Genes that protected coastal First Nations from ancient pathogens brought “catastrophic” vulnerability to European diseases

The immune system genes that protected north coast First Nations from possibly dangerous local pathogens thousands of years ago likely increased their vulnerability to European diseases in the nineteenth century, resulting in the disastrous population crash, a new genetic study has discovered.

The study which included members of the Lax Kw’alaams and Metlakatla First Nations at Prince Rupert “opens a new window on the catastrophic consequences of European colonization for indigenous peoples in that part of the world,” the study authors said in a news release.

The study, published today in Nature Communications, looked at the genomes of 25 individuals who lived 1,000 to 6,000 years ago in what the study calls PRH—the Prince Rupert Harbour region– and 25 of their descendants who still live in the region today.

The study is a follow up to one published in 2013 that used DNA to prove that the remains of a woman from 5,500 years ago was tied directly through the maternal line to members of today’s Metlakatla Nation.

“This is the first genome-wide study – where we have population-level data, not just a few individuals – that spans 6,000 years,” said University of Illinois anthropology professor Ripan Malhi, who co-led the new research with former graduate student John Lindo (now a postdoctoral researcher at the University of Chicago) and Pennsylvania State University biology professor Michael DeGiorgio. Both studies were carried out with the consent and cooperation of the Coastal Tsimshian people.

The new study analyzes the “exome,” the entire collection of genes that contribute to a person’s traits.

The ruins of a Haida longhouse at Tanu. Smallpox and other diseases brought a catastrophic population crash among coastal First Nations in the nineteenth century. (Robin Rowland/Northwest Coast Energy News)
The ruins of a Haida longhouse at Tanu. Smallpox and other diseases brought a catastrophic population crash among coastal First Nations in the nineteenth century. (Robin Rowland/Northwest Coast Energy News)

“Oral traditions and archaeological evidence to date have shown that there has been continuous aboriginal occupation of this region for more than 9,000 years. This study adds another layer of scientific data linking the actual ancestral human remains to their modern descendants through their DNA over a span of 6,000 years,” said Barbara Petzelt, a co-author of the study and a liaison to the Metlakatla community. “It’s exciting to see how this tool of DNA science adds to the larger picture of Coast Tsimshian pre- and post-contact history – without the taint of historic European observer bias.”

In the new study, the team found that variants of an immune-related gene that were beneficial to many of those living in the region before European contact proved disadvantageous once the Europeans arrived.

The genes, the human leukocyte antigen gene family, known as HLA, helps the body recognize and respond to pathogens, or disease causing bacteria and viruses.

The authors say the “the immunological history of the indigenous people of the Americas is undoubtedly complex.”

As people came to the American continents about 15,000 to 20,000 years ago “indigenous people adapted to local pathogens.”

Statistical analyses revealed that the ancient genes were under “positive selection” before European contact. Natural selection meant that those ancient people with genetic resistance to those local diseases had an advantage that resulted in the genes becoming part of the population.

But the study indicates “those adaptations would have proven useful in ancient times but not necessarily after European colonialists altered the environment with their pathogens, some of which may have been novel. Existing genetic variation as a result of adaptation before European contact could thus have contributed to the indigenous population decline after European contact.”

The “positive selection” genes found in the remains of ancient members of the Coast Tsimshian people, has been replaced by another gene among the modern descendants that “has been associated with a variety of colonization-era infectious diseases, including measles and tuberculosis, and with the adaptive immune response to the vaccinia virus, which is an attenuated form of smallpox,” the authors wrote.

One of the genes is “64 percent less common today among the Coast Tsimshian people than it was before original European contact, which is a dramatic decline,” Lindo said.

The modern Coast Tsimshian show a “reduction in ‘effective population size’ of 57 per cent,” the researchers reported.

“’Effective population size’ is a population genetic concept that is different from what we normally think of with census population size,” Malhi said in an e-mail to Northwest Coast Energy News. “It basically means that there was a large drop in genetic diversity after European contact that could have been due to disease, warfare or other things that would result in this large population decline.”

The dramatic die-off occurred roughly 175 years ago, about the time that European diseases were sweeping through the First Nations of British Columbia.

While some members of the Coast Tsimshian community have intermarried with people of European descent over the past 175 years, the genetic changes cannot be solely attributed to what geneticists call “admixture.” The timing coincides with the documented smallpox epidemics of the 19th Century and historical reports of large-scale population declines. A majority of the “European admixture in the population likely occurred after the epidemics,” the study says.

