191 History Inside Frog DNA

[Music] Ah, lots of tiny frogs from Costa Rica. Alright, full disclosure, this isn't the Costa Rica month. No, because this is a Panamanian frog, isn't it? Er, who's so name? [Sigh] What could it be? So Ben, you've got a guess. I'll give you a clue. It's a microendemic. Oh good, a microendemic. That means that I could pick almost anywhere and be completely wrong. Yes, microendemic. Okay, well, I would put it in a cast landscape. If that was the case, oh that's for lizards. So frogs, frogs like it weather, limestone, dunes, do you think? Yeah. Er, microendemic, because it's on a tiny island. It lives on Trinidad. It's the Trinidad, uh, chipping frog. No, it's a good guess, but in fact, it was the Baylon pygmy frog, microheila, baylonensis, baylonensis meaning of baylon and microheila meaning, oh my god, it's a small frog. So, um, yeah, this was actually sent to us by Dalin Kohler, Patreon, Facebook, and her, her total is working in China. And yeah. So complete, like, so what you're saying is I was complete wrong side of the world. Yes, yes. Okay, that's okay. You were the wrong side of the earth. That's about as far as I could possibly be. Apparently they're very loud calls. And it's a really beautiful creature actually. I have a picture of it, which I thought you might like to see, which was sent along with it from Dalin, um, showing I believe, if I'm not mistaken, possibly the actual frog that you just heard. So I'll put this, Oh, the cobra itself. For you to see, there is the culprit. Um, it's a really beautiful little creature. Very small. Dalin said they only get to about 2.5 centimeters long. Um, they're very round, bellied frog with little legs and a very pointy nose. And they have sort of this gray, mottled flank with a nice brown top with some big markings. What, where have you put this picture? In general, in discord. Uh, have you actually sent it? No, I have not presented. There we go. I hate how you have to present it. I'm not a big pressing entity guy. Um, yeah. So there you go. Can you see it now? Nope. That's disappointing. Well, when you come up for it, we'll, we'll, we'll talk about how you think it looks. But yeah, they're found in Bayland. There it is. Oh, classic microhaila. Absolutely. Like classic, beautiful little, chubby microhaila. Yeah, with a nice patterned back. Yeah, very beautiful. A very beautiful patterned bag. And they're found in the Bayland district of Zai Zhang province on the east coast of China. Yeah, really small microhendemic. And yeah, Danin said, I thought this would make a tricky call to guess. So I wanted to share it. And I think that's undeniably what happened. It was awesome. I mean, to be fair, I think it's much harder to find a call that isn't tricky. But even so, microhendemic does. Yeah, all right. I'm not going to feel too bad. I'm guessing that one. Yeah. But yeah, microhaila with a narrow mouth or rice frogs. Yeah, really common across Asia. At least lots of parts of Asia. Incredibly high diversity of species. Yeah. Cool species. So yeah, thanks to Danin for saying that. Yeah, if I'm right. If I'm right, I've got frog calls or other animal sounds. Send them in. We'll check them out. Yeah, let's move on to our paper, shall we? Okay, this is by Moran, Bossy, Marian, and Halfwork, published in 2024. Genomic footprints of pre-colonialism. Population declines in urban and forest Tungara frogs, coincident with historical human activity published in molecular ecology. So we're talking about the Neotropical Tungara frog. Angus, domops, postulosis. Which is this small three centimeters long, this one. Three centimeters long snouts of ant-nate, Neotropical frog that lives on the ground spawns throughout the year. So you can hear them calling and spawning throughout the year. They're unusual in that they don't have any teeth. They have a very specialized diet. They are Memecafagus bands. Oh, adorable. And also termites. Yeah, they eat termites, mites, and ants. And this study takes place in Panama. Obviously being called the Neotropical Tungara frog we knew would be in the Americas, and we are in Panama. And yeah, this was a genetics paper. So they have sequencing whole genomes of over 103 individual Neotropical Tungara frogs. Obviously whole genomes, you can kind of take your genetic analysis to the next level. To the next level. Looking for where you've got whole genomes to work. So, look for whatever you want. Look for whatever you want and you can find it if you know what you're looking for. But they were looking for predominantly runs of homozygosity. So this is where both alleles at a particular locust. So too, you get a copy from your mom or a copy from your dad. At least if you're a diploid organism. And yeah, basically homozygosity is where you get to the same from both parents. It's a classic symptom of inbreeding and can cause inbreeding depression, where animals have negative traits or lose their ability to adapt. Because weak, deleterious alleles, which are normally hidden as heterozygous, where you have two different conditions. They're usually lots of bad things hidden because the dominant alleles are healthy and the recessive rubber sheet heterozygous ones are bad, bad, bad, bad. But if your mum and dad knew each other too well, if they're cousins or brothers and sisters, then they might have two copies of this same deleterious allel and then you end up with inbreeding depression where these like bad traits come to the surface because there's a lack of diversity. And they were kind of looking at this inbreeding