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.

Eel grass really a flower that stores more carbon than tropical forests, genome reveals

Eel grass is not a seaweed but a flowering plant that migrated to the sea, say scientists who have now mapped the eel grass genome. The study also shows that eel grass ( Zostera marina) is crucial in absorbing carbon dioxide in the soft sediments of the coasts.

Eel grasses form a carbon dioxide sink: “they store more carbon than tropical forests,” says Jeanine Olsen of the University of Groningen in the Netherlands who led the study.

Coastal sea grass ecosystems cover some 200,000 square kilometers, the study says. Those ecosystems account for an estimated 15 per cent of carbon fixed in global ocean, and also impact sulphur and nitrogen cycles.

The scientists argue that since sea grasses are the only flowering plants to have returned to the sea that is the most extreme adaptation a terrestrial (or even freshwater) species can undergo.

The science team says the Zostera marina genome is “an exceptional resource that supports a wide range of research themes, from the adaptation of marine ecosystems under climate warming and its role in carbon burial to unraveling the mechanisms of salinity tolerance that may further inform the assisted breeding of crop plants.”

A seagrass meadow. (Christoffer Boström)
A seagrass meadow.
(Christoffer Boström)

Sea grasses form the backbone of one of the most productive and biodiverse ecosystems on Earth, rivaling coral reefs and rain forests in terms of the ecosystem services they provide to humans.

Sea grass meadows are part of the soft-sediment coastal ecosystems found in all continents, with the exception of Antarctica. They not only form a nursery for young fish and other organisms, but also protect the coastline from erosion and maintain water clarity. ‘

The study, which sequenced the genome of the eel grass taken from the Archipelago Sea off Finland. published today, in the journal Nature, is the work of an international consortium of 35 labs, most of them in Europe, working with researchers from the U.S. Department of Energy Joint Genome Institute.

The study showed that eel grasses are completely submerged marine flowering plants, called by science angiosperms. It shows that eel grass is a member of the ancient monocot family.

The monocots include about 60,000 species, flowering plants that first appear above the soil as a single leaf. They include orchids, “true grasses,” as well as rice, wheat, maize and “forage grasses” such as  sugar cane, and the bamboos. According to Wikipedia, other economically important monocot crops include  palms  bananas , gingers, onions, garlic, lilies, daffodils,  irises, amaryllis,  bluebells and tulips.

Zostera marina is the first marine flowering plant have its genome fully sequenced. As well as finding the eel grass’s genetic ancestors the researchers were interested in understanding how the plant–and by extension other plants in the ecosystem–adapt to climate change.

As it adapted to  an underwater, coastal lifestyle, eel grass gained genes that allowed it to live in saltwater but lost genes involved in traits associated with land-based plants.

Olsen called this “arguably the most extreme adaptation a terrestrial (and even a freshwater) species can undergo.”

What she describes as the “use it, lose it, or change it” scenario, eelgrass modified its cell walls. The eel grass cell wall is very different from normal plant cell walls and more like that of sea algae, similar to the cell in seaweeds. The eel grass has lost genes associated with light-sensing, pollination and regulation of internal water balance.

Eel grass lost its stomata (which are used by land plants to ‘breathe’) but also all of the genes involved in stomatal differentiation. “The genes have just gone, so there’s no way back to land for sea grass,” Olsen says. Sex is entirely underwater involving long naked sperm filaments especially adapted for underwater fertilization of the tiny flowers.

The team compared the eel grass genome to duck weed, one of the simplest flowering plants and Zostera marina’s closest sequenced relative. They noted differences in genes related to cell wall structure due to adaptations to freshwater or terrestrial conditions. For example, plants such as duckweed have seemingly lost genes that help plants retain water in the cell wall, while eel grass has regained these genes to better deal with osmotic stress at low tide.

“They have re-engineered themselves,” said Olsen of the changes affecting the eelgrass cell walls. “Crop breeders may benefit from lessons on how salt tolerance has evolved in these plants.”

Eel grass distribution. (Wikipedia Commons(
Eel grass distribution. (Wikipedia Commons(

With Zostera marina meadows stretching from Alaska to Baja California, and from the White Sea to southern Portugal, Olsen noted that these ecosystems afford researchers “a natural experiment to investigate rapid adaptation to warmer or colder waters, as well as to salinity tolerance, ocean acidification and light.”

