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Post by exoticimports on Jun 29, 2021 6:48:56 GMT -8
"modern DNA trees cannot be used to determine reproductively-isolated taxa..." Speyeria atlantis and S. hesperis species boundaries, Scott & Guppy, Lep Soc News, Summer 2021
"These levels of divergence across the genome...were not reflected at the same levels in mtDNA (COI haplotype diversity...)...and Tajima's D was negative...suggesting potential problems with relying on just MtDNA..." Genomic Data Support the Elevation of the Federally LIsted El Segundo Blue...to Species Status, Journal Lep Soc June 2021
My knowledge of modern scientific genome analysis is "use DNA to differentiate." END.
I keep reading about "other methods" and "other markers", even to the point now of authors severely criticizing other authors for not-looking-at-this, or not-analyzing-that.
Can somebody give me a Dummy's version of what these markers/ methods are?
Thanks,
Chuck
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Post by eurytides on Jun 29, 2021 8:59:53 GMT -8
Do these papers mention what specific markers or methods? There are many.
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Post by exoticimports on Jun 29, 2021 9:11:22 GMT -8
Do these papers mention what specific markers or methods? There are many. Typically yes. And other aspects like DNA ratios or something. It’s all like reading Greek. |
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Post by eurytides on Jun 29, 2021 9:21:20 GMT -8
If you provide some specific names, I might be able to provide some info (what little I think I know).
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Post by jshuey on Jun 29, 2021 9:43:50 GMT -8
I have not yet seen the articles in question so don't know the specifics. But maybe that is good - and the generalities are better. I don’t claim to be an expert about this stuff at all – but I have a passing familiarity with it. So here goes – of the top of my head… First thing to remember, is that these are just tools like everything else. A microscope lets you count segments on antennae. These tools let you see DNA sequences inside an animal. But here’s the basic idea and problem. If two entities are different species, then they cannot have identical nuclear DNA. But the problem often is that people only look at one or a few genes – not the entire genome. In theory differences found on the smaller subsample should reflect the entire genome – but who knows for sure if this is true. That gives you a lot of room to complain about other people’s work if you are so inclined. There are a really two different approaches to this type work. You most often hear about mtDNA (aka mitochondrial DNA, DNA barcodes) because it’s straight forward and now streamlined to perform. First mitochondria are organelles inside your cells that have their own genetic code. They are passed on as clones from your mother. But over time, errors occur in the genetic code, and these accumulate creating what people call a genetic clock. The more evolutionary time that has passed between two species forming from a common ancestor, the more different the mtDNA will be. Some people think that if mtDNA differ at some pre-determined level – often 3% is used – then they are different species. John Burns illustrated that while this is often true, there are very easily recognized species (wing patterns, genitalia, host plants) that differ by less than 0.1%. Alternately, there are many species for which the adults cannot be separated based on wing patterns – think Astraptes fulgerator – which is really at least 12 species now. They all look alike, but they have consistently different mtDNA, the larvae look different, and they feed on different host plants. Burns’ point is – mtDNA is a tool that you need to evaluate in conjunction with other characters. In the Astraptes case, mtDNA helped collaborate what Dan Janzen was discovering as he reared thousands of these caterpillars from Costa Rica. They acted like separate species as larvae, but all looked the same as adults. mtDNA proved that they had been isolated from each other for a very long time – millions of years most likely. They are species. mtDNA also gave is Hermeuptychia intricata Grishin in the eastern US. Only after Nick described the bug as new, did people reliably figure out how to tell it apart from H sosybius. The vast majority of work has been performed with this mtDNA analysis – barcodes if you will. The “barcode” is just a subsample of the genetic material inside the mitochondria. The barcode part refers to a specific standardized segment - hence the barcode analogy. It’s a tool, open to interpretation. Contrast with nuclear-DNA – which is what sex is all about and is the gene pool as you know it. Like I said before, if you sequence the entire genome of two distinct species, they will be consistently different. Nick Grishin sometimes dives this deeply into sequencing – and you can find an amazing paper that uses whole genomes in hairstreaks here - www.researchgate.net/profile/Robert-Robbins-2/publication/349208719_A_switch_to_feeding_on_cycads_generates_parallel_accelerated_evolution_of_toxin_tolerance_in_two_clades_of_Eumaeus_caterpillars_Lepidoptera_Lycaenidae/links/604f615a299bf13c4f090521/A-switch-to-feeding-on-cycads-generates-parallel-accelerated-evolution-of-toxin-tolerance-in-two-clades-of-Eumaeus-caterpillars-Lepidoptera-Lycaenidae.pdfWith