depression issue across two kinds of population. So they were looking to see if ones in urban areas were more affected by inbreeding depression than ones from more wild areas. Which is a sensible thing to study. They had sort of two competing potential scenarios for this urbanisation, right? This idea of urban fragmentation, where you have a population that gets split up by urbanisation, and therefore you've got smaller populations and sort of boosting that chances of inbreeding. And like you're saying, the deleterious alleles becoming more prominent. But, alternatively, you've got species that do exceptionally well in urban habitats. I mean, you only have to sort of think about how rats and dogs make use of subways and things. But to sort of, again, there's plenty of species that make fantastic use of the things people have done to the planet. And in those cases, you might actually have the urban populations doing essentially much better and sort of helping along. And you wouldn't see this inbreeding at all. You'd actually see a potential boost in diversity as they're making use of some new niches and having enhanced gene flow in these areas. So it could go even one. They could be winners. They could be losers if you want to sort of look at it through those, those, that sort of framework. Yes. And so like you say, they compared the sites between urban and sort of more wild areas. Expect, I mean, for me, I would have expected to see that urbanization or possibly more recently, like the Kitchertvungas, was causing inbreeding depression. So a reduction in genetic variability nearer to urban centres. Of course, by like a bottleneck. Basically, a big chunk of the population has been removed, who you're left with, lower genetic diversity because you've lost all these frogs from disease and land use change essentially with urbanization. Yeah. Exactly. Yeah. And so, yeah, that's what, yeah, they it's probably, I mean, I think realistically probably expected to see that urbanization was causing this. But yeah, urban frogs generally did have these larger runs. So more like long sequences, which were homozygous. So both from the same parent showing, potentially inbreeding depression. But it was driven by just a few samples really that massively skewed it. And there was a large amount of variation between individuals even within the urban or non-urban population. So whether or not they were urban didn't really adequately describe or there wasn't a strong enough correlation between being urban and having reduced genetic variability, basically. Small, there was a difference, but the difference was so small that it doesn't really look sort of biologically relevant would be the way to sort of frame it. It's like, okay, it's different, but not different enough that it's a concern. or a serious impact. So essentially modern urbanization, you know, the last sort of like a couple of hundred years, doesn't seem to have had a massive, massive effect on the genetic variability of these populations. However, which I mean, to be fair to this area of Panama, we're looking at a section of Panama around the Panama Canal, correct? Where their study sites were. So in terms of a location that has undergone change, you know, a bunch of, a bunch of sort of apes with high ideals coming along and carbon, carbon, a big stretch of water through the middle linking two oceans. Pretty dramatic. I think I would, I'd put that pretty high up in terms of the first. Famous engineering. Yeah, frogs famously not good with salt water. They don't like it. It turns them all shriveled. It's bad. And so yeah, you know, if you were to look at this place on a map right now, it looks like forest, doesn't it? It looks like nice forest mostly, but that you don't have to go back that far and the Panama Canal was being built. So yeah, basically, their results, what they noticed was that something had happened in the genomes of these frogs, but it was quite a long time ago. So yes, they have undergone sharp declines in genetic variability, and across the board, there was, there was kind of evidence of imbreeding depression, but it wasn't due to recent urbanization. It was actually probably due to colonization by Europeans. So it's been inhabited this area since 13,000 years ago. Native Americans inhabited it 13,000 years ago. And then European colonists arrived in the 16th century, and at that time there was a lot of deforestation, a lot of changes in land use agriculture came along, and this kind of continued through to the construction of the Panama Canal in the late 19th century, and then there's like ongoing agricultural and urban development. And so yeah, what they looked at was to see when these kind of like population declines that the genomes showed were actually happening, and yeah, essentially it looks like the declines in their sort of genetic variability began several centuries ago. So before urbanization, but yeah, still caused by people. So there was one big period of population decline between 800 and 1600 years ago, which is the pre-colonial era. So you know, the beginnings of agriculture when people were doing a lot of fires, linked sort of starting off agriculture, you know, like reason realistically it's sort of like between 700 and a thousand years ago. So the native peoples of America were starting to use fire to sort of slash and burn, and this this caused a huge decline in the frogs, and that's evidenced in their genomes. There was this big crash, and then there was a second big crash around between 100 and 400 years ago, and that