Wikipedia:Reference desk/Archives/Science/2023 July 24

= July 24 =

Potato and tomato phenotypes
Today I've read that the genetic difference between tomato and potato is just 8%, with remaining 92% of genome being similar.

However, to me morphological differences between the two are too stark for that percentage: potatos' smooth and rounded leaves vs tomato's edgy and serrated ones, different shape and color of petals, underground tuber vs. surface juicy berry, etc. When these are compared to species within some other fruit-bearing genera, e.g. Malus (and even to humans and chimps who have roughly the same genetic similarity), the phenotypic differences look more pronounced in potato and tomato than in Malus species. Why is that? 212.180.235.46 (talk) 18:21, 24 July 2023 (UTC)


 * I find 8% a remarkably high difference, but don't know how such a percentage is calculated.
 * Things like the colour of the flowers or shape of the leaves can be controlled by a single gene. Think of Mendel's peas: one species can have both white and pink flowers and this is controlled by just one gene. In tomatoes and potatoes, the genetic differences just happen to be very noticeable for humans. PiusImpavidus (talk) 08:10, 25 July 2023 (UTC)
 * Note sure where you're getting your figure for humans compared to chimps from. The generally cited figure for humans and chimpanzees is 98-99% [//www.science.org/content/article/bonobos-join-chimps-closest-human-relatives] [//www.amnh.org/exhibitions/permanent/human-origins/understanding-our-past/dna-comparing-humans-and-chimps] which is a lot more similar than 92%. Our article Human evolutionary genetics says the genetic distance is under 2%. Note however that these soundbite figures should probably be treated with care with due consideration of what they're actually comparing and what it means. Nil Einne (talk) 09:23, 25 July 2023 (UTC)
 * Second the "due consideration". Depending upon how you work out the figures, male humans are closer to male chimps than to female humans (and likewise female humans to female chimps)! Martin of Sheffield (talk) 10:34, 25 July 2023 (UTC)
 * Also I think you overestimate the importance of some minor obvious outward phenotypical features. You seem surprised that potatoes and tomatoes are much more similar than either are to Malus but I think to most biologist who study them in any fashion for a long time, this doesn't seem surprising in any way. Both potatoes and tomatoes are in the genus Solanum. The most you can say about Malus and Solanum seems to be that they are both Eudicots, so without looking further into their evolutionary history, it seems likely they're quite far apart. While there are sometimes some disputes between genomic approaches to taxonomy and more traditional ones, and I know almost nothing about how these play out with Solanum as per Tomato, it was actually Carl Linnaeus who first put the tomato and potato together in Solanum albeit with some later dispute (but I don't think there was much dispute that they were fairly closely related, much more closely related to Malus). So traditional taxonomic methods were enough to show this relatedness, because such methods rely on more than just superficial phenotypical similarities. Nil Einne (talk) 09:39, 25 July 2023 (UTC)
 * As for how traditional taxonomists noticed these similarities, it's a bit outside my wheel house, but things like careful examination of their leaves, flowers, fruits and other features and how these develop is I think generally the way. To ask an obvious question, do you know what potato fruit look like? I didn't either, but I'm not surprised given their closeness that they seem much more similar to tomatoes than to apples. I'd also note that per Tomato, when it was brought to Europe, it was recognised as a relative of nightshade which gave rise to toxicity concerns. The presence of toxins like Solanine in potatoes has also I think been known about for a long time, our article mentions it's a problem with their fruit. This is less of a problem with tomatoes, and the primary glycoalkaloid seems to be Tomatine but while such details probably weren't known until somewhat recently it's possible that the presence of a toxin in the leaves etc causing similar effects was recognised earlier. Nil Einne (talk) 09:59, 25 July 2023 (UTC)
 * I would add that you should also be careful when comparing any plant with significant selective breeding as even more so than their wild relatives, we would often expect significant convergence from said selective breeding e.g. in fruit or tuber size. Nil Einne (talk) 22:31, 25 July 2023 (UTC)
 * You seem surprised that potatoes and tomatoes are much more similar than either are to Malus
 * Malus_sargentii_0zz.jpg That is not what they said.
 * ... differences look more pronounced in potato and tomato than in Malus species.
 * Here "in" means "between". The surprise that that Solanum is as similar to other Solanum as Malus is to other Malus. They are comparing apples with apples. Card Zero  (talk) 11:39, 25 July 2023 (UTC)
 * You're right I misunderstood and in sorry that. With the I think now correct understanding of what the OP is saying I'd point out there doesn't seem to be any reason to think potatoes and tomatoes have the same level of genetic distance or similarity as Malus species to each other. The fact they are on the same genera for each doesn't mean much on that level. I mean if two species were only 70% genetically similar, we'd probably question if they should be in the same genera but it's easily possible these Malusspecies you are comparing are more on the order of 95% or something. We don't have a figure for any two different Malus species. And as I said earlier even if we did you'd need to make sure these are looking at the same thing and what these figures actually mean. But also what Malus species are being compared? You can't say well most Malus look more similar to each other compared to these two specific examples of Solanum which for all we know could be the most distantly related. To be clear, I doubt they are but I don't know so unless you do it's a bit meaningless to say well they are more dissimilar than most Malus. I'd emphasise though that while we should consider all such things, we also shouldn't be surprised if some features of Malus or whatever are more similar than such features in potatoes vs tomatoes yet they are more genetically dissimilar. Nil Einne (talk) 22:50, 25 July 2023 (UTC)
 * Potato fruit look very like the fruit of the tomato. DuncanHill (talk) 09:54, 25 July 2023 (UTC)
 * 8% seems like a very large difference to me. The genetic distance between humans and domestic cats is only 10%. CodeTalker (talk) 17:24, 25 July 2023 (UTC)