To guard against what the study called “false positives” the genomes were also compared to individuals in the 1,000 Genome Project including 25 Han Chinese from Beijing as well as other indigenous peoples in the Americas including the Maya, the Suruí do Pará people of Brazil and a sample of Anzick DNA from the 12,000 year old remains of a child found buried in Montana.

“First Nations history mainly consists of oral stories passed from generation to generation. Our oral history tells of the deaths of a large percentage of our population by diseases from the European settlers.
“Smallpox, for our area, was particularly catastrophic,” said Jocelynn Mitchell, a Metlakatla co-author on the study. “We are pleased to have scientific evidence that corroborates our oral history. As technology continues to advance, we expect that science will continue to agree with the stories of our ancestors.”

The same vulnerability for smallpox, measles and tuberculous likely also contributed to the vulnerability to influenza, Malhi told Northwest Coast Energy News “It is important to note that any of these infectious diseases (measles, tuberculosis, smallpox, flu) could have resulted in the patterns that we are seeing. We just provided a few possibilities but not all possibilities.”

The study says the project was made possible through the active collaboration of the Metlakatla and Lax Kw’alaams First Nations.
The first collaborative DNA study began in 2007 and 2008. The scientists visited the communities each year “to report the most recent DNA results and obtain feedback on the results.”

“The two communities agreed to allow DNA analysis of ancestral individuals recovered from archaeological sites in the region and currently housed at the Canadian Museum of History. During and after community visits and extensive consultation, a research protocol and informed consent documents—agreed on by the indigenous communities and researchers—was approved by the University of Illinois Institutional Review Board. All individuals signed an informed consent document.”

These results were reported to the community and the scientists continue to visit the First Nations to report on this and related studies.

The study is titled “A time transect of exomes from a Native American population before and after European contact” and appeared in the Nov. 15, 2016, edition of Nature Communications.

First Nations historical herring harvest offers “deep time perspective” to modern managers, SFU study says

SFU archaeologists
Iain McKechnie and Dana Lepofsky examine ancient herring fish bones that tell the story about how gigantic herring fisheries were for thousands of years in the Pacific Northwest. (SFU)

The herring, now dwindling on on the Pacific Coast, was once “superabundant” from Washington State through British Columbia to Alaska and that is a warning for the future, a new study says.

A team of scientists lead by Simon Fraser University argue that the archaeological record on the Pacific Coast offers a “deep time perspective” going back ten thousand years that can be a guide for future management of the herring and other fish species.

An archaeological study looked at 171 First Nations’ sites from Washington to Alaska and recovered and analyzed 435,777 fish bones from various species.

Herring bones were the most abundant and dating shows that herring abundance can be traced from about 10,700 years ago to about the mid-nineteenth century with the arrival of Europeans and the adoption of industrial harvesting methods by both settlers and some First Nations.

That means herring were perhaps the greatest food source for First Nations for ten thousand years surpassing the “iconic salmon.” Herring bones were the most frequent at 56 per cent of the sites surveyed and made up for 49 per cent of the bones at sites overall.

The study was published online Monday, February 17, 2014, in Proceedings of the National Academy of Sciences (PNAS). Simon Fraser University researchers Iain McKechnie, Dana Lepofsky and Ken Lertzman, and scientists in Ontario, Alberta and the United States are its co-authors.

The study is one of many initiatives of the SFU-based Herring School, a group of researchers that investigates the cultural and ecological importance of herring.

“By compiling the largest data set of archaeological fish bones in the Pacific Northwest Coast, we demonstrate the value of using such data to establish an ecological baseline for modern fisheries,” says Iain McKechnie. The SFU archaeology postdoctoral fellow is the study’s lead author and a recent University of British Columbia graduate.

Co-author and SFU archaeology professor Dana Lepofsky states: “Our archaeological findings fit well with what First Nations have been telling us. Herring have always played a central role in the social and economic lives of coastal communities. Archaeology, combined with oral traditions, is a powerful tool for understanding coastal ecology prior to industrial development.”

The researchers drew from their ancient data-catch concrete evidence that long-ago herring populations were consistently abundant and widespread for thousands of years. This contrasts dramatically with today’s dwindling and erratic herring numbers.

“This kind of ecological baseline extends into the past well beyond the era of industrial fisheries. It is critical for understanding the ecological and cultural basis of coastal fisheries and designing sustainable management systems today,” says Ken Lertzman, another SFU co-author. The SFU School of Resource and Environmental Management professor directs the Hakai Network for Coastal People, Ecosystems and Management.

