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Topic: Papilio machaon from Sichuan, Identification please. | Author: Wu Ming Hsuan | Replies: 16 | Views: 1228
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Re: Papilio machaon from Sichuan, Identification please.

by Chuck » Fri Oct 25, 2024 9:22 pm

adamcotton wrote: Fri Oct 25, 2024 9:08 pm
Chuck wrote: Thu Oct 24, 2024 7:42 pm And just like that, because somebody has to over-analyze a well established species, Oregon loses an entire species!
Actually Oregon hasn't lost a species at all, the name has just changed but the butterflies are still there.

Adam.
Tell that to Kevin. He had machaon, now all he's got are bairdii. That's worse than when Alaska "lost" its own ssp of canadensis. :lol:

Thanks for your insights Adam.

To my mind, all this reinforces my (current) belief to compile series - "Catch 'em all and let the scientists sort 'em out." Except Papilio polyxenes, which I'm told nobody wants more of; that said I never know in the Appalachians when that polyxenes might be joanae.
Topic: Papilio machaon from Sichuan, Identification please. | Author: Wu Ming Hsuan | Replies: 16 | Views: 1228
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Re: Papilio machaon from Sichuan, Identification please.

by adamcotton » Fri Oct 25, 2024 9:08 pm

Chuck wrote: Thu Oct 24, 2024 7:42 pm And just like that, because somebody has to over-analyze a well established species, Oregon loses an entire species!
Actually Oregon hasn't lost a species at all, the name has just changed but the butterflies are still there.

Adam.
Topic: Papilio machaon from Sichuan, Identification please. | Author: Wu Ming Hsuan | Replies: 16 | Views: 1228
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Re: Papilio machaon from Sichuan, Identification please.

by adamcotton » Fri Oct 25, 2024 9:06 pm

The important distinction between the tree from Condamine et al. (2023) in the figure above and COI trees of Tiger Swallowtails is that the tree above is based on a number of both mt and nuclear genes.

A number of species groups in Papilionidae (and I am sure many other taxa) do not separate into neat clusters in a COI analysis, machaon and its relatives is one of those. I suspect that only trees based on multiple nuclear genes as well as COI and a few other mitochondrial genes will be able to produce well resolved trees.

Adam.
Topic: How Genetic studies reveal new relationships, species | Author: Chuck | Replies: 35 | Views: 19675
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Re: How Genetic studies reveal new relationships, species

by Chuck » Fri Oct 25, 2024 9:00 pm

adamcotton wrote: Fri Oct 25, 2024 8:54 pm
I am a little confused by Gen 1 and Gen 7 in the figures, unless 'Gen 7' actually means the 7th generation ancestor. The oldest 'parent' in the lineage should be at the top of the pyramid with the offspring at the bottom, but perhaps I am misinterpreting your unusual pyramid.
Gen 7 is a singular individual. It's parents are directly below it; and six more generations below (Gen 1) you see it's great-great-great-great-great-great grandparents.

This demonstrates the number of individuals that donate DNA to a single individual, exactly like all of my ancestors who donated their DNA (except in some cases MtDNA.)
Topic: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail | Author: Chuck | Replies: 55 | Views: 3576
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Re: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail

by Chuck » Fri Oct 25, 2024 8:56 pm

adamcotton wrote: Fri Oct 25, 2024 8:30 pm With regard to Papilio bjorkae and other 'glaucus' putative taxa, it is good to put a name to those that can be defined morphologically and then see what genomics uncovers.

Adam.
Really? But all I've read for decades is big fights over what's not a valid subspecies (which predates genetics) and synonymization. I'm so confused.

So then, since our Spring Form is not bjorkae, and the one up on the lakeshore isn't the same either, I should describe two new...species? Subspecies? The ones on the lakeshore I suspect are hybrids, because as one goes east 70km around the end of Lake Ontario, there must be a heavily hybridized zone, because 30km north of there they are canadensis.

Would one name a suspected hybrid?