this type analysis, you can definitively say how each of the species is different and measure the magnitude of those differences. In this case, they wanted to look at any gene that may have helped larvae process the deadly poisons in cycads. But most efforts subsample the genome – so their analysis is reduced to “tool” status. They cannot say definitively how two species are different – but they can compare those segments of the genes they analyzed. If two groups of populations interbreed, differences should be minor. If they do not interbreed, you should be able to find consistent differences between the populations if: 1. Enough time has passed that random mutations have accumulated, 2. You sampled enough of the genome to pick up real differences, and 3. You are looking at a segment of the genome that has actually mutated. But if you did not choose the correct part of the genome or you just looked at a little snippet – you may easily conclude that two lineages are in fact the same (because you simply missed the differences). Other "markers and sequences" refer to the part of the genome that individual researchers sequenced. Unlike the "mitochondrial Barcode" segment, there is no standardized part of the nuclear genome that people sequence. They will always tell you what they sequenced, but it's up to you to see if that they same segment that other authors may have used. So, let’s confuse this even further - in addition to problems associated with sampling different parts of the genome – you also have to define “species”. Some people would say that any lineage that is on its own unique evolutionary pathway is a distinct “evolutionary species”. In this case, any consistent DNA differences between populations would signify that they are distinct species. But some of those differences may have accumulated because the populations became separated, and if given the chance, these could indeed still interbreed – think subspecies if you will. This is the biological species concept. And there are lot's of other species definitions as well... So, despite what we’d like to think, species are not very “real”. They are concepts, based on your assumptions of what contributes a species (which may well be different than my concept of a species). I lean strongly towards an evolutional lineage species concept – in part because I’ve spent my life trying to protect biodiversity – and these lineages are the core entities that create biodiversity. But who knows if two authors debating some of these issues are actually using the same species concepts. Note that I’ve been confused by species for a long time… Many moons ago, I published a paper entitled “The morpho-species concept of Euphyes dion, with the description of a new species”. People must have liked what I did there, because Euphyes bayensis - an entity that confused the hell out of me at the time, is still recognized. John |
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Post by exoticimports on Jun 29, 2021 10:45:06 GMT -8
John, that is EXACTLY what I was looking for! Thank you!
Aside from cost/ time, why not sequence a larger part of the genome? Or is that the problem?
In my lifetime we've discerned sp/ssp morphologically and geographically, then with foodplants, now DNA. Amazing.
Now, when I see two barcodes I can say "ooh those are really different!" or "hmm...just two little spikes of yellow." In contrasting humans, we have white skinned, blue-eyed blubber eaters, and blue-black skinned omnivores with perfect eyesight. I'm told they we a singular species, not even subspecies. Clearly, the DNA has different "markers." Who determines which markers are significant(? probably wrong word) enough to claim sp/ssp status? If morphology doesn't always determine status, and phermones don't (different paper on Hemileuca), and even DNA may not, then do we really know, even if "species" is defined?
Thanks again John, that was perfect.
Chuck
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Post by eurytides on Jun 29, 2021 10:59:11 GMT -8
John, thanks for taking the time to write that!
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Post by jshuey on Jun 29, 2021 13:32:34 GMT -8
Aside from cost/ time, why not sequence a larger part of the genome? Or is that the problem?
It’s a lot of extra time and cost. mtDNA samples go into a rack and an auto sampler puts in the reagents, shakes the rack, pulls the sample back out and spits out results (most of the time). There is nothing standardized about the whole genome analyses, and it takes serious computing power to re-assemble the data into the correct spots within the genome. A lab with good equipment can turn out a few hundred barcodes a day. It takes several days to turn out a small batch “everything” sequences.
Now, when I see two barcodes I can say "ooh those are really different!" or "hmm...just two little spikes of yellow."
But keep in mind – that they are still just one piece of evidence that two bugs are different or the same. It’s just some information that you still have to think about.
Who determines which markers are significant(? probably wrong word) enough to claim sp/ssp status?
