6 ms·

Not sure if a troll given I address this in the OP. You can't just upload images. Internal dissections, DNA sequences, imaging at SEM scale, all of these are n

by xipho 6y ago

Not sure if a troll given I address this in the OP. You can't just upload images. Internal dissections, DNA sequences, imaging at SEM scale, all of these are not rare requirements, they are the norm. Specimens have to be meticulously collected, preserved, and vouchered in Natural History collections as part of this process (Science should be replicable to some degree). It's a wonderful aspiration to live in a society where anyone will have the free time to "level-up" to a taxonomists level of experience by making, literally, millions of observations, then "power-up" with their free access to SEMs, sequencers, high-powered microscopes and lighting, digital imaging systems (etc.) then "farm for $" to get access to travel and gear then gain "clan-clout" to navigate collecting policies and permitting, etc. etc. Something to strive for, but sadly not a reality anytime soon.

MattGaiser 6y ago
Do they actually have lots of species which look the same but are impossible to tell apart except for DNA?
- hospadar 6y ago
  Look into mushroom identification - many little brown mushrooms (LBMs) are differentiated only by careful microscopic analysis of their spores or DNA sequencing. Mushrooms are especially difficult because many of the potentially useful identifying features are only present at certain (short - hours or a day or two) phases of the lifecycle of the fruiting body.
  - tp3 6y ago
    Finally, for those who think genomic/genetic studies are being used inappropriately, consider that while they may seem to me to be, in practice, just another sort of 'data processing' (which they are not - they are often just generalised (or even generalized), and their application to new contexts is not that different to simply applying similar analysis to previous contexts) it is possible, for example, that, for example, the study of the DNA sequences of fungi actually (if you want to make a broader and very broad claim about fungus genomics) might in the future yield, in this particular case, a much more detailed, more reliable (and possibly more objective) classification (if not entirely a direct one) of some of the fungi and their eukaryotes in our immediate neighbourhood. I've also got to say that for the same reason, I don't have a lot of confidence in the 'fungal genomic analysis' thing in particular, because, on the whole, it seems to me to be so easily manipulated.
  - oasisbob 6y ago
    Fungal taxonomy is especially interesting. Some argue that latin binomials should be abandoned, see "Against the naming of fungi": https://doi.org/10.1016/j.funbio.2013.05.007 https://doi.org/10.1016/j.funbio.2013.05.007
- dwiel 6y ago
  I occasionally use iNaturalist to help identify plants and fungus while out on hikes. The community there has a ton of specialists and it is extremely common to get messages like this on observations that are months old. Here is one I got this morning about a random mushroom I took a picture of in the woods of Indiana: Russula sanguinea was described from a European mushroom and therefore probably isn't here in North America at all. The name has been applied to many red Russula in N. A. adding to the confusion. Out west where it may be sorted it is being called Russula rhodocephala which itself is a lookalike for Russula americana but under different trees according to Danny Miller here [1]. Mushroomexpert's Kuo and Mycoquebec say that a lookalike under oaks in the east is Russula tenuiceps or R. sanguinaria under conifers/pines, but it is probably a group of species, and also not the same as the European one in the case of R. sanguinaria. We are trying to downvote these identifications for this reason. Hopefully, any people interested in identifying mushrooms will pitch in and help to vote any Russula that is being called Russula sanguinea in the eastern US back to genus level anyway, but we are concerned with a few other species too. Read fungee's journal post here [2]. Check out the master list here [3]. Another thing that is daunting for Russula ID, there are well over a hundred known red Russula in the east, many are not named yet, and, if they are, the name is not in use. [1] http://www.alpental.com/psms/ddd/Russula/index.htm http://www.alpental.com/psms/ddd/Russula/index.htm [2] https://www.inaturalist.org/journal/fungee/46596-new-ai-computer-vision-first-for-android https://www.inaturalist.org/journal/fungee/46596-new-ai-comp... [3] https://forum.inaturalist.org/t/computer-vision-clean-up-wiki/7281 https://forum.inaturalist.org/t/computer-vision-clean-up-wik...
  - dmix 6y ago
