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Post by exoticimports on Dec 5, 2021 9:48:25 GMT -8
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. <snip> 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
Back up on this topic. I noted that A New and Rare Ithomiini from Northeastern Brazil (Lepidoptera: Nyphalida: Danainae) Journal of LepSoc, March 2021 presents a new ssp based solely on morphology and geography. There are no references to genetic tests whatsoever. I'm surprised that Journal would approve/ peer review a ssp without genetics these days. Comments? Then I went further, reading this critique of the description of Papilio appalachiensis: insectnet.proboards.com/thread/1576/news-on-papilio-appalachiensis. This series of critiques discusses from perspectives which John Shuey has already shared with us. Of further interest from a different perspective, the critiques author, starlightcriminal, registered only months before his input on appalachiensis, and "disappeared" two months after posting it. He seems, from my perspective, knowledgeable on the subject of taxonomy and genetics (at least far beyond me) and I suspect he's a professional. So what's the benchmark for naming a new ssp? Clearly genetic tests are not required, even for LepSoc Journal. Or maybe it's political? Why do I get the feeling if I name a new ssp without genetics (or likely even with) it would fail peer review? Thoughts? Chuck
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Post by Adam Cotton on Dec 5, 2021 10:31:38 GMT -8
Subspecies are not always genetically different from other subspecies of the same species, whereas USUALLY different species have significantly different sequences of commonly recognised genes such as COI, ND5 etc. However even between species there can be very low differences between these genes; such as in the case of Papilio eurymedon and rutulus, which have almost identical COI but are obviously different species.
It is not necessary to provide genetic evidence when naming a new subspecies. Mainly it can be used to provide evidence that the new taxon is the SAME species as the one it is being named under, rather than to show that the subspecies is genetically different to other subspecies of the same species.
Having said that, there are often small differences between sequences of subspecies within a species, and these can be used to support subspecies status. It was proposed some years ago that a 2% difference is a good indicator of specific difference but this is not a consistent value that can be applied across species.
Generally a subspecies is regarded as phenotypically separable by a character or characters from other subspecies in most specimens of the included population. Usually a minimum of 80% of specimens is accepted, but this figure doesn't always hold either.
Even a new species can be validly described without any genetic analysis. There is no 'requirement' for DNA work, particularly if morphology is clearly conclusive, especially if there is significant genitalic difference. Some journals certainly prefer genetic data to be included, but it really is not mandatory and definitely not political.
Adam.
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Post by exoticimports on Dec 5, 2021 13:00:25 GMT -8
Thanks Adam. For reference, I found this article that claims the best MtDNA for Papilio studies. pubmed.ncbi.nlm.nih.gov/33490531/So what about self-sustaining populations of hybrid with limited ingress of DNA from the parent species? At what point do they get considered a species? Chuck
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Post by jhyatt on Dec 5, 2021 17:12:21 GMT -8
I've come to think that mtDNA analysis, and the host of related techniques, simply provide another character to use in studying species. No more or less valuable than other characters, such as wing pattern, food plant associations, larval setae, etc etc. Some folks seem to thing that DNA techniques are the end-all and be-all of systematic studies, but for all the reasons John Shuey pointed out, they aren't necessarily more valuable than all the other, older, techniques in every case.
That's my two cents worth...
jh
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Post by jshuey on Dec 6, 2021 9:51:02 GMT -8
Thanks Adam. For reference, I found this article that claims the best MtDNA for Papilio studies. pubmed.ncbi.nlm.nih.gov/33490531/So what about self-sustaining populations of hybrid with limited ingress of DNA from the parent species? At what point do they get considered a species? Chuck The key thing to ponder is species are more of a concept than reality. There are multiple definitions of species, but I think most of the public thinks about biological species - a core tenant of which is that if two populations can't successfully interbreed, then they are two different species. But there are all kinds of shades of gray with this concept - and the mention of hybrid species is a great example. I'm personally more attune to concepts aligned with distinct evolutionary lineages. That is that populations that have distinct evolutionarily histories need to be recognized, even if they look the same. This is where mDNA often comes in, because it provides a "molecular clock" that can be used to show that two lineages have been isolated. But how long is long enough to count as a new species? That is the question.\ So, there are no black and white rules about any of this. It really comes down to usefulness of our various concepts of species. In most cases, the biological concept is pretty useful - think Celastrina in North America. In other cases, species may be so similar (as adults at least) that the lineage concept is more useful. "nothing is real"... John
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Post by exoticimports on Dec 6, 2021 10:30:22 GMT -8
I'm personally more attune to concepts aligned with distinct evolutionary lineages. That is that populations that have distinct evolutionarily histories need to be recognized, even if they look the same. This is where mDNA often comes in, because it provides a "molecular clock" that can be used to show that two lineages have been isolated. But how long is long enough to count as a new species? That is the question.\ My interests are similar. Case in point is the recent revision to Hemileuca; it seemed that the experts were grasping at straws trying to find a scientific basis to determine that the Bog Buckbean moth was something other than just ordinary maia. Glad you said "molecular clock", as I have been quandarizing. Does voltanism come into play? Say there's a 2% difference between two populations that are both double brooded, that would yield X years of separation. If they were univoltine, it would be 2X years? If one were bivoltine, and the other univoltine, it would be 1.5X years? A number of people have told me there is a "catalog" of MtDNA for some NA papilio; damned if I can remember where this is or how to find it. Chuck
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Post by exoticimports on Feb 8, 2022 10:43:27 GMT -8
Thanks guys for bringing me up to speed a bit on MtDNA and genetics. So the papers I've read use, and refer to BOLD. BOLD is awesome. But I have questions: 1. How the heck to I read this? I suppose I have to know what I'm looking at? Ex. end of page v3.boldsystems.org/index.php/Public_RecordView?processid=GBGL3919-072. How we (amateur) do a comparison of one or more specimens? I know the pros use analytic software; is this available? Does it provide a dummy's summary? 3. How would one get specimens tested and into BOLD? Chuck
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Post by LEPMAN on Feb 8, 2022 18:36:06 GMT -8
Hi Chuck, Hopefully I can answer your questions.