Anyone who wants to! Of course, if they want to publish, they have to know something about the subject to get it past peer review. But the main difference between most of the examples in butterflies and the case you mention in humans, is that in butterflies – there are fixed differences that make it easy to say, this bug never breeds with that bug. Or not – think white admiral versus red spotted purple. A couple of genes are fixed in both subspecies, but you get blends where they mix. And other genes also seep through that blend zone as well. Then look at the Eumaeus paper linked above. There are completely different genetic pathways for detoxification in these closely related species.
I’m in the process of writing a paper that says- even though the male and female genitalia of these two bugs are identical, and for the last 100 years people never questions the species status of the two populations, barcodes consistently separate the populations (but with ~0.5% difference – so very low) and using the subtle wing patterns differences that I’ve discovered, I can visually separate them. Therefore, these two bugs, one in western Mexico, the other in the east and south through Costa Rica, are different species. As long as I state my rational (and it holds up to peer review) – it’s my call. So if I can do it - pretty much anyone can...
john
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Post by exoticimports on Jun 30, 2021 3:06:44 GMT -8
Thanks John! That explains some of the critique going on.
Curious if the mentioned geographically isolated species you mentioned will produce viable offspring.
Chuck
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leptraps
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Post by leptraps on Jun 30, 2021 3:48:24 GMT -8
I read these post's with great interest. I am no scientists nor a Biologist who can create such documents/articles. I am amazed that some of you can use such information.
On the other hand, I design and create the equipment that you can use to collect the specimens you study.
Each one of us contributes to increasing our knowledge of the Lepidoptera, or any other living organisms we choose to study.
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Post by cabintom on Jul 27, 2021 4:18:38 GMT -8
I’m in the process of writing a paper that says- even though the male and female genitalia of these two bugs are identical, and for the last 100 years people never questions the species status of the two populations, barcodes consistently separate the populations (but with ~0.5% difference – so very low) and using the subtle wing patterns differences that I’ve discovered, I can visually separate them. Therefore, these two bugs, one in western Mexico, the other in the east and south through Costa Rica, are different species. As long as I state my rational (and it holds up to peer review) – it’s my call. So if I can do it - pretty much anyone can... john
Out of curiosity, why have you decided to separate the two as species and not subspecies? Or should I just wait for the paper? 
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Post by jshuey on Jul 27, 2021 9:09:37 GMT -8
I’m in the process of writing a paper that says- even though the male and female genitalia of these two bugs are identical, and for the last 100 years people never questions the species status of the two populations, barcodes consistently separate the populations (but with ~0.5% difference – so very low) and using the subtle wing patterns differences that I’ve discovered, I can visually separate them. Therefore, these two bugs, one in western Mexico, the other in the east and south through Costa Rica, are different species. As long as I state my rational (and it holds up to peer review) – it’s my call. So if I can do it - pretty much anyone can... john Out of curiosity, why have you decided to separate the two as species and not subspecies? Or should I just wait for the paper? Ha! You just hit the "what is a species" question on the head. I can go either way on this one, but my tendency is to view evolutionary lineages as species. This one has three things pointing to a distinct linage. Obviously, the bar codes are distinct (but barely). There are consistent wing-pattern differences (distinct enough that I can ID over 80% of photos on iNaturalist). And the two things are geographically isolated by high mountain ranges. A different person would look at this evidence as very minor - and say subspecies... john |
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Post by cabintom on Jul 30, 2021 7:31:37 GMT -8
I can go either way on this one, but my tendency is to view evolutionary lineages as species.
Meaning that you'd view all subspecies as full species? |
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Post by jshuey on Jul 30, 2021 11:50:57 GMT -8
I can go either way on this one, but my tendency is to view evolutionary lineages as species. Meaning that you'd view all subspecies as full species? No - there are definitely cases where two subspecies are the result of selection pressure - think red-spotted purples and white admirals. There are lots of examples like this where a species gradually changes pattern over its range, and people have named some of the forms as subspecies. But at least in the tropics, there are lots of subspecies that are clearly allopatric, often separated by mountain ranges or even oceans. They obviously share common ancestors, but are different enough that they are recognized subspecies. These are the things that I'd prefer to recognize as different species. It all comes down to " personal judgement" - you often hear about lumpers and splitters - I lean towards splitter. Largely because I work as a conservation ecologist, and as such, want to conserve as many evolutionary lineages as possible. If you are a lumper, then these lineages tend to get lost. John |
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Post by cabintom on Jul 31, 2021 11:22:46 GMT -8
Interesting. Thanks for sharing your perspective John!
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