    I dabbled in mycology and identifying mushrooms is super hard, probably one of the hardest taxonomy things. I wouldn’t want to be the expert in that field getting asked all the time with a single iPhone photo. /r/mycology had to say stop posting “please identify this mushroom” because it was so common. I’d imagine its easier with insects. And you don’t have as many people who care because they aren’t trying to eat them as often. I still like to ID random bugs I find in my house and backyard and it’s always a probability exercise. Those tree identification apps by taking a photo never work. I used it at a UofT garden where every tree was labelled and it got it wrong every time. So even the ML is way off.
- xipho 6y ago
  Good question, increasingly we can judge for ourselves. Go to BOLD (COI barcoding) [0]. Search for "Apidae". That's just one family of bees, in this case the one that includes 27+ (IIRC, probably way off) subspecies of what we know as the honeybee. The important bit is the count in "BINS", e.g. hypothesis of speciation typically based on a single gene, COI. That's only the specimens that have been sequenced and archived at BOLD. That doesn't include the various other bee families, notably Halictidae, Colletidae, Melittidae, and others roughly all the "sister groups" in the Apoidea [1]. An example of why is this important? The Africanized honeybee, known perhaps from bad horror movies, is characterized (identified) as a hybrid of two species. It can be more or less aggressive (to the point of killing you if you don't GTFO) depending on then nature of its DNA. Hybridization has blurred the limits of the species in many areas, including in the US. Sequencing specimens is the only way to confidently determine which of the species you have, A (friendly bee honey), AB (grumpy bee honey), or B (deadly bee honey) (gross simplification here, not Mendelian). [0](http://www.boldsystems.org/index.php/Public_BINSearch http://www.boldsystems.org/index.php/Public_BINSearch). [1](here: https://www.catalogueoflife.org/?taxonKey=625GP https://www.catalogueoflife.org/?taxonKey=625GP)
  - throwanem 6y ago
    > The Africanized honeybee, known perhaps from bad horror movies You're talking about The Swarm (1978), which is absolutely so-bad-it's-good. Fans of Michael Caine will I think in particular find it rewarding, and I was especially impressed with its frankly prescient treatment of the drawbacks inherent in mass insecticide application given that the ongoing research increasingly points to exactly that as the culprit for pollinators disappearing.
    - artificial 6y ago
      Sounds similar to Jaws starting a shark panic.
      - throwanem 6y ago
        Well, you're considerably more likely to run into a wild colony of "Africanized" hybrids than you are a great white shark, for one thing. For another, while I wasn't around at the time, I understand the movie was more made in response to sensationalistic reporting than a cause of it - I might be wrong about that part, though. That said, my understanding is that A. m. scutellata x A. mellifera hybrids aren't unusually aggressive in nest defense by the standards of social hymenopterans generally, but only by the standard of the European honeybee (A. mellifera). I can't claim close familiarity with the relevant literature on bee hybrids, but from what I have seen, their nest defense behavior seems roughly comparable in aggressiveness to that of many yellowjacket (Vespula, Dolichovespula) species. On the other hand, a wild bee colony is likely to be one or two orders of magnitude greater in size than a wild yellowjacket colony, which means that a comparable level of aggression in nest defense could pose a significantly greater hazard. Using the figures from the Wikipedia article [1] and its relevant source [2], it looks like A. m. scutellata x A. mellifera are responsible for an average of around 15 human deaths per year since the introduction of A. m. scutellata into Brazil in 1956. So I don't really see that there's very much to worry over here, in any case. [1] https://en.wikipedia.org/wiki/Africanized_bee https://en.wikipedia.org/wiki/Africanized_bee [2] https://www.si.edu/spotlight/buginfo/killbee https://www.si.edu/spotlight/buginfo/killbee
- rmah 6y ago
  Yes. And to make it even more confusing, there are often plants/animals that have wildly varying appearance but are actually the same species: e.g. great danes/chihuahuas or cabbage/broccoli
- underbluewaters 6y ago
  Yes, and this even applies to vertebrates and can sometimes work in reverse. I was part of a team of research divers that did fish counts in California. This was in the early 00's so in several instances genetic research found that seemingly identical fish were different species depending on region. In one case groups of fish that looked quite different turned out to be the same species. Very frustrating when you are putting in so much work underwater! That whole experience made me very skeptical of citizen-science projects once I knew how much training was required to do good work. While they are a great compliment to professional research they are no replacement (though often funders are treating citizen science as just that).