Worse, when I was in PA chasing MST I caught some Speyeria cybele because they were (1) right there and (2) looked much darker. I just pulled a pair off the board. Now that you've said that, I looked at iNat and couldn't find a match, so I pulled some more out of the freezer (these were going to go to Dr. Hyatt.) So how would I know if these are a unique ssp or a form?

This has rather turned my methods upside down. I have tons of specimens that don't match the nominate, accepted morphology.
Topic: How Genetic studies reveal new relationships, species | Author: Chuck | Replies: 35 | Views: 19675
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Re: How Genetic studies reveal new relationships, species

by adamcotton » Fri Oct 25, 2024 8:54 pm

Chuck wrote: Fri Oct 25, 2024 4:00 pm From a more practical perspective, what does this mean? Below, the Gen 1 female passes the MtDNA to the next generation, and IF that individual is a female she too will pass along this MtDNA.

In this example, if the Gen 1 female (and only the female) is Papilio glaucus, then that glaucus MtDNA will continue down the line of females only and the Gen 7 (whether male or female) will have the same MtDNA as the Gen 1 female.
I am a little confused by Gen 1 and Gen 7 in the figures, unless 'Gen 7' actually means the 7th generation ancestor. The oldest 'parent' in the lineage should be at the top of the pyramid with the offspring at the bottom, but perhaps I am misinterpreting your unusual pyramid.
Chuck wrote: Fri Oct 25, 2024 4:00 pm Note too, for the Gen 7 individual, which I've selected to be male, his MtDNA will not be passed down, so all of the MtDNA shown in this tree is at a dead end, so far as his offspring are concerned; it's like they never existed.

So what use is MtDNA? First, it's a pretty good indicator of mutations. Second, it's inexpensive to extract and analyze.

Note too in the above drawings, it's unlikely that two parents produce only one viable offspring, so in any given population the MtDNA will be passed around in that population.
The last sentence answers the question ... the original male at the top of your pyramid almost certainly had many sisters who passed on the same mtDNA as the male to other members of the population. The main problem with mtDNA is when there is interspecific hybridisation involved. A first generation hybrid and all offspring down the female lineage of that hybridisation event will carry the mtDNA of the female parent species of the original hybrid. This can be problematic in the event that a single specimen is sequenced, IF that specimen was the result of hybridisation in the past. Whole genome analysis (expensive) solves this potential problem, and it may be the only solution for the glaucus-group, which has clearly undergone hybridisation events.

Adam.
Topic: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail | Author: Chuck | Replies: 55 | Views: 3576
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Re: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail

by adamcotton » Fri Oct 25, 2024 8:36 pm

I should add also that under the ICZN Code, a new taxon only needs to be PURPORTEDLY different for the published name to be available.
13.1. Requirements. To be available, every new name published after 1930 must satisfy the provisions of Article 11 and must
13.1.1. be accompanied by a description or definition that states in words characters that are purported to differentiate the taxon,
It doesn't actually matter whether the stated characters really do differentiate the taxon ... that is for a subsequent taxonomist to decide, and is an important distinction between the purpose of the ICZN Code to govern nomenclature only, not taxonomy.

Adam.
Topic: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail | Author: Chuck | Replies: 55 | Views: 3576
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Re: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail

by adamcotton » Fri Oct 25, 2024 8:30 pm

With regard to Papilio bjorkae and other 'glaucus' putative taxa, it is good to put a name to those that can be defined morphologically and then see what genomics uncovers. I suspect that it will take much more than just COI to sort out this complex.

Adam.
Topic: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail | Author: Chuck | Replies: 55 | Views: 3576
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Re: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail

by adamcotton » Fri Oct 25, 2024 8:25 pm

Chuck wrote: Fri Oct 25, 2024 12:23 pm
adamcotton wrote: ↑Mon Oct 21, 2024 1:12 am
If two populations are consistently visibly distinct in the vast majority of specimens then they should deserve subspecies status whether or not they are genetically different at all.
This shocked me so much I had to ponder it for days.

