Taxonomy, the study of how living organisms relate to one another as species, has been around since the 1700s. Though scientists and philosophers have long debated what makes a species a species, taxonomists treat each species as a group of organisms that share common biological characteristics.

Discovering and describing new species is essential to biology researchers and conservationists because they use species as a unit of analysis. Species are also economically important to agriculture, hunting and fishing, and have special legal status, such as under the U.S. Endangered Species Act.

Despite this, scientists have been able to formally name and describe only an estimated 10% of species on the planet, based on discovery trends over the years.

This gap in knowledge is known as the Linnean shortfall. It remains unclear whether poor research methodology, disagreements on how to define a species, or other factors are to blame for this gap.

We are scientists in evolutionary biology, and figuring out ways to better identify species is central to our research. Using genetic analysis and artificial intelligence, we were able to disentangle hidden species that have been lumped together in a single group and predict where and what types they might be. Our findings also pinpoint a potential cause for this shortfall in species identification: an underinvestment in the science of taxonomy.

Hidden species remain to be discovered

For this study, we chose to focus on mammals. Because of their relatively large size and importance to people as a source of food, companionship and entertainment, we predicted that it was more likely that a large proportion of mammalian species have been already been identified.

Our first task was to identify known species that might actually contain two or more species. To do this, we analyzed 1 million gene sequences from 4,300 named species, identifying clusters of sequences that showed high genetic diversity and fitting the data to an evolutionary model.

We found potentially hundreds of hidden species that were previously classified as a single group. This finding was expected, as it mirrors results from previous studies, albeit on a larger scale.

Where and what are these hidden species?

Once we identified the presence of these potentially hidden species, our second task was to determine what specific traits they have in common. To do this, we used a data science technique called random forest analysis, a form of machine learning that draws information from a large number of different variables in order to make a prediction about a particular outcome. It’s similar to the technique that Netflix uses to suggest shows you might be interested in watching.

In our case, we wanted to predict whether a known species contained hidden species. The predictor variables we used spanned environmental factors, such as the climate of common mammalian habitats, and species-specific factors, such as physical traits, geographic range, reproductive and survival patterns. We also included research-based factors on the techniques scientists used to conduct their studies. In total, we collected some 3.8 million data points to build our model.

Based on our model, we found that three types of predictor variables stood out the most.

The first type comprised attributes of the species itself, such as body mass and geographic range. These results suggest that small mammals with relatively large ranges are more likely to have hidden species. This makes sense as, all things being equal, it is more difficult for scientists to recognize physical differences in smaller animals than larger ones.

The second type was climate – there are likely to be more hidden species in wet, warm areas with a large difference in day and night temperatures. This likely reflects the fact that tropical rainforests tend to have very high levels of mammalian diversity.

The third type was research effort, including the geographic dispersion of samples in museum collections and the number of recent publications mentioning the scientific name of a known species. This implies that researchers are generally effective in identifying new mammals, as how much attention the scientific community has focused on a specific mammal predicts whether that creature is identified. This is supported by how the general characteristics we’ve identified match new mammalian species described over the past 30 years, as well as the fact that our model recognizes areas that scientists are already investigating for hidden species.

Unknown species face extinction

At a time when Earth is facing its greatest extinction crisis since an asteroid killed off the dinosaurs, we believe that identifying and describing the many undiscovered species on Earth is crucial to aiding the preservation of its biodiversity.

Even though our study still found a large number of mammals waiting to be discovered, mammalian diversity is already relatively well captured compared with that of other species. We found that roughly 80% of existing mammal species have already been described, a proportion far higher than in nonmammal groups with even higher diversity such as beetles or mites.

Discovering and describing new species, as with all scientific research, takes a village. Natural history museums are largely responsible for collecting the raw data we analyzed, and genetic and biodiversity databases provided the infrastructure to make it accessible to us. A culture of information sharing among peers and large computer networks supported the thousands of hours of computation time we needed. Our work was made possible only by ongoing investments in taxonomic research.

Biodiversity scientists are racing to better understand the processes that create and maintain biodiversity while in the midst of the planet’s sixth mass extinction, one that is entirely caused by human actions. Taxonomists face the challenge of describing the species around us before they go extinct. As our findings suggest, there is still a long way to go.

Danielle Parsons, PhD Candidate in Evolutionary Biology, The Ohio State University and Bryan Carstens, Professor of Evolutionary Biology, The Ohio State University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

A new omicron subvariant of the virus that causes COVID-19, BA.2, is quickly becoming the predominant source of infections amid rising cases around the world. Immunologists Prakash Nagarkatti and Mitzi Nagarkatti of the University of South Carolina explain what makes it different from previous variants, whether there will be another surge in the U.S. and how best to protect yourself.

