Poop scanners… scoop it up, plop it in, and it tells you what pooped it. Given that many critters have a natural inclination to poop when stressed, perhaps just putting that bug in the receptacle is enough to have it poop and then you can release the bug and have the scanner do its thing. That way you don’t even have to take it’s leg and blend it up!
3 Likes
Several strains of DNA without an egg, a shell and a brooding hen will not end up in a chick, though ;-)
4 Likes
If you really want to boil it down to the most materialistic explanation – and I suspect most of us probably don’t – the genetic code is all that matters. The organism built by that code is merely the machinery that allows the code to protect itself and then replicate and perpetuate itself into the next generation. How the environment shapes the organism from conception through its reproductive period is merely some tweaking of the machinery that might or might not help in getting the code into the next generation. That’s the Richard Dawkins gene’s-eye view of the world, more or less.
2 Likes
Or, as I have seen it simplified for laypersons, “A chicken is just an egg’s way of making another egg.”
4 Likes
I think you’re missing the point. The only thing that gets copied faithfully with any longevity is the genetic material. Because of that, every organism has an unbroken line of ancestry going all the way back to the very beginning of lfe. And this also connects every organism together into single tree of lfe. Whatever may happen during the lifetime of each individual has no part to play in that, because acquired charactistics aren’t inherited.
2 Likes
Nevertheless, the hen also had to pass through the genetic eye of the needle to get here, just like every other hen before it.
2 Likes
Unless they are acquired through Horizontal Gene Transfer. 
3 Likes
It is important to keep in mind that the technique used in the barcoding system is premised on the presence of base pairings that are weakly selected or neutral. The theoretical basis of the technique is that weakly selected sites act as clocks for measuring isolation. Over time they accumulate random mutations. Organisms that are isolated from each other will accumulate different neutral mutations at different sites and taxonomically distant groups will be more different than taxonomically close ones. The method has been pretty robust and it is being applied widely.
Technology changes how we do things. A few years ago I needed to consult primary literature to identify birds in many places. Then field guides proliferated. Then on-line guides with audio became real. Now I can post a crappy photo to iNat and get an ID from somebody with actual knowledge. I still collect field guides and I still try to ID things on my own. Having a tricorder won’t change that. If anything it will increase the speed at which I learn to identify new things.
2 Likes
I know that acquired characteristics cannot be inherited, just as I understand that DNA is the foundation of life. What I was trying to say is that the expression of genetic information can differ between individuals in different circumstances. This may or may not have a difference on long term selection, and I really don’t want to debate this. The original post is about gene sequencing replacing morphology as a method of identifying species. Given that two individuals can differ slightly in their genetic makeup but look the same (or be identical and look very different), does a slight change in genetic information denote a different species?
1 Like
But the data to date indicate that the barcode method correlates well with other means of identifying and that the cryptic species it has revealed are as real as any other species. So what’s the issue?
I guess the question I have, and others seem to (at least by my reading of the threads parts of which go beyond the knowledge base of someone like me whose primary interest is biogeography, not genetics) is can genetics ever overcome the same barrier that morphology has, which is figuring out where the division line between intra-species variability and speciation is ?
Is that something there is any consensus or literature on?
3 Likes
If morphology has figured that out in a manner that applies consistently and universally to all living things it hasn’t done a very good job of communicating it. There is no definitive morphological definition of species. All species concepts have exceptions and inconsistencies.
1 Like
@cmcheatle Honestly, I don’t know. I saw the article, and thought it would be an interesting topic for discussion. I do have some strong feelings about genes being the be all and end all to life, but those are more philosophical. Here is one of the original papers regarding Lepidoptera -https://www.pnas.org/content/101/41/14812 My question is that if the adults are morphologicaly similar, then there must be something stopping them from breeding. Since they are all from the same small region, it would seem to be pheromone attraction is the main cause. Is this caused by speciation, or feeding on different host plants. I don’t know the answer.
