“We’ve shown that by using high quality transcriptomic data we can answer a long-standing question to the best of our current techniques,” said Dr. Konstantin Khalturin, Staff Scientist in OIST’s Marine Genomics Unit and first author of the paper published in Science Advances.

A genome is the full set of genetic information found in every cell. It is subdivided into genes. These genes are made up of DNA base pairs and each gene contains the instructions needed to create a protein, and thus leads to the proper care and maintenance of a cell. For the instructions to be carried out, the DNA must first be transcribed into RNA. A transcriptome is the result of this, like the reflection of a genome but written in RNA base pairs rather than DNA.

This genetic information differs among species. Those who are closely related have very similar genetic information, while a greater evolutionary distance results in more genetic differences. By using this data, researchers have improved our knowledge of animal evolution, but some questions still prove difficult to answer.

As Kamptozoa and Bryozoa are closely related to mollusks, annelids, and nemertea, small mistakes in the dataset, or missing data, can result in an incorrect placement on the evolutionary tree. Furthermore, while collecting these tiny animals, it’s easy to pick up other organisms, such as algae, that contaminate the sample. Dr. Khalturin highlighted that they were careful to avoid contamination and later screened their dataset for RNA of algae and small animals to remove any that might have come from them.

In total, the researchers sequenced the transcriptome of four species of Kamptozoa and two species of Bryozoa, but to a far higher quality level than had previously been achieved. While past datasets had completeness of 20-60%, in this study, the transcriptome completeness was over 96%.

Using these transcriptomes, they predicted proteins and compared them to similar data of 31 other species, some of which were closely related to Kamptozoa and Bryozoa, such as clams and bristleworms, and others which were more distant, such as frogs, starfish, insects, and jellyfish. The high-quality datasets meant that they could compare many different genes and proteins simultaneously. Dr. Khalturin credited the powerful computational capabilities that the researchers could access at OIST.

“Our main finding is that the two phyla belong together,” said Dr. Khalturin. “This result was originally proposed in the 19th century by biologists who were grouping animals based on what they looked like.”

While Dr. Khalturin stated that this question had now been answered to the best ability available, he also highlighted that the dataset could answer other fundamental evolutionary questions — such as the more precise location of mollusks and annelids on the tree of life, and how life diversified.

The paper in the journal Science Advances brought together experts in salmon ecology, watershed science, mining impacts and mining policy to integrate knowledge across research fields that often work independently from one another. Led by UM researchers at the Flathead Lake Biological Station, the team found past and present mining pressures are extensive across the region and often overlap with important populations of salmon, trout and char.

“Our paper highlights the mosaic of more than 3,600 active and abandoned mines sitting amongst some of the most valuable fish habitat in western North America,” said Chris Sergeant, an FLBS research scientist and the paper’s lead author. “The largest of these mines processes around 160,000 metric tons of earth every day.”

Sergeant said not all mines pose the same level of risk, but their review revealed that harm from mining can be severe and long-lasting. The extent of mining pressures on these watersheds underscores the importance of accurately assessing risk to water, fish and communities.

The study reviewed the ecological complexity of rivers and how mines can impact culturally and economically important fish species such as salmon by contaminating waters with heavy metals, burying stream habitat and diverting water for processing ore. When not managed properly, these cumulative impacts can be impossible to reverse and degrade landscapes for decades to centuries.

“Unfortunately, in some cases, we are learning the hard way that mines can have profound impacts on aquatic ecosystems, leaching far down the watershed from the actual mine site, at scales that were not anticipated in the original impact assessment,” said Erin Sexton, a paper co-author and FLBS senior scientist. “For example, impacts from the Elk Valley coal mining complex in southeast British Columbia have been documented over 155 miles downstream of the mines, crossing the U.S.-Canada international boundary.”

The authors emphasize that up-to-date and transparent science has an important role to play in managing the potential impacts of mines. Emerging science on salmonid ecology, cumulative effects and how climate change is altering these landscapes can improve risk assessment of mines.

The authors highlighted four key issues that will be foundational to modern, science-based risk assessment and mitigation: understanding stressor complexity and uncertainty, accounting for cumulative effects of mining activities across a mine’s life cycle, developing realistic mitigation strategies and recognizing the potential for climate change to magnify risk.

“Emerging science is revealing the complex realities of how salmon watersheds work in this era of climate change and also the many different risk pathways posed by mines,” said co-author Jonathan Moore of Simon Fraser University in British Columbia. “Informed decision-making will need risk assessments that embrace these challenging topics, ranging from cumulative effects to climate change.”

While a low-carbon future will depend to some extent on mined minerals, it is important to consider whether current and future mining projects are operated in such a way that protects fish, water and well-functioning watersheds.

“Our paper is not for or against mining, but it does describe current environmental challenges and gaps in the application of science to mining governance,” Sergeant said. “We identify a need and opportunity for strong science-based and transparent risk assessment, as well as the integration of goals and values of impacted communities. In the end, it is possible that some specific places might just be too valuable to risk with major mines.”

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