First, it really caught me off guard that Adam, of all people, being so taxonomy-minded would hold such a liberal perspective; I thought Adam would be more strict and "by the book."

Beyond that though, doesn't it open the door to commercial dealers naming forms as species?
Commercial dealers like Oberthür and many others?

Actually my statement was not 'liberal'. It is generally accepted that if two populations of the same species can be distinguished consistently in the vast majority of specimens then they are worthy of subspecies status. Of course the new subspecies must also be distinguishable from the other subspecies of the same species, not just one of them.

My point was that subspecies often have very little (or no) genetic difference to other subspecies of the same species, at least in their COI 'barcode' gene.

Adam.
Topic: RIP Jackie Miller | Author: Chuck | Replies: 4 | Views: 396
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Re: RIP Jackie Miller

by bobw » Fri Oct 25, 2024 7:04 pm

I heard about this soon after she died. I only met het once at a Lepsoc meetimg in Washington state in 2010, but she was very helpful. Obviously we shared a mutual interest in Castniidae on which she wrote her PhD dissertation. We had a long conversation about these bugs. RIP Jackie.
Topic: RIP Jackie Miller | Author: Chuck | Replies: 4 | Views: 396
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RIP Jackie Miller

by Chuck » Fri Oct 25, 2024 5:47 pm

Wow, I jumped on the McGuire website to search something, and I get slapped in the face with "Remembering Jackie Miller". Oh no.


Jacqueline Miller, Allyn curator emerita at the McGuire Center for Lepidoptera and Biodiversity at the Florida Museum of Natural History, passed away peacefully earlier this year on July 8.

https://www.floridamuseum.ufl.edu/scien ... ne-miller/

Though we'd never met face-to-face, we'd corresponded and I found her to be delightful. She helped me out once when I really needed it. I suppose I should have made a greater effort to get there sooner.
Topic: Papilio machaon from Sichuan, Identification please. | Author: Wu Ming Hsuan | Replies: 16 | Views: 1228
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Re: Papilio machaon from Sichuan, Identification please.

by Chuck » Fri Oct 25, 2024 5:30 pm

If two populations are consistently visibly distinct in the vast majority of specimens then they should deserve subspecies status


...also officially split as a species, sister to...

Going back to this statement posted elsewhere, and the tree above where everything fits into nice little boxes at the end of lines:

In looking at COI trees for the Tiger Swallowtails, I see many branches that do not fit into the nice boxes. Some are individual specimens, some are groups of; some fit closely next to known clades, and some are sisters to well established species (i.e., at the same level.) I'm not going to count them, but of the eastern Tiger Swallowtails in BOLD, I'll bet 1/3 don't fit in a nice box, and that includes boxes like MST that haven't yet been described but are known.

So Adam, you MUST be aware of "sister" specimens / groups that don't fit into the nice machaon/ indra/ etc boxes, right? As complex as the tree is for those clades already, I'm assuming there are "outliers" - and more than in the eastern Tigers. Is that correct? I'll bet there are some right in USA. And if so, what do you make of them?
Topic: How Genetic studies reveal new relationships, species | Author: Chuck | Replies: 35 | Views: 19675
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Re: How Genetic studies reveal new relationships, species

by Chuck » Fri Oct 25, 2024 4:00 pm

Mitochondrial DNA (MtDNA) is a foundation of current genetic taxonomy. It is not comprehensive, it is not the latest and greatest.

MtDNA, beside being a partial snapshot, has one critical flaw- it is only passed down by the females. None of the male MtDNA is passed down.

So let's look at this.


This is a basic heredity tree, showing how each individuals is a product of one male (red) and one female (green) parent. Various types of DNA are passed from each of the parents. You are a sum of your ancestors- sort of.

Image


However, MtDNA is only passed down from the female mother (green.) For the father (red), when the MtDNA from generation X-1 is passed to generation X, that MtDNA "disappears"- it does not get to the generation X individual. NOTE important- but other DNA does, otherwise you'd look like your mother.