1. How the heck to I read this? I suppose I have to know what I'm looking at? Ex. end of page v3.boldsystems.org/index.php/Public_RecordView?processid=GBGL3919-07
The sequence you see at the end is the FASTA sequence. You don’t necessarily “read” this unless you are wanting to do specific genetic work but considering this is the CO1 gene (codes for cytochrome oxidase protein/enzyme) you most likely would not be doing this. CO1 is used mainly for DNA barcoding.
2. How we (amateur) do a comparison of one or more specimens? I know the pros use analytic software; is this available? Does it provide a dummy's summary?
It is easy to do phylogenetic comparisons between specimens (I think this is what you mean by comparing) best way to do this is download the FASTA sequence and upload it to a phylogenetic tree maker. These are available easily online with a simple search. The more complex software’s cost and have additional functions that can complicate things. The phylogenetic tree software should be able to give you relatedness. It can also give you the "family tree" for the group you may be looking at. If you have an unknown sequence that you are trying to ID you can “BLAST” the sequence. To do this you go to the BLAST database or NIH GenBank and submit the FASTA sequence. The program will compare your sequence to all the known sequences and give you a % similarity for each species.
3. How would one get specimens tested and into BOLD? Steps: 1. submit a specimen record (photograph) to BOLD and get a specimen ID. 2. Sequence the CO1 sequence. There is multiple options for this – some expensive some less expensive. 2a. If you know how to do PCR and amplify the CO1 gene then you can just buy degenerate CO1 primers and go at it. Afterwards you purify DNA and submit it to a company like eurofin or university for sequencing. 2b. If you don’t know how to do the step above or don’t have a lab you can send a leg or tissue sample to a company that does DNA Barcoding. One of the most well known is the university of Guelph in Canada. They are the ones who helped found BOLD and do thousands of sequencing. Only con? They only do large sequencing batches of 1000+ specimens. If you are looking to do a smaller number, you can find a company that accepts smaller number of specimens or you can find a taxonomist who does Barcoding and ask to include a few specimens along their batch. Without a grant and/or university affiliation it can be difficult to access some of these services. I tried to simplify everything and define any terms that I used but if anything Google is your best friend (:
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Post by exoticimports on Feb 9, 2022 5:16:36 GMT -8
Thanks Lepman,
#2 you are way over my head, I guess I have more reading to do.
One thing I'm trying to find is a modern/ recent analysis of Papilio glaucus vs. canadensis vs. the intergrade zone. This was done a long time ago, presumably with whatever method was available at the time. Specifically, the intergrade hybrids from MI were studied, but not the non-contiguous population in NY. But even if I had the data, I don't know how to read it.