Map of First Nations sites with fish bones
Map of First Nations’ archaeological sites with high numbers of fish bones. Herring is abundant in sites throughout the Strait of Georgia. In 71% of sites, herring makes up at least 20 per cent of the bones found at the site. (SFU/PNAS)

Heiltsuk tradition

The paper says that the abundance of herring is additionally mirrored in First Nations’ place
names and origin narratives. They give the example of the 2,400-y-old site at Nulu where herring
made up about 85 per cent of the fish found in local middens. In Heiltsuk oral tradition, it is Nulu where Raven first found herring. Another site, 25 kilometres away at the Koeye River, has only has about 10 per cent herring remains and is not associated with herring in Heiltsuk tradition.

(In an e-mail to Northwest Coast Energy News, McKechnie said “there is a paucity of archaeological data from Kitimat and Douglas Channel. There is considerable data from around Prince Rupert, the Dundas Islands and on the central coast Namu/Bella Bella/ Rivers Inlet area and in southern Haida Gwaii.”)

The study says that the archaeological record indicates that places with abundant herring were consistently harvested over time, and suggests that the areas where herring massed or spawned were more extensive and less variable in the past than today. It says that even if there were natural variations in the herring population, the First Nations harvest did not affect the species overall.

It notes:

Many coastal groups maintained family-owned locations for harvesting herring and herring roe from anchored kelp fronds, eel grass, or boughs of hemlock or cedar trees. Herring was harvested at other times of the year than the spawning period when massing in local waters but most ethnohistorical observations identify late winter and springtime spawning as a key period of harvest for both roe and fish.

The herring and herring roe were either consumed or traded among the First Nations.

Sustainable harvests encouraged by building kelp gardens,wherein some roe covered fronds were not collected, by minimizing noise and movement during spawning events, and by elaborate systems of kin-based rights and responsibilities that regulated herring use and distribution.

Industrial harvesting

Industrial harvesting and widespread consumption changed all that. Large numbers of herring were harvested to for rendering to oil or meal. By 1910, the problem was already becoming clear. In that year British Columbia prohibited the reduction of herring for oil and fertilizer. There were reports at that time that larger bays on the Lower Mainland were “being gradually deserted by the larger schools where they were formerly easily obtained.”

But harvesting continued, in 1927 the fishery on eastern Vancouver Island, Columbia, processed
31,103 tons of herring. The SFU study notes that that is roughly twice the harvest rate for 2012 and would also be about 38 per cent of the current herring biomass in the Strait of Georgia.
In Alaska, reduction of herring began in 1882 and reached a peak of 75,000 tons in 1929.

As the coastal populations dwindled, as with other fisheries, the emphasis moved to deeper water. By the 1960s, the herring populations of British Columbia and Washington had collapsed. Canada banned herring reduction entirely in 1968, Washington followed in the early 1980s.

In the 1970s, the herring population off Japan collapsed, which opened up the demand for North American roe, which targeted female herring as they were ready to spawn. That further reduced the herring population so that the roe fishery is now limited to just a few areas including parts of the Salish Sea and off Sitka and Togiak, Alaska.

The First Nations food, social and ceremonial herring fishery continues.

Government fishery managers, scientists, and local and indigenous peoples lack consensus on the cumulative consequences of ongoing commercial fisheries on herring populations. Many First Nations, Native Americans, Alaska Natives, and other local fishers, based on personal observations and traditional knowledge, hypothesize that local herring stocks, on which they consistently relied for generations, have been dramatically reduced and made more difficult to access following 20th century industrial fishing

Deep time perspective

The SFU study says that some fisheries managers are suggesting that the herring population has just shifted to other locations and other causes may be climate change and the redounding of predator populations.

But the study concludes, that:

Our data support the idea that if past populations of Pacific herring exhibited substantial variability, then this variability was expressed around a high enough mean abundance such that there was adequate herring available for indigenous fishers to sustain their harvests but avoid the extirpation of local populations.

These records thus demonstrate a fishery that was sustainable at local and regional scales over millennia, and a resilient relationship between harvesters, herring, and environmental change that has been absent in the modern era.

Archaeological data have the potential to provide a deep time perspective on the interaction between humans and the resources on which they depend.

Furthermore, the data can contribute significantly toward developing temporally meaningful ecological baselines that avoid the biases of shorter-term records.

Other universities participating in the study were the University of British Columbia, University of Oregon, Portland State University, Lakehead University, University of Toronto, Rutgers University and the University of Alberta.

 

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