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This month, George Tiley began his NC State appointment as an assistant professor of plant and microbial biology. Right before his Aug. 1 start date, Tiley and colleagues published a piece in the Proceedings of the National Academy of Sciences on the shifting nature of the way researchers think about evolution, particularly so-called reticulate evolution, which examines evolution in terms of "family webs" rather than "family trees."

The paper was part of a special journal called "Monitoring and Restoring Gene Flow in the Increasingly Fragmented Ecosystems of the Anthropocene," which brought together research from across the speciation genomics and conservation biology communities to address the pressing challenges of anthropogenic habitat fragmentation and biodiversity loss.

The Abstract spoke with Tiley about the paper.

The paper's title is 'Phylogenetic Networks Empower Biodiversity Research.' What are phylogenetic networks?

It is a really new concept in the sense that biologists have thought about hybridization (the process in which two organisms from different species or distinct populations interbreed) or gene flow (the transfer of genetic material from one population to another) between populations for a long time. Examples of this are sunflowers for their hybridization; a really classic example from grasses is wheat.

We've seen these ancient hybridization events that were also accompanied by whole-genome duplication, and this is a common mechanism by which we get really useful plants, whether we want to think about wheat or another big one from NC State—the sweet potato. But until fairly recently, and for good reasons, we thought about evolution as very treelike; this goes back to Darwin and views on shared ancestry.

One of the reasons we continue to use family trees, with plants especially, is because they are computationally convenient—they are mathematically convenient. Estimating trees from genetic data is a lot easier in terms of programming that structure and doing the computation behind it.

We've had big jumps in the last 20 years in probability theory that allowed us to say, "Here's the likelihood of a network," and that was accompanied with computational advances as well. Now we find ourselves revisiting a lot of biodiversity research with networks, where we know there is some history of gene flow between species.

In other words, we're replacing 'the tree of life' with 'the web of life?'

Exactly, and that's a term some people will use now. It's not a tree of life. It's a web of life to reflect these types of ancient gene-flow events in addition to gene flow that we might experience between modern-day populations. We try to distinguish between the two that you can have populations of the same species that exchange genes, and then you have these more ancient events that have often led to a lot of confusion in the tree of life, too.

If you went back to the study of evolution back in the 1990s, you would sequence a plant's chloroplast gene and get that family tree. You'd find some well-supported relationships and you'd find some weak ones. And then you'd say, well, as biotechnology advances, what we need is more data.

Now we sequence whole genomes. We have all the data there is, and we still find that—in the plant tree of life—there are some relationships that have a lot of uncertainty, despite having all the data. It's not just well, we need more data. There are other processes going on, and sometimes the web of life explains these reticulate processes, which can sometimes lead to a lot of clarification and insight about the evolution of important traits across plant groups.

How can these networks affect conservation of plants and animals?

Sometimes we'll find what we call a microendemic species. It seems to be distinct genetically; it might have some different traits. But there's a lot of consternation about whether hybrids deserve protection or not.

And this is sometimes what we find in research where you'll have these sort of narrow hybrid zones, and these species, by definition, have kind of a limited range, and if somebody were to do an assessment, you'd say, well, it has a small population size. It has a very small range. It's a distinct species. Are we dealing with something that has been an evolutionarily independent unit for a long time? Or is this something that represents a relatively recent hybridization event?

And it's not to say that hybrids don't deserve protection, but in conservation there are limited resources. There are decisions that need to be made. And this can be another tool that helps, say, conservation policy managers or other conservation groups set their priorities. And it's another piece of information that we think is really important, as genetic data becomes more and more integrated with extinction risk assessments.

How can these networks influence biodiversity research?

When we think about biodiversity, broadly, sometimes people will approach that from a context of what is the sort of alpha species diversity, if we had to count the number and abundance of named species in a given area. Others will approach that from a standpoint of phylogenetic diversity. How much evolution is in this space? How divergent are the paths on average? So, I think this can just be another clarifying layer to that in terms of understanding.

When we have, say, a high species count in an area, how many of those might not represent what we would call an evolutionarily distinct unit where we get these more ephemeral relationships popping up?

Because one thing that we can learn from studying reticulate processes is that extinctions do happen as well, and that tends to be a common mechanism for these relationships, where you'll have hybridization, you have back crossing to the parent. The hybrids are not as selectively advantaged as their parental species in a given area, but some signatures of gene flow remain.

So, I think one thing we want to do is just make sure researchers are aware that these are viable tools to use now. For a long time, they were kind of disregarded. Researchers would say, "We understand these processes happen. But it's not computationally feasible. So we're not going to use these tools." We want to make sure people know that these are tools that are available to them when they might be appropriate to use.

Is there a biodiversity example in the Southeast that people would recognize?

A really good example that we can think about in terms of biodiversity in North Carolina is the pitcher plant. They are really, really cool, hyper-diverse in terms of their group. But we are aware that there have been these types of ancient gene-flow events, and understanding their evolution might clarify the species distributions and the processes that gave rise to their current diversity, and also how some people might set conservation statuses for them.

Where do you see your future work trending?

We're showing that these are useful tools for studying biodiversity. But there's a bit of a disconnect between what's been happening in this fundamental evolutionary biology space, and how do we connect that with, say, plant breeders or people who really want to understand the genetics of agriculturally important traits? Because, again, understanding these particular evolutionary processes is important for understanding a lot of our agriculturally and industrially useful crop plants.

And that's where I see my lab going. How do we take what we've done so far and maybe retool some of that to be useful for finding, perhaps, the genes that are underlying these ancient hybridization events that could be useful for plant breeders as well? How do we take this and make it into a useful tool that can help solve really challenging problems in evolutionary biology?