadily and is poised for continued growth in 2021 based on environmentally responsible, science-based policies and practices,” said Keith Colwell, Minister of Fisheries and Aquaculture for Nova Scotia. “Our Atlantic partnership continues to help the industry grow sustainably.”

Cooperation between the provinces and the aquaculture industry has led to improvements in pest management, environmentally sustainable aquaculture methods, aquatic animal health and policies to support the shared use of marine and freshwater resources. It also aims to align regulation and policy between the provinces to make the regulatory requirements easier to understand by industry and the public.

Each province has a comprehensive and robust legislative and regulatory framework to ensure environmental sustainability, economic prosperity and public accountability. The provinces update their legislation and regulations regularly. Nova Scotia revamped its regulatory framework in 2015; New Brunswick received Royal Assent for a new Aquaculture Act in 2019 and is working on the supporting regulations; Newfoundland and Labrador completely revised its aquaculture policy in 2019; and Prince Edward Island has recently drafted a new Aquaculture Act.

The ministers have agreed to continue to use science-based evidence for management decisions, thereby increasing public and investor confidence in the Atlantic Canadian aquaculture industry.

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Ecology

COMING SOON: A Healthy Environment and a Healthy Economy 2.0

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We all want the same thing: a clean and responsible energy future for our children and future generations while continuing to enjoy a high standard of living.

On December 11, 2020, the Prime Minister announced a new climate plan which he claimed will help achieve Canada’s economic and environmental goals.

The proposed plan by Environment and Climate Change Canada (ECCC) entitled “A Healthy Environment and a Healthy Economy” will have an initial investment of $15 billion of taxpayer’s money. It is built on 5 pillars of action:

  1) Making the Places Canadians Live and Gather More Affordable by Cutting Energy Waste

2) Making Clean, Affordable Transportation and Power Available in Every Community

3) Continuing to Ensure Pollution isn’t Free and Households Get More Money Back

4) Building Canada’s Clean Industrial Advantage

5) Embracing the Power of Nature to Support Healthier Families and More Resilient Communities  

In my paper, “A Healthy Environment and a Healthy Economy 2.0” I will objectively critique each pillar in the government’s new climate plan and provide alternative solutions to the same issues.

  This is an alternative plan that supports workers, protects lower income earners and creates economic growth while respecting the environment and focusing on the dignity of work.

  This plan abandons virtue-signaling projects and relies on Canadian ingenuity to build our economy and restore Canada’s role of responsible leadership in the world.

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