whimsicalism 6y ago
> imaging at SEM scale I can't see how that would possibly be a requirement for determining the species of a bee. Wouldn't DNA be cheaper and easier?
- throwanem 6y ago
  Not at this time. Sequencing is cheap and easy, but hymenopteran genomics is a young field with many more open questions than answers; morphological taxonomy is much more mature, and aided besides by highly specific genital configurations which are, in no small number of cases, the only way currently known reliable of telling two macroscopically indistinguishable species apart. Too, in order to evaluate genomic relatedness precisely enough to update taxonomy, you need your sequence database to be broad as well as deep - unless you already have a broad and deep sequence database of other solitary bees, for example, it's hard to get very precise results out of a given solitary bee's genome. It may not even tell you anything you didn't already know. In any case, it's not rare in the literature to encounter whole genera categorized almost entirely through analysis of the males' aedagi, with microscopic imagery and line drawings included to highlight features by which distinctions are made. Some of these features are only easily distinguished at SEM scale, so that's what is used. That said, it's thought among at least some taxonomists that these unique and incompatible genital configurations may be the only thing that prevents interfertility among individuals of these otherwise separate species. So it's going to be really interesting to see what comes out of genomics as applied to the Hymenoptera over the next decade or so - something else that's not rare in the literature is to encounter reclassifications and rearrangements of large branches of the family's taxonomic tree, as phylogenetic research heavily revises prior results. Beyond that, there's a lot else coming out of genomic research into the family, including a rare example of heritable mutualism between a virus and a eukaryote in the form of Bracovirus [1] [2]. So, while yours is a fair question, there is a lot going on with hymenopteran genomics and phylogenetics these days, and my understanding as an interested amateur who does a great deal of reading in the literature is that, for the moment at least, established taxonomical methods still are likely to provide a more precise, albeit still provisional, placement of an otherwise ill-characterized species. In a decade or two, though, that might no longer be the case. [1] https://en.wikipedia.org/wiki/Bracovirus https://en.wikipedia.org/wiki/Bracovirus [2] https://jvi.asm.org/content/87/17/9649 https://jvi.asm.org/content/87/17/9649
Dylan16807 6y ago
> Not sure if a troll given I address this in the OP. You can't just upload images. Internal dissections, DNA sequences, imaging at SEM scale, all of these are not rare requirements, they are the norm. Specimens have to be meticulously collected, preserved, and vouchered in Natural History collections as part of this process (Science should be replicable to some degree). Take the comment a little more gently. You didn't really address that by just saying "many of which require internal dissection, or molecular methods". And even with this followup, it's not fully addressed. Dissection takes an expert, sure. But DNA extraction doesn't require deep knowledge about the species. And preservation requires skills but not taxonomy skills. Does SEM imaging for this purpose usually require species expertise? I'm not saying you're wrong overall here, I'm just saying there are pretty obvious points where the average person won't know the answer or which of these skills end up mattering the most. > It's a wonderful aspiration to live in a society where anyone will have the free time to "level-up" to a taxonomists level of experience I don't think that's what they were suggesting.
- xipho 6y ago
  My apologies if it sounded harsh, I read it and a "go look it up on Wikipedia" type concept flashed in my head. > But DNA extraction doesn't require deep knowledge about the species. The act of extraction doesn't, but interpretation of the results does. So to does actually knowing where to get the specimens in the first place. So to does building up experience knowing where to look, how to collect, building up a feeling for the diversity and variation in the group you study. Without these tools in hand all the images, sequences, and assays etc. in the world will a) cost you way more than anyone wants to pay and b) will have you floundering around in a giant pool of dirt-common species that are well known rather than pulling that series of uncommon and ultra-rare specimens and making a contribution that really extends our knowledge. It takes years to know where to focus precious time, this isn't peculiar to taxonomy.

