New analysis techniques transforming the study of evolution and genetics

It’s clear to anyone that an African elephant and a garden snail are different species, but the lines blur around closely related animals. In fact, many biologists suggest there isn’t a clear-cut definition of what a “species” really is.

It turns out that speciation is an even more complicated and messy process than previously thought.

A recent study, published in the Proceedings of the National Academy of Sciences (PNAS), looked at the separation of polar bears and brown bears into distinct species, discovering that the process of speciation is not as clear cut as we might like to believe.

Scientists have known for some time that the delineation of polar and brown bears did not stop them from mating with each other. The results presented in the paper involve an expanded dataset – including genetic sequencing of an ancient polar-bear tooth – to gain insights into the split between the species.

The research has implications beyond bears. The findings have similarities to discoveries about our own species’ evolution, and speciation more broadly.

“What is a species? That’s the question,” laughs Peter Cowman, senior curator of biosystematics at Queensland Museum Network, and co-appointed senior researcher at the Centre of Excellence for Coral Reef Studies at James Cook University. “A species is a concept, and it’s important to understand that it’s a human construct. We need species to understand the world that we live in and the biodiversity of our planet, but nature and evolution don’t necessarily care what we think a species is. As scientists we have different concepts of what a species is.

“A lot of people use biological species concept – the ability of two individuals to successfully produce viable, fertile offspring – but that’s not always the case. The polar bear and brown bear, although it’s uncommon, are involved in hybridisation across the two species.

“A lot of people use biological species concept – the ability of two individuals to successfully produce viable, fertile offspring – but that’s not always the case.”

Peter Cowman, Queensland Museum Network

“Because I’m a phylogeneticist, or bioinformatician, I tend to lean towards what we call the ‘phylogenetic species’ concept. This is all about using family trees or molecular phylogenetic trees to understand how closely related individuals are within a population or across species. But that doesn’t always give the right answer, either.”

Cowman told Cosmos that the PNAS paper highlights how new analytic tools are transforming the way in which we study evolution and genetics. In turn, this provides opportunities for us to better understand the basics of what a species is and where organisms fit in the ecosystem.

“We really are getting into the science-fiction end of things,” says Cowman. “We’ve got a desktop sequencer that can sequence a genome in 48 hours or less. It’s the same size as an iPhone. The data we’re producing now is what future technology will be based on. All you have to do is look at the response to the COVID pandemic – we can get genetic data and analyse it very quickly. Overnight, you get new trees for different COVID strains and understanding how new strains are popping up.

“It’s the same in biodiversity analysis. All these things add to how we can analyse this data really quickly and understand how different species are interacting, and especially how they’re going to change under the climate-change scenario.

“Museums are a goldmine for these types of analysis, especially with this changing technology. Like analysing DNA from fossils, we’re able to analyse DNA from samples that are collected 80 to 100 years ago. We’re able to get DNA that can solve different puzzles.”

“We’re able to analyse DNA from samples that are collected 80 to 100 years ago. We’re able to get DNA that can solve different puzzles.”

Peter Cowman, Queensland Museum Network

An example of the power of new analysis techniques, particularly involving ancient DNA, is shown in our developing understanding of our own evolution.

Scientists once thought a common ancestor simply split into modern humans and Neanderthals. But researchers have found Neanderthal DNA in modern Eurasian people. This implies that modern human populations received an influx of genes from Neanderthals at some point in their shared evolutionary history.

The researchers of the PNAS paper, which included, scientists from the US, Finland, Norway, Denmark, Singapore and Mexico, explain that it was only later that scientists realised that this genetic intermingling also supplemented Neanderthal populations with modern human genes. In other words, interbreeding is complex and not necessarily one way.

“The formation and maintenance of species can be a messy process,” says study co-author Charlotte Lindqvist, associate professor of biological sciences at the University at Buffalo and a bear genetics expert.

“We find evidence for interbreeding between polar bears and brown bears that predates an ancient polar bear we studied,”

Charlotte Lindqvist, University at Buffalo

“What’s happened with polar bears and brown bears is a neat analogue to what we’re learning about human evolution: that the splitting of species can be incomplete,” she says. “As more and more ancient genomes have been recovered from ancient human populations, including Neanderthals and Denisovans, we’re seeing that there was multidirectional genetic mixing going on as different groups of archaic humans mated with ancestors of modern humans. Polar bears and brown bears are another system where you see this happening.”