Below, all the yellow MtDNA disappears when passed to the next generation because the males do not pass along MtDNA; the green is all that's passed down to the individual marked "Gen 7"

Image


From a more practical perspective, what does this mean? Below, the Gen 1 female passes the MtDNA to the next generation, and IF that individual is a female she too will pass along this MtDNA.

In this example, if the Gen 1 female (and only the female) is Papilio glaucus, then that glaucus MtDNA will continue down the line of females only and the Gen 7 (whether male or female) will have the same MtDNA as the Gen 1 female.

COI is the analysis of some MtDNA, so the heredity of any individual, based on the COI Bar Coding, tracks only mutations in the MtDNA that came along a direct path on the maternal line.

Below, let's say that the green line of females are glaucus; however, the Gen 7 individual also has (obviously) a male father, which has ancestors, and in this case every single one, male and female is Papilio canadensis (yellow.) COI Bar Coding though would concretely put this Gen 7 individual in the Papilio glaucus clade.

Image

Note too, for the Gen 7 individual, which I've selected to be male, his MtDNA will not be passed down, so all of the MtDNA shown in this tree is at a dead end, so far as his offspring are concerned; it's like they never existed.

So what use is MtDNA? First, it's a pretty good indicator of mutations. Second, it's inexpensive to extract and analyze.

Note too in the above drawings, it's unlikely that two parents produce only one viable offspring, so in any given population the MtDNA will be passed around in that population.

Hope this helps.
Topic: Tiger Swallowtails of NY: Finger Lakes, Part II | Author: Chuck | Replies: 182 | Views: 610394
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Re: Tiger Swallowtails of NY: Finger Lakes, Part II

by Chuck » Fri Oct 25, 2024 2:56 pm

Cabintom wrote: Tue Oct 22, 2024 6:17 pm Just came across this paper: "Determination of a New Spring-flying Species of the Pterourus glaucus Complex (Papilionidae) in Southern New England" https://digitalcommons.unl.edu/cgi/view ... ext=taxrpt
Thanks Tom, I do appreciate your flagging this!

Now, when do we get an update from you????
Topic: Lepidoptera Decline | Author: 58chevy | Replies: 2 | Views: 258
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Re: Lepidoptera Decline

by Chuck » Fri Oct 25, 2024 2:55 pm

Unfortunately it's behind a wall that wants an email address, at the least.
Topic: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail | Author: Chuck | Replies: 55 | Views: 3576
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Re: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail

by Chuck » Fri Oct 25, 2024 12:23 pm

The sidebar discussion on publishing the description of a new taxon which has taken most of this thread is quite interesting. It will make a good reference, perhaps it should be pulled out and lumped under a more applicable topic.

Rules, including ICZN, as well as academic "suggestions", formats of the paper and terminology, and preferences (e.g., genetic testing) stratifies the ability to publish a new taxon description such that the ability to do so is largely outside the ability of smaller institutions, citizen scientists, and those who live amongst the subject taxon.

To itemize some of the challenges to the lesser-endowed:
1. No money for $200 reference books
2. Publications hidden behind paywalls
3. No money for travel to institutional collections
4. English (and certainly Lepidoptery) as a second language
5. No credentials or membership as required to participate & publish
6. No money for even COI testing, no lab within 1500km

On it's face, a citizen scientist from, for example, Solomon Islands is in a perfect position- it would take less than a week to find a new taxon that is clearly unique; they have word processors and computers and the internet. So presumably nothing would stop said enthusiast from describing a new species- except the reality of the academic environment.

adamcotton wrote: Sun Oct 20, 2024 6:12 pm If two populations are consistently visibly distinct in the vast majority of specimens then they should deserve subspecies status whether or not they are genetically different at all.
This shocked me so much I had to ponder it for days.

First, it really caught me off guard that Adam, of all people, being so taxonomy-minded would hold such a liberal perspective; I thought Adam would be more strict and "by the book."