Eel grass endangered

Jeremy Schmutz, head of the US Department of Energy’s genetic plant program, emphasized that while eel grasses are key players in coastal marine ecosystem functions and considered the “lungs of the sea,” they are also endangered. “There are estimates that nearly a third of the eel grass meadows worldwide have been destroyed by runoff into the ocean,” he said, “reducing their potential capabilities as carbon sinks. Thus, studying the adaptive capacity of eel grass is urgent to assist conservation efforts.”

An overarching question for Olsen’s team is how quickly eel grass can adapt to rapid climate change. The fact that Zostera marina grows along the coastline from Portugal to Scandinavia is being used as a natural experiment to investigate adaptation to warmer or colder water, as well as to salinity, ocean acidification and light.

Genetics show stronger pine beetle evolving; stream flow increases in infected forests: studies

A new study, based at the University of Alberta, released this week, indicates that natural selection may be making the mountain pine beetle more tolerant of colder temperatures and that the beetle may be evolving the ability to fly longer distances.

A second study, from the Colorado School of Mines, also released this week, is tracking how the extent of pine beetle infected or killed trees in forests is changing ground water and stream flows.

The mountain pine beetle infestation has wreaked havoc in North America, across forests from the American Southwest to British Columbia and Alberta. Millions of hectares of forest have been lost, with severe economic and ecological impacts from a beetle outbreak ten times larger than previous ones.

Dust from beetle killed wood is believed partially responsible for the explosions at the Lakeland Mill in Prince George and the Babine Forest Products mill in Burns Lake. The explosion in early 2012 at the Babine Forest Products mill killed two workers and injured another twenty. The Lakeland Mill explosion killed two workers and injured twenty four others.

As part of the fight to contain the mountain pine beetle, scientists recently sequenced the pine beetle genome.

Using that genome, Jasmine Janes and colleagues at the University of Alberta, with assistance from the University of British Columbia and the University of Northern British Columbia, used genetics to track how the pine beetle was able to expand its range so rapidly. The study was published in Molecular Biology and Evolution.

Studied at molecular level

While teams of researchers have tracked the path of the pine beetle across BC on the ground, how the beetle spread so easily “is only beginning to be understood at the molecular level,” the study says.

Pine beetles were collected from 27 sites in Alberta and British Columbia. The University of Alberta scientists were especially interested in how the pine beetle was able to jump across the Rockies, something that earlier researchers believed would not happen.

By looking at the genetic markers, the team concluded that the pine beetle may have been able to spread by adjusting its cellular and metabolic functions to better withstand cooler climates and facilitate a larger geographic dispersal area.

In an e-mail to Northwest Coast Energy News, Janes said the research looked at genomic signatures to find out how the beetle had been able to spread into Alberta – where did it come from, what route did it take and how did it overcome the physical and climatic barriers that we had always assumed?

The research discovered that there are two genetically different populations of pine beetles, one from the south of British Columbia and Alberta and one in the north. Another group of pine beetles, found near Valemount, “were harder to classify as being from either north or south genetically. The beetles in this area were showing higher genetic diversity.”

The pine beetle has always been around and killed older trees (called “low quality hosts”), helping to renew the ecosystem. There were also larger five-year infestations that occurred on a 20 to 40 year cycle. The current pine beetle “epidemic” in BC has gone on now for more than 20 years, with the pine beetle “observed in previously unrecorded numbers” over a much wider area

It is generally believed that climate change has help the pine beetle survive milder winters.

The study notes:

Successful establishment of mountain pine beetle on pure jack pine in northern Alberta has raised concerns that the mountain pine beetle will continue to expand its range into the vast boreal forest of jack pine that extends across North America from the Northwest Territories to the Atlantic Coast.

The teams concludes that one group of the beetles originated in southwestern BC perhaps from Whistler or Manning Park. Then the beetles spread north up the west coast of BC toward Houston “with rapid population size increases in central and northern BC and then dispersed long distances with prevailing winds toward the east and Alberta.”

Some of the beetles from southwestern BC appear to have taken a different route, moving more slowly eastward in the south of BC toward Crowsnest Pass area and then moving northward along the base of the Rockies, Janes said, adding. “Our research suggests that these two routes have then met in the middle again, around Valemount and that is why we see the genetic patterns across the landscape that we observed.”

Selective pressure

The second part of the research was answering the question of how the beetles were able to do this. How could they withstand the colder temperatures to spread further north and east?

To answer the scientists used the same genetic markers (single nucleotide polymorphisms) to conduct “selective sweeps” of the beetle genome. The sweeps look for unusual genetic markers that could indicate the beetles are under “selective pressure.”

