Into the 'Mammalverse': Genomics advances unlock secrets hidden within mammals' genetic blueprints

Article from ASU professor explores future, implications of mammal genomics

May 24, 2023

An Arizona State University researcher recently co-authored a perspective article as part of the special section “Zoonomia” in the renowned journal Science. School of Life Sciences Assistant Professor Nathan Upham and Michael Landis, assistant professor at Washington University, explore the implications and main advances of six publications by the Zoonomia Consortium on evolutionary history and give their view on the future of mammal genomics.

“I think this article expertly highlights some of the most important features of the largest release of mammalian genomes ever,” said Melissa Wilson, an expert in genetics and associate professor in the School of Life Sciences. Portrait headshot of Assistant Professor Nathan Upham with greenery behind him. ASU Assistant Professor Nathan Upham published a perspective article that explores the implications and main advances of six publications by the Zoonomia Consortium on evolutionary history. Photo courtesy Nathan Upham

The “mammalverse” – as referred to by Upham – encompasses the universe of diverse mammal species, ecologies and genomes to be investigated. Mammal genomics — studying the genes and DNA of mammals — is a fast-growing area of research that can help us learn more about how mammals have evolved and are related to each other, and even discover new ways to improve human and animal health.

Mammals include monkeys, cats, whales, mice, bats and humans. This fascinating group of species has complex genetic codes that determine their characteristics and traits.

Geneticists use advanced techniques and technologies to examine the DNA sequences of different mammals and compare how their genes work. Genomic datasets containing hundreds of mammals’ DNA (or RNA) sequences can provide critical information about evolutionary relationships, genetic diversity and potential health implications.

The Zoonomia Consortium’s new dataset of 240 species’ genomes has unlocked new research at the molecular, individual and population levels among mammals. In their perspective article, Upham and Landis explore such publications and provide additional insights into the field.

“The alignment of whole genomes for these 240 species of placental mammals shows how much we can learn about humans by studying nonhumans,” Upham said.

“We can now better explore all the mammal diversity that is alive today on Earth (6,500 species), including their wide variety of ecological traits (flying to burrowing to fully aquatic) and genomic diversity (transposable elements, enhancers, transcription factors and protein-coding genes). All of this diversity is now beginning to be explored using datasets and tools like those presented in these Zoonomia articles,” he said.

Various cutting-edge techniques and technologies, including high-throughput sequencing, comparative genomics and computational analyses, have allowed scientists to explore the vast complexities of mammalian genomes, including previously unexplored regulating elements.

“The sequencing of genomes from wild mammal species is far more feasible now than it was 20 years ago, thanks to new ultra-long read sequencing technologies that are now able to traverse the highly repetitive DNA regions that are abundant in mammal genomes,” Upham said. As one article in the package found, this “dark matter” of mammal genomes makes up approximately 25–65% of DNA content for typical species.

Shown is the consensus timescaled phylogeny from Upham et al. (2019) and genome data downloaded from NCBI on 9 February 2023.

Genomes for 675 mammal species relative to the Mammalia phylogenetic tree of 5,911 living species shows the disproportionate representation of large-bodied species related to cats, dogs, whales, monkeys and some marsupials. Shown is the consensus time-scaled phylogeny from Upham et al. (2019) and genome data downloaded from NCBI on Feb. 9. Photo courtesy Nathan Upham

“As a result, studying the diversity and abundance of different types of transposable elements is now feasible for the first time,” Upham said.

Despite all the significant advances in the field of mammal genomics, there are still several limitations.

“The alignment of these 240 genomes (from the Zoonomia Consorium’s new dataset) is a big advance, but they highlight how little is actually known about the mammalverse of 6,500 living species’ genomes. Only 675 species of mammals have yet had their genomes sequenced, and many of those are low-quality assemblies," Upham said.

In addition, he said there is a large bias in which species have been sequenced, mostly large-bodied and high-latitude species (e.g., species related to cats, dogs, whales, cattle and monkeys). As a result, there is a need to sequence small-bodied bats, rodents and shrews to even out the sampling of genomes.

“Future sequencing of genomes in small-bodied mammals will be valuable, as these species are expected to evolve more rapidly because of large population sizes and short generation times. However, both dynamics can be flipped when small species are range restricted (for example, on mountains or islands) or long lived (such as in some bats like Myotis species), which underscores their value for comparative genomic studies,” Upham and Landis wrote in the article.

Nonetheless, the article shows that the field holds immense potential for enhancing our understanding of mammalian biology, evolution and health, ultimately paving the way for advancements in medicine, conservation and evolutionary biology.