Birds and Pterodactyls
I learned throughout my life that birds didn't go extinct after the Chixclub impact because they could fly and weren't heavily impacted. But my question is- why did Pterodactyls (and Pterosaurs in general) go extinct but not birds? 104.187.66.104 (talk) 19:38, 24 July 2023 (UTC)
 * Very few bird species survived and the ones that did seem to have been small ground dwelling ones - the survivors diversified later. Small size seems also to have been a feature of the few mammals that survived the event. But that does not seem to have been enough of itself - lots of dinosaurs were fairly small. NadVolum (talk) 22:48, 24 July 2023 (UTC)
 * Well one theory is that the surviving birds nested underground. Then they could survive incineration of the surface of the Earth. Graeme Bartlett (talk) 00:32, 25 July 2023 (UTC)


 * Another study, published in 2016, suggested that avian dinosaurs survived their relatives because they were small seed eaters and better able to cope with the available produce in the wake of the extinction. The same reasoning might explain why, despite both being capable of flight, birds lived while pterosaurs perished.
 * Smithsonian Magazine - What Doomed the Pterosaurs?
 * The 2016 study is Dental Disparity and Ecological Stability in Bird-like Dinosaurs prior to the End-Cretaceous Mass Extinction
 * Alansplodge (talk) 11:44, 25 July 2023 (UTC)


 * One thing to note is that, given the amount of devastation caused by the KT event, there's bound to be a certain capriciousness in the survival of some of the species. The only commonalities seem to be the size of the species involved, nearly all megafauna and megaflora died out; the plants could not efficiently photosynthesize, and the animals could not get enough calories as either primary or secondary consumers to survive on the meager plant life that was left after the event.  The only common theme is that smaller things did better, as they needed less resources to survive in general, and that omnivores and scavengers did better than pure herbivores or pure carnivores.  However, even among smaller species, there isn't necessarily a "one size fits all" explanation as to why population "X" survived, but population "Y" did not.  The KT extinction, for example, killed of all of the Enantiornithes, which were avian (bird-like) dinosaurs that were the most diverse clade among all mesozoic life.  There's a shocking number of species of different body plans and sizes and diets and whatnot, and they all died out at the event.  Ammonites all died out, but other similar clades of mollusks seem to have come through unscathed.  So, other than "larger gone, small maybe survived", there's not always a clean explanation as to who made it through the event.  Evolution as a whole is arbitrary and capricious, and not purposeful, and that's also going to be true of extinctions often.  -- Jayron 32 16:49, 25 July 2023 (UTC)
 * I think this is always worth keeping in mind, especially as it is not the most intuitive aspect of understanding the mechanisms of natural selection. A genetic population/species/clade can have an immensely well-adapted set of traits for it's ecological niche and still just run into pure misfortune.  Selective pressures are the results of essentially unfathomably large sets of fitness checks and there's no guaruntee of success under what random chance might bring even under relatively stable ecological epochs.  When you mix in cascade effects, keystone species deaths, and general ecological collapse, all bets are truly off and even when examining the highest levels of selective pressures, fitness can capitulate to pure dumb chance.


 * All of that said, I'm going to break with my usual distaste for speculation here and share two other possible factors with the OP which may have played a role here: I've heard it previously speculated that two of the major advantages that smaller mammal species (even as compared against their relatively larger cousins in close mammalian clades of the time) had were that they used burrows and may have had some of the relatively full fur coats, both of which would have been advantages in the fallout of the K-pg event (the other factor of their very small caloric needs in a devastated biomes I think has already been referenced). The ancestors of modern avians may very well have had similar advantages from their feathers and own nesting habits, compared against other sauropsids, including pterosaurs--though I will admit I do not know if this speculation converges with established research. SnowRise let's rap 10:17, 28 July 2023 (UTC)
 * Certain species require warmer climates and that could have been true for pterodactyls. Thus, they preferentially populated areas, although perhaps wide, but near equator. Birds at the same time known to populate very wide areas. Since the impact was at the Yucatan peninsula or near, the resulting dust and gases were blown off with prevailing winds which are close to the tropics. That could have affected the pterodactyls the strongest. It is possible that areas close to the poles although to have gotten their dose of sediment, the intensity of the secondary impact for them was smaller. AboutFace 22 (talk) 02:36, 30 July 2023 (UTC)
 * There are two major factors involved in 'the survival of the fittest'. One is a short breeding cycle (the period from seed to seed), which gives a species the ability to rapidly diversify and therefore adapt to changing environmental conditions. Our shrew-like ancestors would probably have had great, great, great […] grandchildren in the time it took for a single pterosaur to reach sexual maturity.
 * The other factor is pure, blind luck. Luck is something that people find hard to comprehend because it isn't particularly comprehensible, so the success of avians after the KT Event, much like the success of mammals, The Beatles or Elon Musk, is often attributed to some sort of unique excellence despite the fact that many entities of equal or greater 'fitness' simply weren't so lucky and fell by the wayside. nagual</b><b style="color:#BBA">design</b></b> 13:52, 31 July 2023 (UTC)