Chuck
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Post by jshuey on Feb 9, 2022 5:31:32 GMT -8
Thanks Lepman, #2 you are way over my head, I guess I have more reading to do. One thing I'm trying to find is a modern/ recent analysis of Papilio glaucus vs. canadensis vs. the intergrade zone. This was done a long time ago, presumably with whatever method was available at the time. Specifically, the intergrade hybrids from MI were studied, but not the non-contiguous population in NY. But even if I had the data, I don't know how to read it. Chuck Just send Mark Scriber an email and explain your issue. Unfortunately, I don't have his email since he retired - so you will have to dig it out on your own. Try the Lep Soc Directory. Mark is a really nice guy who spent his entire, very successful, career studying tiger swallowtails. He loves the group, and the research on tigers was very kind to him over the years (Chair at Michigan State, lots of grants, elected member of the National Academy of Science). If you are on to something, Mark will have the connections to get your bugs sequenced (or he will know who already has the data hidden away from some past effort). And you will get him excited! John
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Post by exoticimports on Feb 9, 2022 7:13:54 GMT -8
Thanks Lepman, #2 you are way over my head, I guess I have more reading to do. One thing I'm trying to find is a modern/ recent analysis of Papilio glaucus vs. canadensis vs. the intergrade zone. This was done a long time ago, presumably with whatever method was available at the time. Specifically, the intergrade hybrids from MI were studied, but not the non-contiguous population in NY. But even if I had the data, I don't know how to read it. Chuck Just send Mark Scriber an email and explain your issue. Unfortunately, I don't have his email since he retired - so you will have to dig it out on your own. Try the Lep Soc Directory. Mark is a really nice guy who spent his entire, very successful, career studying tiger swallowtails. He loves the group, and the research on tigers was very kind to him over the years (Chair at Michigan State, lots of grants, elected member of the National Academy of Science). If you are on to something, Mark will have the connections to get your bugs sequenced (or he will know who already has the data hidden away from some past effort). And you will get him excited! John I asked Mark, and another expert in that field, and despite an ongoing discussion, neither responded. I took this to mean it's under study and they didn't want to say, perhaps to keep more fingers out of the pie. A third author/expert did respond, with info that conflicts with other publications, so it appears to me at least there is some contention in the focus groups. In the bigger picture, the recent focus on MtDNA and taxonomy is, as you know, very new to me so I'm trying to absorb both the methods and results. For example, right now COI and ND5 mean nothing to me. Spring form and summer form must have the same DNA, but other than winter I don't know what determines which, or how. I didn't know if I could send somebody a leg and voila here's what you want to know, or if I have to have to have an "in" with a pro or specialist (those questions I believe are now answered!) I'm confused about dates of divergence based on what appears to be a fixed rate of genetic change, when clearly there are expert papers that indicate real-time genetic change as a result of environmentally-induced change. So hope experts don't mind some questions. Yes, I use Wikipedia and other sources as well. Thanks, Chuck
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Post by LEPMAN on Feb 9, 2022 9:50:29 GMT -8
Just send Mark Scriber an email and explain your issue. Unfortunately, I don't have his email since he retired - so you will have to dig it out on your own. Try the Lep Soc Directory. Mark is a really nice guy who spent his entire, very successful, career studying tiger swallowtails. He loves the group, and the research on tigers was very kind to him over the years (Chair at Michigan State, lots of grants, elected member of the National Academy of Science). If you are on to something, Mark will have the connections to get your bugs sequenced (or he will know who already has the data hidden away from some past effort). And you will get him excited! John I asked Mark, and another expert in that field, and despite an ongoing discussion, neither responded. I took this to mean it's under study and they didn't want to say, perhaps to keep more fingers out of the pie. A third author/expert did respond, with info that conflicts with other publications, so it appears to me at least there is some contention in the focus groups.
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Post by LEPMAN on Feb 9, 2022 9:52:06 GMT -8
In the bigger picture, the recent focus on MtDNA and taxonomy is, as you know, very new to me so I'm trying to absorb both the methods and results. For example, right now COI and ND5 mean nothing to me.
Answer: COI and ND5 are just the abbreviations for the genes that encode something. They are found in mitochondria and used to study change over time. It could theoretically be any gene that has a consistent and predictable change over time. The change we refer to are actually mutations that accumulate over time (part of the process known as evolution) and the predicted rate of change can be used to determine the time and relatedness of two individuals.
Spring form and summer form must have the same DNA, but other than winter I don't know what determines which, or how. Answer: Yes, there is a concept of genomic equivalence where all cells in an organism would normally have the exact same genome. But its not about the geneome, its about the expression of the genes in the genome. Each cell goes through a process known as differential expression which is what turns totipotent embryonic stem cells into differentiated cells like wing or muscle cells. The difference in expression can result from any of the hundreds of translation and transcription regulatory pathways. These pathways can respond to environmental cues like daylight and temperature. When this happens there are hormones released like ecdysome and signaling ligands. These will bind to receptors in the cells or trigger an organ like ganglia to release different ligands (molecule signals) that trigger morphological phenotype changes. Seasonal forms are dictated through ecdysome as a result of daylight length but not all forms are dictated in the same way but all share similarities that are conserved across eachother.
I didn't know if I could send somebody a leg and voila here's what you want to know, or if I have to have to have an "in" with a pro or specialist (those questions I believe are now answered!) I'm confused about dates of divergence based on what appears to be a fixed rate of genetic change, when clearly there are expert papers that indicate real-time genetic change as a result of environmentally-induced change.
Answer: Its important to know that rate of change is a prediction! If you predict something as millions of years or thousands of years of divergence the % error is low. But when doing it in one year or a dozen year you could have results that vary between populations and etc. In general, there are many things that can affect rate of mtDNA mutations. Mutagens, a lineage dying etc. and mtDNA is very effective but not perfect. Secondly, environmental changes can lead to selections for inheritable genetic mutations that increase the offspring's change at passing along their genes. It dosent mean that this mutation is in the mitochondria but there could be a confounding variable effect where one mutation masks the other variable. e.g. a organism that happens to have an above average mitochondrial mutation rate passes on its genes because it also happens to have beneficial mutations. End result is a sudden increase of mt mutations over a short period of time but when you average everything out you get a consistent rate all across. This has to do with the sampling theory - the larger the sample the less errors.
I'm glad you asked about genetics and butterfly wing patterns/phenotypes as the molecular mechanisms that give rise to these is an active area of research for me which once published I may share on here!
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