coincides with European colonialists arriving again, subsequent massive changes to the area using again another big peak in agriculture essentially. So it kind of seems like these frogs, although they have been impacted by human pressures, it isn't the modern urbanization that people thought it would be. It's actually historically when humans have first rocked up to this environment, and then again, subsequently when new humans came again and started treating it differently, this is caused big challenges you can see in the genomes. I mean, so it's not so it's yeah, certainly a rival of new humans for the colonial one, but the prior one might have been a shift in practice as opposed to people rocking up right or a shifting population density. I try to, you know, to be fair, I didn't try all that hard, but I want this to get an idea of like how many people were sort of around and about this sort of area, and it seems like it's reasonably tricky to work out between two million and 200,000 seems to be the wide range. So you've got a pretty sizeable number of people there presently. So you can see how crop cultivation and sort of disturbance from fire would have led to some sort of impact on these frogs. Like it is, that's a lot of people to sustain and support. Yeah, and these frogs, although they are torrent of sort of human areas, they have their limits and there comes a point where frogs can't really carry on anymore. Yeah. Really intense farmland or urbanized areas. Frogs just can't cope, they just can't deal, they need certain things which aren't there, they need water, they need trees, they need shade, all this stuff, yada yada. So yeah, and basically human, it's throughout human history, these frogs have been under pressure from people and it was a surprise result. They thought it would be straightforward. They thought we like, oh, we've got urban areas, we've got non-urban areas, the ones in the urban areas are probably undergoing bottlenecks and declines. No, modern things aren't that big of a deal. It's actually historical changes which of course already existing declines. These historic changes can still be sort of seen today. Like these are cumulative effects essentially, right? They haven't rebound, the diversity hasn't rebounded. Is the analysis capable of spotting or rebounding in diversity? That's a good question I don't know. Because I do wonder whether the urbanization now doesn't have a distinct signature on the genome because the impact it would have has already occurred. So there's the inbreeding, how much more inbreed can you get while still being viable? Yeah. Yeah. But I think the main thing that I find cool about this paper is that like even now when you're studying populations of animals, you think you've got two groups. You think you've got an urban and an unurban where these ones are existing in relatively pristine environments. It's not so. We've been around for so long causing changes to the environment that like you really have to go back quite a long way to actually recognize what human influence is. Which I think is really cool because yeah, I feel like I feel like a lot of studies probably miss out on this as a dynamic at all. Yeah, it's not completely. Absolutely. I mean partly because it the amount of work that's gone into to work this out and then even end towards the end of the paper, they're sort of saying, you know, you've got to be a little bit cautious with the estimations of when these bottlenecks are occurring because you change a couple of parameters like mutation rate, recombination rate, and your estimates of when things are occurring are going to shift. And when you're working on such broad scales as, you know, 5,000, 8,000 years ago, I change your 10% suddenly knocks your 100 years down the line or 200 years down the line and you're going to reinterpret that in a different way because you're going to have to connect it to different sort of human activity that you know about. So it's yeah, it looks damn difficult to pull off and the fact that they've yeah, identified these two sort of key time periods at all is, is well, it just kind of feels like magic, doesn't it? History trapped in the DNA of frogs. It really is cool. Yeah, it really is cool. And like all credit to these authors, their figures are amazing. Yeah, really nice. Some of their color choices wouldn't help the color blind, but mostly they're just gorgeous figures. Yeah, I really like them actually. Yeah, a little bit inspiring this one. So yeah, let's, we got anything else to say about these frogs. These are near tropical Tungara frogs. I mean, I don't think that I think basically highlighting the paper pretty much says a lot more than what we've gone over quite briefly. There was a lot of lines of evidence that they've explored. I was sort of picking the highlights. So it is worth a read. Yeah, I can't wait for this sort of, you know, this sort of study be done in other locations and to sort of pick up other historic changes be them natural or anthropogenic. Yeah. Yeah, so have you got any other business for this episode? I do not. I have no any other business. Okay, so I've got a couple of bits. One just to say that a British holiday maker was bitten by a blunt headed, a blunt nose viper from Cyprus while on holiday. This poor lady got bitten by one. It sounds like it was not too serious, but you know, seriously enough, she had to go to hospital for a bit. Yeah, and then had to sit on a wheelchair to get around for a while. Yeah, she got bitten by a blunt nose viper while on holiday, which