“We find evidence for interbreeding between polar bears and brown bears that predates an ancient polar bear we studied,” Lindqvist adds. “And, moreover, our results demonstrate a complicated, intertwined evolutionary history among brown and polar bears, with the main direction of gene flow going into polar bears from brown bears. This inverts a hypothesis suggested by other researchers that gene flow has been unidirectional and going into brown bears around the peak of the last ice age.”

Sixty-four modern polar and brown bear genomes were studied by the researchers.

“It’s exciting how DNA can help reveal ancient life history,” says co-first author Kalle Leppälä, a mathematical sciences researcher from Finland’s University of Oulu. “Gene flow direction is harder to determine than merely its presence, but these patterns are vital to understanding how past adaptations have transferred among species to give modern animals their current features.”

The genomes included several new ones from Alaska, where both species are found. Also analysed was a new, more complete ancient polar bear genome. DNA was extracted from a tooth attached to a subfossil (not fully fossilised) jawbone found in Norway’s Svalbard archipelago. The bear would have lived 115,000 to 130,000 years ago.

Cowman was particularly impressed with the inclusion of the subfossil’s genome in the study, which he says is “very rare”.

“Normally we analyse contemporary genetic samples from living species, living lineages, whereas here they’ve managed to include an ancestral, a fossil lineage. And it really highlights how speciation is on a continuum.

“It’s not just a switch where two populations, over a certain amount of time, become separate species overnight. It really shows that they can interact and when they do come back into contact, there is the possibility for the sharing of genetic material.

“Gene flow direction is harder to determine than merely its presence, but these patterns are vital to understanding how past adaptations have transferred among species to give modern animals their current features.”

Kalle Leppälä, University of Oulu

“I’m quite jealous! I’ve got a background in studying fish and corals, and it would be nigh on impossible to get similar data from a fossil fish! This comes with the advances that we’re seeing in these genetic methods.

“Being able to get viable DNA material from a fossil 10 years ago would have been nearly unheard of. It’s not just these fossils that can be analysed – think of all of the specimens in museums that are preserved in formalin or new preservation techniques. Getting ancestral DNA is a new field and revolutionised how we study these patterns of speciation.”

Using the expanded dataset, the team estimated that polar bears and brown bears began to separate into distinct species between 1.3 and 1.6 million years ago. Lindqvist says that interbreeding and limited fossil evidence have made this timing hard to pinpoint.

Polar bears, soon after becoming a separate species, saw a dramatic decline in numbers, leading to a prolonged genetic bottleneck. The new research suggests that this has led to much less genetic diversity than is seen in brown bears.

The researchers found a remarkably similar story between the bear species as that between modern humans and Neanderthals. Their analysis found evidence of hybridisation in the genomes of both polar bears and brown bears. The influx of genetic information from the other species is particularly strong in polar bears. Earlier research suggested this was the other way around.

The team believes its findings may be of interest in studies concerned with the impact of climate change on threatened species.

Polar bears, adapted to the icy Arctic north, have been found to capture genetic material from brown bears, which are adapted to life in lower, warmer latitudes. As global warming sees a decline in Arctic sea ice, the two bear bears may intermingle more frequently as their ranges overlap. Lindqvist says this makes studying their shared evolutionary history all the more intriguing.

“Population genomics is an increasingly powerful toolbox to study plant and animal evolution and the effects of human activity and climate change on endangered species,” says team leader Luis Herrera-Estrella, from Mexico’s National Laboratory of Genomics for Biodiversity and Texas Tech University in the US. “Bears don’t provide simple speciation stories any more than human evolution has. This new genomic research suggests that mammalian species groups can hide complicated evolutionary histories.”

“The implications of the results are that this ancestral polar bear lineage may have been able to get some novel gene from this expanding boreal brown bear and potentially that helped it to adapt to a changing climate,” says Cowman. “And the implication is that if it’s done it once, it can do it again.

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“That has implications across a lot of other species. But I think it’s important to understand that we’re using the past to try to predict the future a lot here. But it shows that there is this interaction between species and it can have all these different outcomes that we may not expect.”

Cowman believes the techniques displayed in the PNAS paper are reflective of a development in our ability to delve into these problems of speciation, though he suggests that speciation remains an unsolved mystery. “I guarantee you if one day, scientists did unite under a common or universal species concept, nature and evolution would say “hold my beer” and show us something completely different,” he says. “I think for me, that’s the beauty of it all. It’s so much fun, and it can be frustrating at times, to study evolution and speciation.”