by xipho 6y ago

MattGaiser 6y ago

Do they actually have lots of species which look the same but are impossible to tell apart except for DNA?

hospadar 6y ago
Look into mushroom identification - many little brown mushrooms (LBMs) are differentiated only by careful microscopic analysis of their spores or DNA sequencing. Mushrooms are especially difficult because many of the potentially useful identifying features are only present at certain (short - hours or a day or two) phases of the lifecycle of the fruiting body.
- tp3 6y ago
  Finally, for those who think genomic/genetic studies are being used inappropriately, consider that while they may seem to me to be, in practice, just another sort of 'data processing' (which they are not - they are often just generalised (or even generalized), and their application to new contexts is not that different to simply applying similar analysis to previous contexts) it is possible, for example, that, for example, the study of the DNA sequences of fungi actually (if you want to make a broader and very broad claim about fungus genomics) might in the future yield, in this particular case, a much more detailed, more reliable (and possibly more objective) classification (if not entirely a direct one) of some of the fungi and their eukaryotes in our immediate neighbourhood. I've also got to say that for the same reason, I don't have a lot of confidence in the 'fungal genomic analysis' thing in particular, because, on the whole, it seems to me to be so easily manipulated.
- oasisbob 6y ago
  Fungal taxonomy is especially interesting. Some argue that latin binomials should be abandoned, see "Against the naming of fungi": https://doi.org/10.1016/j.funbio.2013.05.007 https://doi.org/10.1016/j.funbio.2013.05.007
dwiel 6y ago
I occasionally use iNaturalist to help identify plants and fungus while out on hikes. The community there has a ton of specialists and it is extremely common to get messages like this on observations that are months old. Here is one I got this morning about a random mushroom I took a picture of in the woods of Indiana: Russula sanguinea was described from a European mushroom and therefore probably isn't here in North America at all. The name has been applied to many red Russula in N. A. adding to the confusion. Out west where it may be sorted it is being called Russula rhodocephala which itself is a lookalike for Russula americana but under different trees according to Danny Miller here [1]. Mushroomexpert's Kuo and Mycoquebec say that a lookalike under oaks in the east is Russula tenuiceps or R. sanguinaria under conifers/pines, but it is probably a group of species, and also not the same as the European one in the case of R. sanguinaria. We are trying to downvote these identifications for this reason. Hopefully, any people interested in identifying mushrooms will pitch in and help to vote any Russula that is being called Russula sanguinea in the eastern US back to genus level anyway, but we are concerned with a few other species too. Read fungee's journal post here [2]. Check out the master list here [3]. Another thing that is daunting for Russula ID, there are well over a hundred known red Russula in the east, many are not named yet, and, if they are, the name is not in use. [1] http://www.alpental.com/psms/ddd/Russula/index.htm http://www.alpental.com/psms/ddd/Russula/index.htm [2] https://www.inaturalist.org/journal/fungee/46596-new-ai-computer-vision-first-for-android https://www.inaturalist.org/journal/fungee/46596-new-ai-comp... [3] https://forum.inaturalist.org/t/computer-vision-clean-up-wiki/7281 https://forum.inaturalist.org/t/computer-vision-clean-up-wik...
- dmix 6y ago
  I dabbled in mycology and identifying mushrooms is super hard, probably one of the hardest taxonomy things. I wouldn’t want to be the expert in that field getting asked all the time with a single iPhone photo. /r/mycology had to say stop posting “please identify this mushroom” because it was so common. I’d imagine its easier with insects. And you don’t have as many people who care because they aren’t trying to eat them as often. I still like to ID random bugs I find in my house and backyard and it’s always a probability exercise. Those tree identification apps by taking a photo never work. I used it at a UofT garden where every tree was labelled and it got it wrong every time. So even the ML is way off.
xipho 6y ago
