Sunday, 21 June 2026

The Genomics of Yellow Bats

In terms of species, bats are the second-largest order of mammals, after the rodents. New species are identified all the time, due in part to the relative difficulty of closely examining night-flying mammals, many of which sleep in hard-to-access caves. The current total stands at over a thousand, representing over 20% of all known mammal species. 

Within this huge group, there is, perhaps, rather more diversity than many people realise. While bats have probably not received the same level of attention as some other mammal groups, scientists have nonetheless long attempted to disentangle the relationships between all these subgroups. (Also, when I say they have received less attention, there's a mammal-centric bias here; it's probably still a lot better than, say lizards, let alone millipedes or the like). 

In the past, we identified different species by their physical appearance and, with bats, we have the added ability to examine differences in their ultrasound calls. While we used this information to make some inferences about which bats might be more closely related to others, there were limits as to how much we could do this without relying on mere guesswork. Today, of course, we have genetic analysis, looking at how invisible changes have occurred in genes as animals evolved, tracing relationships we could never see before. Over the last two decades, this has continued to improve as we become able to sample larger and larger sets of genes and use increasing computing power to spot common patterns in the correspondingly vast databases we build up.

These sorts of analyses have enabled us to confirm that the 21 recognised families of bat are, indeed, distinct evolutionary lineages, and how they relate to one another. This has helped us understand how and when echolocation evolved, with most modern studies suggesting that echolocating bats do not share a unique common ancestor. (Thus, it either evolved twice or one subgroup later lost the ability.)

At a higher level, we have been able to determine how bats relate to other mammals. The general consensus here is that they are something of a side branch, splitting off from the group that would later lead to both carnivorans and hoofed mammals before they even split from each other.

At the opposite end of the scale, however, things can often be more intractable. Twenty years ago, when we could only compare single genes across multiple species, this wasn't such an issue. But improved modern methods, while promising more accurate detail, produce correspondingly more data, making them hard to compare across a large group. This is especially true of the vesper bat family, partly because it's the largest of all the bat families, but also because it underwent a rapid burst of diversity around 35 million years ago, at the dawn of the Oligocene. Such rapid changes are difficult to disentangle, since the key thing you want to know is what order they happened in - and they almost (but not quite) happened all at once.

However, it is possible to perform these sorts of analyses on smaller numbers of closely related species. This provides a different kind of information than that we get from the "big picture" studies of how families and orders relate. Instead, it can reveal how species responded to climatic changes such as the Ice Ages, and how geography, dispersal behaviour, and vicarious events led to them being what (and where) they are now. 

While it isn't the first of its kind, one such study was published in April, looking specifically at a group commonly known as the yellow bats. There is some debate as to exactly how these particular bats should be classified. We know that they are distinct evolutionary group, more closely related to each other than to anything else, and we also know that their closest relatives are the red bats (Lasiurus spp.)

The argument purely concerns whether they are different enough from the red bats to be given their own genus or not. While the case has been made, so has the counter-argument that there's just no need, and, as of this writing, this is the stance taken by sources such as the American Society of Mammalogists and the Batnames Database, and that I will therefore be using here.

That aside, what we can agree is that there are four currently recognised species of yellow bat. The northern yellow bat (Lasiurus intermedius) lives in southern and eastern Mexico and along the southern coastal regions of the US from Texas to South Carolina, with two isolated populations further north along the Atlantic seaboard, the most northerly reaching the outskirts of New York city. The western yellow bat (Lasiurus xanthinus) inhabits northern and central Mexico and the border regions of the US as far north as Los Angeles. The southern species (Lasiurus ega) is the most widespread, being found through southern Mexico, Central America, Colombia and Peru west of the Andes and almost the whole of the rest of the continent on the eastern side, reaching as far south as northern Argentina. 

These were all discovered and named in the 19th century, although the western yellow bat was not raised to full species status until 1988. More recently, an additional, rarer species, the Cuban yellow bat (Lasiurus insularis), being split off from the northern species in 1995 and living only in its eponymous island country. They are all fairly regular-looking bats aside from their yellowish fur, and live in forests and patches of semi-arid woodland, where they roost in trees during the day - most often palm trees or amongst Spanish moss, although it depends exactly where they live. They feed on bugs, flies, beetles, and other flying insects.

The researchers took samples from 125 specimens stored in natural history museums from across the bats' ranges and looked at sequences across the genome, allowing for more thorough coverage than had been possible with earlier methods. They then used specialised software to analyse the differences between the samples, making it possible to build up a family tree and, by calibrating against the known age of relevant fossils, provide an estimate of when different branches of that tree appeared.

The overall picture this produced matched that from most earlier studies, with the Cuban and northern species being the most closely related. Even this much is a positive, however, since a 2020 study had seemed to indicate that the Cuban yellow bat couldn't be a distinct species after all. By sampling a wider section of the genome to obtain a complete picture, this seems to put that one to bed. Which is good news for the Cuban bats, since their low population and declining, exposed, habitat make them a Vulnerable species, a conservation status they would lose if they weren't a species in the first place.

The dates are, however, perhaps more significant. The Cuban bats diverged from their mainland kin 1.25 million years ago, during the Ice Ages, while their common ancestor split from the southern species 3 million years ago, in the Late Pliocene (the "long autumn" before the Ice Ages). 

Interestingly, the study also threw up some ancestral branching within the southern yellow bats. The ancestors of the bats from Ecuador seem to have split from the ancestors of other sampled members of the species over 1.5 million years ago, well before the Cuban bats became a species. While it may be a stretch, based on this alone, to argue that the Ecuadorian bats represent a previously unknown species, if distinct physical differences could be identified, describing them as a "new" subspecies may be perfectly justifiable. (The two known subspecies of the northern yellow bat, incidentally, show up clearly in the data, having diverged 780,000 years ago, while the currently recognised southern subspecies do not, and may not really exist.)

The western yellow bats are the oldest species, as had previously been suspected, with the estimated divergence time here being a little over 5 million years ago, very roughly at the Miocene/Pliocene boundary. Because such studies include closely related animals outside of the group being studied in order to calibrate the starting point, it's also possible to say that the common ancestor of yellow bats diverged from that of the other red bats over 13 million years ago, marking the origin of the group. (Doubtless, those arguing for a separate yellow bat genus will be heartened by this, because it is very early for a group smaller than a genus, but it's no clincher).

These dates, combined with what we know of ancient climates, allow us to build a picture of how this one small group of mammals evolved. The researchers believe that yellow bats first evolved in North America, and began to branch into different species when some of them (later the western bats) adapted to drier conditions than the others. 

Suitable habitat would have been available to them in South America from the Pliocene onwards, but only in the south of the continent, so it seems unlikely they reached it until the Ice Ages. The cooling climate forced the bats further south, leading to the distribution we have today. Similarly, warmer periods between the Ice Ages would have allowed them to move north and inland, into regions where they no longer live. Indeed, in the 1960s, a fossil identified as belonging to a yellow bat was discovered in Kansas, and dated to the last interglacial, 120,000 years ago. 

Of course, this is just one small group of mammals, and not one of great significance to many people. They are not of noticeable economic importance, and only the Cuban yellow bat, which we already knew was distinct, is under any known conservation threat. But it illustrates a principle, of how advancing scientific techniques - in this case, genomics - can lead to new understanding, bringing a picture of the world's past into clearer view.

[Photo by Juan Corzado Cortés, from Wikimedia Commons.]

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