What is BA.2, and how is it related to omicron?

BA.2 is the latest subvariant of omicron, the dominant strain of the SARS-CoV-2 virus that causes COVID-19. While the origin of BA.2 is still unclear, it has quickly become the dominant strain in many countries, including India, Denmark and South Africa. It is continuing to spread in Europe, Asia and many parts of the world.

The omicron variant, officially known as B.1.1.529, of SARS-CoV-2 has three main subvariants in its lineage: BA.1, BA.2 and BA.3. The earliest omicron subvariant to be detected, BA.1, was first reported in November 2021 in South Africa. While scientists believe that all the subvariants may have emerged around the same time, BA.1 was predominantly responsible for the winter surge of infections in the Northern Hemisphere in 2021.

The first omicron subvariant, BA.1, is unique in the number of alterations it has compared to the original version of the virus – it has over 30 mutations in the spike protein that helps it enter cells. Spike protein mutations are of high concern to scientists and public health officials because they affect how infectious a particular variant is and whether it is able to escape the protective antibodies that the body produces after vaccination or a prior COVID-19 infection.

BA.2 has eight unique mutations not found in BA.1, and lacks 13 mutations that BA.1 does have. BA.2 does, however, share around 30 mutations with BA.1. Because of its relative genetic similarity, it is considered a subvariant of omicron as opposed to a completely new variant.

Why is it called a ‘stealth’ variant?

Some scientists have called BA.2 a “stealth” variant because, unlike the BA.1 variant, it lacks a particular genetic signature that distinguishes it from the delta variant.

While standard PCR tests are still able to detect the BA.2 variant, they might not be able to tell it apart from the delta variant.

Is it more infectious and lethal than other variants?

BA.2 is considered to be more transmissible but not more virulent than BA.1. This means that while BA.2 can spread faster than BA.1, it might not make people sicker.

It is worth noting that while BA.1 has dominated case numbers around the world, it causes less severe disease compared to the delta variant. Recent studies from the U.K. and Denmark suggest that BA.2 may pose a similar risk of hospitalization as BA.1.

Does previous infection with BA.1 provide protection against BA.2?

Yes! A recent study suggested that people previously infected with the original BA.1 subvariant have robust protection against BA.2.

Because BA.1 caused widespread infections across the world, it is likely that a significant percentage of the population has protective immunity against BA.2. This is why some scientists predict that BA.2 will be less likely to cause another major wave

However, while the natural immunity gained after COVID-19 infection may provide strong protection against reinfection from earlier variants, it weakens against omicron.

How effective are vaccines against BA.2?

A recent preliminary study that has not yet been peer reviewed of over 1 million individuals in Qatar suggests that two doses of either the Pfizer–BioNTech or Moderna COVID-19 vaccines protect against symptomatic infection from BA.1 and BA.2 for several months before waning to around 10%. A booster shot, however, was able to elevate protection again close to original levels.

Importantly, both vaccines were 70% to 80% effective at preventing hospitalization or death, and this effectiveness increased to over 90% after a booster dose.

How worried does the US need to be about BA.2?

The rise in BA.2 in certain parts of the world is most likely due to a combination of its higher transmissibility, people’s waning immunity and relaxation of COVID-19 restrictions.

CDC data suggests that BA.2 cases are rising steadily, making up 23% of all cases in the U.S. as of early March. Scientists are still debating whether BA.2 will cause another surge in the U.S.

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Though there may be an uptick of BA.2 infections in the coming months, protective immunity from vaccination or previous infection provides defense against severe disease. This may make it less likely that BA.2 will cause a significant increase in hospitalization and deaths. The U.S., however, lags behind other countries when it comes to vaccination, and falls even further behind on boosters.

Whether there will be another devastating surge depends on how many people are vaccinated or have been previously infected with BA.1. It’s safer to generate immunity from a vaccine, however, than from getting an infection. Getting vaccinated and boosted and taking precautions like wearing an N95 mask and social distancing are the best ways to protect yourself from BA.2 and other variants.

Prakash Nagarkatti, Professor of Pathology, Microbiology and Immunology, University of South Carolina and Mitzi Nagarkatti, Professor of Pathology, Microbiology and Immunology, University of South Carolina

This article is republished from The Conversation under a Creative Commons license. Read the original article.