Good question, increasingly we can judge for ourselves. Go to BOLD (COI barcoding) [0]. Search for "Apidae". That's just one family of bees, in this case the one that includes 27+ (IIRC, probably way off) subspecies of what we know as the honeybee. The important bit is the count in "BINS", e.g. hypothesis of speciation typically based on a single gene, COI. That's only the specimens that have been sequenced and archived at BOLD. That doesn't include the various other bee families, notably Halictidae, Colletidae, Melittidae, and others roughly all the "sister groups" in the Apoidea [1]. An example of why is this important? The Africanized honeybee, known perhaps from bad horror movies, is characterized (identified) as a hybrid of two species. It can be more or less aggressive (to the point of killing you if you don't GTFO) depending on then nature of its DNA. Hybridization has blurred the limits of the species in many areas, including in the US. Sequencing specimens is the only way to confidently determine which of the species you have, A (friendly bee honey), AB (grumpy bee honey), or B (deadly bee honey) (gross simplification here, not Mendelian). [0](http://www.boldsystems.org/index.php/Public_BINSearch http://www.boldsystems.org/index.php/Public_BINSearch). [1](here: https://www.catalogueoflife.org/?taxonKey=625GP https://www.catalogueoflife.org/?taxonKey=625GP)
- throwanem 6y ago
  > The Africanized honeybee, known perhaps from bad horror movies You're talking about The Swarm (1978), which is absolutely so-bad-it's-good. Fans of Michael Caine will I think in particular find it rewarding, and I was especially impressed with its frankly prescient treatment of the drawbacks inherent in mass insecticide application given that the ongoing research increasingly points to exactly that as the culprit for pollinators disappearing.
  - artificial 6y ago
    Sounds similar to Jaws starting a shark panic.
    - throwanem 6y ago
      Well, you're considerably more likely to run into a wild colony of "Africanized" hybrids than you are a great white shark, for one thing. For another, while I wasn't around at the time, I understand the movie was more made in response to sensationalistic reporting than a cause of it - I might be wrong about that part, though. That said, my understanding is that A. m. scutellata x A. mellifera hybrids aren't unusually aggressive in nest defense by the standards of social hymenopterans generally, but only by the standard of the European honeybee (A. mellifera). I can't claim close familiarity with the relevant literature on bee hybrids, but from what I have seen, their nest defense behavior seems roughly comparable in aggressiveness to that of many yellowjacket (Vespula, Dolichovespula) species. On the other hand, a wild bee colony is likely to be one or two orders of magnitude greater in size than a wild yellowjacket colony, which means that a comparable level of aggression in nest defense could pose a significantly greater hazard. Using the figures from the Wikipedia article [1] and its relevant source [2], it looks like A. m. scutellata x A. mellifera are responsible for an average of around 15 human deaths per year since the introduction of A. m. scutellata into Brazil in 1956. So I don't really see that there's very much to worry over here, in any case. [1] https://en.wikipedia.org/wiki/Africanized_bee https://en.wikipedia.org/wiki/Africanized_bee [2] https://www.si.edu/spotlight/buginfo/killbee https://www.si.edu/spotlight/buginfo/killbee
rmah 6y ago
Yes. And to make it even more confusing, there are often plants/animals that have wildly varying appearance but are actually the same species: e.g. great danes/chihuahuas or cabbage/broccoli
underbluewaters 6y ago
Yes, and this even applies to vertebrates and can sometimes work in reverse. I was part of a team of research divers that did fish counts in California. This was in the early 00's so in several instances genetic research found that seemingly identical fish were different species depending on region. In one case groups of fish that looked quite different turned out to be the same species. Very frustrating when you are putting in so much work underwater! That whole experience made me very skeptical of citizen-science projects once I knew how much training was required to do good work. While they are a great compliment to professional research they are no replacement (though often funders are treating citizen science as just that).