Sorry if I was not clear in what I wrote, what I meant is that inability to define the dividing line exists in morphology, but can it be overcome with genetics ?
At a minimum, it would require sequencing large numbers of any suspected species to try and work it out I assume?
1 Like
Also, do not discount epigenetic changes. I remember that there is a mollusk, I forget which one, where the color of shell is determined not by the organism’s genetic material, but by the epigenetic state inherited from the mother at the time of birth/conception, which determines the following mother’s shell color. And so on, e.t.c. I remember this from my Genetics class because the professor remembered the different colors of the shells as Belgian Chocolates! 
4 Likes
If we want to define that line by presence and extent of current gene flow between putative taxa, genetics is certainly a more direct way to get at that question than morphology (which serves as a more convenient, but also more noisy, proxy for what is going on genetically). But it involves much more than a simple “barcode,” or some measure of overall genetic similarity between samples of the taxa. The amount of sampling and analysis required to quantify gene flow between populations is never likely to be possible quickly or outside of a laboratory environment.
So I think morphology will continue to be indispensable as our best first approximation of what is going on. And in many cases it can be enough.
3 Likes
Genetic analysis is great! It’s really helpful! But it’s not a cure-all. Genetics help figure out where the lines are between taxa. If the distinction is clear – if the taxa have been separate for a long time – genetic analysis can find the difference. But in most (not all) cases, morphology can find that difference, too. Where morphology gives unclear answers, genetics may – or may not.
In the unclear cases, genetics provides more evidence but it can’t give us simple answers because there are no simple answers. Two populations are diverging, becoming two species. Will they continue? Will they merge back together? At what point should we call them different species? Genetics can’t answer those questions.
Two populations are similar but differ slightly and don’t interbreed because they’re geographically separated. They probably would interbreed if they met, but they don’t meet Should they be called one species or two? The answer must be a matter of human judgement, nothing else. Genetics can’t provide the answer.
People sometimes seem to think that a certain amount of genetic differentiation makes two populations different species. That isn’t true. Sometimes a small genetic difference or a chromosome rearrangement with little genetic sequence change causes two populations to be reproductively isolated. In other cases, a single species with clearly interbreeding populations is genetically variable.
We treat species like nice, neat, mutually exclusive categories because that’s what we need our words to be. Animals, plants, and other organisms have no need for our neat words. Our learning to analyze genetics doesn’t change that.
8 Likes
Very nicely put. In the article that started all this, there is a quote from Linnaeus - “God created, Linnaeus organised,” he immodestly told people."
I don’t think humans, as a group, are comfortable with the ideas of randomness, chance etc. Or, if you like, an element of chaos. Like you, I see Life existing in a somewhat chaotic manner, with nothing certain, nothing “organized”. In a state of flux. As a side issue, I think this is why people have a hard time accepting things like climate change. It’s random, slow, and uncertain. If it was more rhythmic and predictable, I suspect more folks would be on board.
These are my beliefs, by the way. I have no proof - it’s just how I understand the world around me.
3 Likes
One point to keep in mind is that a genetic analysis requires a good morphological foundation to properly match current names and genetic results.
Unfortunately, taxonomy of many large genera is poorly known. All we have is papers more than a century old, short and obscure descriptions, and type specimens often badly preserved.
In my small field of interest i can make the examples of beetles Melyris or Astylus, where providing reliable specific names to attach to specimens could be often a real challenge .
5 Likes
I am open to adopt new names created on the basis of genetcs but if this will be the new standard then a new concept of species shall be elaborated. For now I am a little bit dubious of cryptic species that are, at least apparently, morphologically undistinguishable. Are we sure that the marker that are currently available are “bullet proof” or are they, at least in some cases, just confusing us showing differences that would be claimed to be significant when they are not significant? As regards, how many times past taxonomic shifts based on genetics have been reverted?
3 Likes