Beyond that though, doesn't it open the door to commercial dealers naming forms as species? In thinking of the COI tree I have for the eastern Tiger Swallowtails, from that it's clear that if Pavulaan names bjorkae and we are naming MST, there are other stand-outs that equally should be described (perhaps even moreso!) To make it more complicated, there are at least two other populations of Tigers (one I have, the other I've seen photos of) that are really, really morphologically distinctive....should those also be described? [these are on my "to look into and get genetics" list]

Further, Pavulaan's bjorkae is described with the subject having a limited range. The other Spring Form throughout US eastern seaboard/ New England are not included in bjorkae. As I've voice, JHyatt's SF and our local SF and the SF an hour north of where I live are each morphologically distinct. My next project plan was to study SF, and while Pavulaan may have scooped me, then again he may not have. I've kept these differences in my mind as perhaps forms, perhaps hybrids; I am hesitant to name each as unique taxon, pending further analysis. That said, reflecting on Adam's comment, is doing so a disservice to science? Each is unique in some way, do they not merit recognition?

On another note, Harry did tell me why he was motivated to describe bjorkae fast, w/o genetics, which is to head-off a potential cluster (American colloquialism) which would exacerbate problems I've been struggling with during my research.
Topic: Papilio machaon from Sichuan, Identification please. | Author: Wu Ming Hsuan | Replies: 16 | Views: 1228
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Re: Papilio machaon from Sichuan, Identification please.

by Chuck » Fri Oct 25, 2024 11:52 am

Thanks Adam. I had seen that, didn't realize it was the latest and greatest. And, of course, no ssp. I have a drawer of "these things" that have data but in most cases no ID, so taking it to ssp will be some work.
Topic: Papilio machaon from Sichuan, Identification please. | Author: Wu Ming Hsuan | Replies: 16 | Views: 1228
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Re: Papilio machaon from Sichuan, Identification please.

by adamcotton » Fri Oct 25, 2024 10:27 am

Here's the tree from Condamine et al. (2023), in which P. bairdii was officially separated from machaon. Note that P. kahli was also officially split as a species, sister to P. brevicauda.

Image

Sorry there isn't a more recent published tree specifically on the machaon-group. Note also that other Asian species (P. everesti, verityi and archias) were separated as species after this paper was published. There were no new trees in those publications.

Adam.
Topic: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail | Author: Chuck | Replies: 55 | Views: 3576
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Re: Papilio bjorkae (Pavulaan, 2024) Tiger Swallowtail

by bobw » Fri Oct 25, 2024 9:16 am

I've been holding off on posting this until I was sure of my facts, but I discussed it with staff at the Natural History Museum yesterday and it appears to be correct.

Obviously accessibility and cost is a barrier to the analysis of genetic material from a specimen, but one other major problem is the Nagoya protocol. This states that in order to extract genetic material from a specimen, you have to have permission from the country of origin of the specimen. This presents multiple problems; first you have to identify who you need to ask in each country, and you could be dealing with multiple countries. Then you have to hope that they will reply, and you have to ask 3 times before a "no reply" is admissable. Then you have to hope that permission is given, which will not always be the case. Evidently the museum employs one full-time member of staff just to deal with these issues.

This is all very well for a large institution like that - and they find it an absolute nightmare, but an amateur researcher would find it almost impossible to jump through all the hoops required, even if they could find the resources to get the samples analysed.

In countries which are signatories to the Nagoya protocol, it's actually illegal to extract genetic samples without the appropriate permission and in theory you could be prosecuted. Of course, one country that hasn't signed up to it is the USA, so I guess they get to do what they like.
Topic: Euphaedra sp. (I.D.) requested | Author: Trehopr1 | Replies: 5 | Views: 510
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Re: Euphaedra sp. (I.D.) requested

by livingplanet3 » Thu Oct 24, 2024 11:09 pm

Euphadra can be difficult, but I'll try:

1. E. zampa (?)
2. E. losinga (?)
3. E. ravola (?) or E. themis (?)
4. E. ravola (?) or E. themis (?)