yeah, I looked to them for two months while I was there and I didn't see one. So, where was this sorry? Cyprus. Cyprus. Yeah. Yeah. Quite close. Thanks. Yeah. Macrover Perra Lebertina. Yeah, it's this big fat viper and obviously blunt nose. It's got short nose. But yeah, really beautiful snake, but yeah, savage that she got bitten, really unlucky. But yeah, I saw that and yeah, apparently she was doing like some kind of outside yoga thing and she got bitten. Obviously, I was a meditation. So she was trying to meditate for a while and this, she got bitten by a venomous snake. That's going to put a little bit of a, yeah, in your meditation, isn't it? That's her chakra is fully skew-width after that. I don't know if Shakras have anything to do with meditation, but yes. Okay, anyway, so yeah, that was one thing I wanted to mention, which I thought was noteworthy. Yeah, just wild. And then another one, which is just this absolutely bizarre story, which I saw on the news, which is, there's this guy, he's got an emotional support alligator. It was called Walligator. And basically this guy had him as a pet. He like cuddles the alligator. I don't know why they call it an emotional support alligator. So I don't know what emotions the guy has that is this alligator specifically supporting. But, just, basically, he'd get this right. This is what's crazy to me is that he took the reptile on holiday with him. So they were on holiday in Georgia, in the US. And I think I don't know where he was, but the alligator was presumably outside. I don't know if, when you take your alligator on holiday, I don't know if it stays in the garden or comes in the house. I don't know what how that works. But the alligator was nearby, possibly in the garden of the property. And some local pranksters, probably teenagers, saw the alligator, jumped over the fence, grabbed it, stole it. And then they took it to their friends house, released it into their pool for a joke. And then animal control came, thought the alligator was just a wild alligator, and let him go back into a swamp. And now the guy whose alligator it is has been completely unable to find him. The alligator just lives in the swamp now. There are so, I am lost for words. There are so many questions that I want answered. Starting with whether I wasn't the way you could keep alligators as pets, I would have thought keeping native species as pets was not allowed. Oh, yeah, man. Now, loads of people in the States have got a man, American. Yeah, bizarre. I would have thought alligator was quite an impractical animal to transport anywhere. Transporting across state lines seems a little bit odd. But again, I don't know the rules. Well, there are no, there are no, keeping, keeping in the garden while you're on holiday. I mean, again, I suppose they had to have to find a pet friendly place to stay. But I doubt alligator is really what people are intending when they say, oh, yeah, pet friendly. Yeah, if someone emailed me and was like, hey, I don't have an Airbnb, they were like, hey, hey mate. Yeah. So I'm looking to come and stay two nights in April, just a couple of things. Pet friendly. Yeah. Is it pet friendly? And if so, can I bring my alligator? I'll be like, no, don't bring your alligator to my house. It's rude to ask. It's rude to ask. Didn't so, yeah, very, very long or anything like that. Little like, little market. I don't know. He just looks like a normal alligator. Yeah. He's nine years old, 182 centimeters, six feet long. Apparently he's really friendly. He won't bite. Yeah. And provide some information. You try to take this, the mate you tried to take is alligator to watch a Philadelphia Phillies baseball game in 2023, but they wouldn't let him in. So that is the line. They can't alligator can go on holiday, but they can't go to baseball games. Interesting. Interesting. That's something to remember. That's a lesson for us all then. Don't take your alligator to go watch baseball because you will be denied entrance. I'd love to know how this alligator is getting on in his new swamp life, whether he's just completely adapted to it or whether he misses his belly rubs. Yeah. I mean, just another question to add to the pile of questions. Yeah. I can only hope he's doing marvelously. I think he's probably fine. Yeah. He's probably just like, oh, so I don't know. How habituated do they get? It's a good question. I have no idea, but usually things that are domesticated don't get domesticated in a generation. Yeah, exactly. But you know, they can lose natural behaviors quite quickly in captivity. So I guess it maybe depends on how many generations things. Crocs are tough. Yeah. Yeah. Alligator, but yeah, the crocodile is pedantry. Yeah, true. So yeah, this guy, where are you, Wally? Fairly well. Fairly well. Have you got any other business beyond that? No, I'll be wondering about that all day now. Yeah, I know. The alligator out there. The Georgian swamps. So yeah, I don't think I've got anything else to say either. Yeah, hoping to get some snake-based fieldwork on the go quite soon. Excellent. Exciting. Well, update on that. I hope you're thinking some transmitters on Adders in the next few weeks or months. So yeah, I think it's across that succeeds and I will provide some updates, but yeah, other than that, I think you can get in touch with us. Herp highlights at gmail.com. If you want to support the podcast, you can patreon.com/herp highlights. Thanks to all of our patrons. Yeah, I think so. That is it. So thank you for listening. Yeah, thanks for listening. [Music]