Anaissa Ruiz-Tejada

Graduate Science Writer, School of Life Sciences

aruiztej@asu.edu

Words matter: How researchers can avoid stigmatizing language

A man in a white doctors coat types on a laptop. Only his hands and part of his arms are visible. There is a stethoscope visible in the foreground.

Word choice matters a lot when it comes to research. That’s the main takeaway from a new article co-authored by Arizona State University Assistant Professor Angel Algarin and published in Health Communication.“Researchers in any field should be cognizant of the language they’re using to describe the people they study so they don’t inadvertently add to the use of stigmatizing language,” s...

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Words matter: How researchers can avoid stigmatizing language

May 24, 2023

“Researchers in any field should be cognizant of the language they’re using to describe the people they study so they don’t inadvertently add to the use of stigmatizing language,” said Algarin, who teaches in the Edson College of Nursing and Health Innovation. A man in a white doctors coat types on a laptop. Only his hands and part of his arms are visible. There is a stethoscope visible in the foreground. A content analysis of HIV-related stigmatizing language found more than 26,000 uses across publications in a 10-year period. Photo courtesy Shutterstock Download Full Image

For the article, Algarin and his co-authors performed a content analysis of HIV-related stigmatizing language published in scientific literature from 2010 to 2020.

They found 26,476 peer-reviewed articles that used variations of the stigmatizing term “HIV/AIDS-infected.” More than a third of these articles came from the United States. And the journal that used the stigmatizing language the most was one that focused on general science and medicine.

“The use of stigmatizing language in science is concerning, as the words we use are read by health care professionals, policymakers and journalists, who in turn use this same language when discussing topics surrounding HIV because they trust that we are the experts,” Algarin said.

The consequences of using terms that stigmatize entire groups of people are well documented. As a social epidemiologist and interventionist, Algarin’s previous work has focused on the impact of stigma on people living with HIV.

In his 2020 articles published in AIDS and Behavior and AIDS patient care and STDs, he found that people living with HIV who experienced higher levels of stigma experienced poorer mental health and HIV care outcomes.

Elijah Palles has experienced stigmatizing language firsthand in peer-to-peer conversations and in health care settings. Shortly after he was diagnosed with HIV, he said he encountered a case manager who was “shocked” that someone “like him” with a job, car and house could be living with HIV.

“I felt stupid because I do have resources and I do know better, but I beat myself up for a while thinking she’s right, I’m not the typical person who would contract this, and then I had to say, 'Well no, I’m just like every other person who contracts this.' So, that interaction fed into my own internalized stigma for a while,” Palles said.

As a Valleywise Health Voices of Hope Speakers Bureau member and Maricopa County Department of Public Health Positively You! Ambassador, Palles regularly shares his story to help raise awareness about available resources, combat misinformation and reduce HIV-related stigma. Recently, he spoke with students at Edson College as part of a public health presentation by the county.

He said Algarin’s work on this issue is important and much needed.

“They are in the driver’s seat of the conversation, and if you’re using a term like 'HIV-infected,' that is very stigmatizing because you’re saying someone is infected and that goes back to this idea of clean versus dirty,” Palles said.

The point of Algarin’s article wasn’t to call anyone out, but instead to highlight the real-world impact of researchers’ work and more specifically how the words they use affect people.

“I understand that people engaged in research may not intentionally be using stigmatizing language, but we should see this as an opportunity to do better,” Algarin said.

David Coon, Edson College associate dean of research initiatives, support and engagement, said there is always room for improvement. And one of the key ways to avoid harmful terminology is to connect with the community.

“At ASU and Edson College, we take our commitment to social embeddedness seriously. So, it’s imperative that we listen to the voices of the communities we work with and do our best at every step in terms of the language we use in how we communicate with them and about them. In doing so, we respect their choices about how they self-identify and want to be represented in research,” Coon said.

Raising the issue has resulted in some positive changes. According to the article, the use of stigmatizing language specific to HIV/AIDS started to decrease after the Joint United Nations Programme on HIV/AIDS released an update to HIV terminology guidelines.

In addition to referencing language guides on appropriate terms to use, Algarin said there are three specific actions researchers can take to reduce the stigma in scientific literature:

Ensure the use of appropriate terms in the manuscripts you’re writing.
Suggest the use of non-stigmatizing terms when serving as a peer reviewer.
If you are an editor, implement a non-stigmatizing terminology policy in the instructions for authors.

“Implementing these practices can show the communities that we work with that we are not only listening, but we are actively making changes to respect preferred, non-stigmatizing terminology. It is my hope that making these changes brings us one step closer to ending the perpetuation of stigma in science,” Algarin said.