The study looked at specific functions in the beetle: the genes that govern “actin filaments” that “control muscle contractions like shivering and moving wings”; “the synthesis of cholesterol that provides energy for metabolic activities” and transport of ions across cell membranes.

Normally, female pine beetles can only fly short distances to find a new host tree to lay eggs. They can travel longer distances if they are up in the tree canopy and are then carried by the wind. Stronger pine beetles that can fly longer distances show the threat is likely evolving.

The study concludes that Canadian Mountain Pine Beetle range expansion:

may continue as populations are currently exhibiting signals of selection. These signals suggest ongoing adaptation of metabolic and cellular processes that could potentially allow them to withstand colder temperatures, shift developmental timing and facilitate longer dispersal flights.

Janes said further research is required to fully validate and understand these signatures of selection, but it does suggest that the beetle is adapting and that is why it “may have been able to breach the Rocky Mountains”

Water and trees

Precipitation samples
Colorado scientists collected precipitation samples to determine their unique chemical fingerprints. ( Lindsay Bearup/Colorado School of Mines)
In Colorado alone, the mountain pine beetle has caused the deaths of more than 3.4 million acres of pine trees. The new research findings show the consequences of an obvious observation: Dead trees don’t drink water

The Colorado study asked how all those dead trees are changing stream flow and water quality?

“The unprecedented tree deaths caused by these beetles provided a new approach to estimating the interaction of trees with the water cycle in mountain headwaters like those of the Colorado and Platte Rivers,” said Reed Maxwell a hydrologist at the Colorado School of Mines.

Maxwell and colleagues have published results of their study of beetle effects on stream flows in this week’s issue of the journal Nature Climate Change.

As the trees die, they stop taking up water from the soil, known as transpiration. Transpiration is the process of water movement through a plant and its evaporation from leaves, stems and flowers.

The “unused” water then becomes part of the local groundwater and leads to increased water flows in nearby streams.

“Large-scale tree death due to pine beetles has many negative effects,” says Tom Torgersen of the US National Science Foundation’s Directorate for Geosciences and program director for the NSF’s Water, Sustainability and Climate program.

“This loss of trees increases groundwater flow and water availability, seemingly a positive,” Torgersen says.

“The total effect, however, of the extensive tree death and increased water flow has to be evaluated for how much of an increase, when does such an increase occur, and what’s the water quality of the resulting flow?”

Under normal circumstances, green trees use shallow groundwater in late summer for transpiration.

Red- and gray-phase trees–those affected by beetle infestations–stop transpiring, leading to higher water tables and greater water availability for groundwater flow to streams.

The Colorado study shows that the fraction of late-summer groundwater flows from affected watersheds is about 30 per cent higher after beetles have infested an area, compared with watersheds with less severe beetle attacks.

“Water budget analysis confirms that transpiration loss resulting from beetle kill can account for the increase in groundwater contributions to streams,” write Maxwell and scientists Lindsay Bearup and John McCray of the Colorado School of Mines, and David Clow of the U.S. Geological Survey, in their paper.

Dead trees create changes in water quality

“Using ‘fingerprints’ of different water sources, defined by the sources’ water chemistry, we found that a higher fraction of late-summer stream flow in affected watersheds comes from groundwater rather than surface flows,” says Bearup.

“Increases in stream flow and groundwater levels are very hard to detect because of fluctuations from changes in climate and in topography. Our approach using water chemistry allows us to ‘dissect’ the water in streams and better understand its source.”

With millions of dead trees, adds Maxwell, “we asked: What’s the potential effect if the trees stop using water? Our findings not only identify this change, but quantify how much water trees use.”

An important implication of the research, Bearup says, is that the change can alter water quality.

The new results, she says, help explain earlier work by Colorado School of Mines scientists. “That research found an unexpected spike in carcinogenic disinfection by-products in late summer in water treatment plants.”

Where were those water treatment plants located? In bark beetle-infested watersheds.

 

The TRIA project (a collaboration of researchers at the University of Alberta, University of British Columbia, University of Montreal, University of Northern British Columbia). The TRIA project investigates the physiology, genetics and ecology of all three players in the mountain pine beetle system – the pines (lodgepole and jack pine, and their hybrids), the beetle and the fungus (several types).

The Colorado study is funded by the National Science Foundation’s (NSF) Water, Sustainability and Climate (WSC) Program. WSC is part of NSF’s Science, Engineering and Education for Sustainability initiative.