whimsicalism 6y ago

> imaging at SEM scale I can't see how that would possibly be a requirement for determining the species of a bee. Wouldn't DNA be cheaper and easier?

throwanem 6y ago
Not at this time. Sequencing is cheap and easy, but hymenopteran genomics is a young field with many more open questions than answers; morphological taxonomy is much more mature, and aided besides by highly specific genital configurations which are, in no small number of cases, the only way currently known reliable of telling two macroscopically indistinguishable species apart. Too, in order to evaluate genomic relatedness precisely enough to update taxonomy, you need your sequence database to be broad as well as deep - unless you already have a broad and deep sequence database of other solitary bees, for example, it's hard to get very precise results out of a given solitary bee's genome. It may not even tell you anything you didn't already know. In any case, it's not rare in the literature to encounter whole genera categorized almost entirely through analysis of the males' aedagi, with microscopic imagery and line drawings included to highlight features by which distinctions are made. Some of these features are only easily distinguished at SEM scale, so that's what is used. That said, it's thought among at least some taxonomists that these unique and incompatible genital configurations may be the only thing that prevents interfertility among individuals of these otherwise separate species. So it's going to be really interesting to see what comes out of genomics as applied to the Hymenoptera over the next decade or so - something else that's not rare in the literature is to encounter reclassifications and rearrangements of large branches of the family's taxonomic tree, as phylogenetic research heavily revises prior results. Beyond that, there's a lot else coming out of genomic research into the family, including a rare example of heritable mutualism between a virus and a eukaryote in the form of Bracovirus [1] [2]. So, while yours is a fair question, there is a lot going on with hymenopteran genomics and phylogenetics these days, and my understanding as an interested amateur who does a great deal of reading in the literature is that, for the moment at least, established taxonomical methods still are likely to provide a more precise, albeit still provisional, placement of an otherwise ill-characterized species. In a decade or two, though, that might no longer be the case. [1] https://en.wikipedia.org/wiki/Bracovirus https://en.wikipedia.org/wiki/Bracovirus [2] https://jvi.asm.org/content/87/17/9649 https://jvi.asm.org/content/87/17/9649

Dylan16807 6y ago

> Not sure if a troll given I address this in the OP. You can't just upload images. Internal dissections, DNA sequences, imaging at SEM scale, all of these are not rare requirements, they are the norm. Specimens have to be meticulously collected, preserved, and vouchered in Natural History collections as part of this process (Science should be replicable to some degree). Take the comment a little more gently. You didn't really address that by just saying "many of which require internal dissection, or molecular methods". And even with this followup, it's not fully addressed. Dissection takes an expert, sure. But DNA extraction doesn't require deep knowledge about the species. And preservation requires skills but not taxonomy skills. Does SEM imaging for this purpose usually require species expertise? I'm not saying you're wrong overall here, I'm just saying there are pretty obvious points where the average person won't know the answer or which of these skills end up mattering the most. > It's a wonderful aspiration to live in a society where anyone will have the free time to "level-up" to a taxonomists level of experience I don't think that's what they were suggesting.

xipho 6y ago
My apologies if it sounded harsh, I read it and a "go look it up on Wikipedia" type concept flashed in my head. > But DNA extraction doesn't require deep knowledge about the species. The act of extraction doesn't, but interpretation of the results does. So to does actually knowing where to get the specimens in the first place. So to does building up experience knowing where to look, how to collect, building up a feeling for the diversity and variation in the group you study. Without these tools in hand all the images, sequences, and assays etc. in the world will a) cost you way more than anyone wants to pay and b) will have you floundering around in a giant pool of dirt-common species that are well known rather than pulling that series of uncommon and ultra-rare specimens and making a contribution that really extends our knowledge. It takes years to know where to focus precious time, this isn't peculiar to taxonomy.