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 Post subject: What is a species subspecies? Layman thoughts...
PostPosted: June 20th, 2017, 9:01 pm 
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Recently read a thread from about a year ago which I chose not to reply to because I didn't want to stir up the misogynistic stuff I don't have the right alleles for to find as funny. The thread (please don't respond there, let it die, make your own choice but please...

viewtopic.php?f=2&t=23520

I am not a scientist but I have faith in science and have loved the concept of the scientific method since it was first explained to me. A tested hypothesis to explain something to the exclusion of other explanations with peer review is a beautiful way to reduce bias that humans tend to have.

Regarding Milksnakes, ever since I found out the species ranged from little tiny representatives in N.E. US to monster six footers in Central America, I have suspected it was actually a species complex of several distinct species. It looks like that is the case.

Anyway, what is a species to me? Ignoring paleo-species we can't directly study, and ignoring parthenogenic species that don't often exchange genes - to me, a species is a population of biological life forms that do not have a barrier to gene flow.

For example, California Kingsnakes and Desert Kingsnakes have an integrade zone where hybrids between the two are recruited into the population of sexually reproducing adults, so they are the same species.

For me, a subspecies is a population within a population that has some significant differences from other populations within the population. Maybe we can detect those differences with DNA or maybe they are the result of epigenetics, but which case it is does not really matter. Those differences may not currently be a barrier to gene flow worthy of species level distinction, but they could lead to such a barrier to gene flow that results in isolation followed by speciation.

So - just because genetics may not be able to distinguish between two populations at the DNA level, if there are distinct enough differences then I would say subspecies level designation is valid and important because it gives us a taxonomic way to note those differences that may be an indication the population is headed for speciation.

T. elegans complex is a good example.

I do not consider Coast Range to be a valid subspecies, I think they are Mountain Garters that sometimes (usually) have a red phase. Some sub-populations of Coast Range don't. I do however consider Wandering Garter to be a valid subspecies. Not only does it look different, but its natural history is different too.

However for making entries into the database, I would enter Coast Range as Coast Range because to my knowledge there is not yet a peer reviewed accepted paper invalidating it as a species, so I go with what science currently suggests.

But as far as lab scientists who want to do away with subspecies, I strongly disagree. I think they are an important designation in studying the process by which sexually reproducing species evolve.

Thoughts?


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: June 23rd, 2017, 1:05 am 
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"For me, a subspecies is a population within a population that has some significant differences from other populations within the population."

BAM...you nailed it, but I would add that the significant difference consists of characteristics that are peculiar to that subspecies and are found everywhere it is found. This is different from morphs, which are not the dominant characteristic of the subspecies. IE...banded cal kings, striped cal kings, and aberrant cal kings. None of those constitutes a subspecies, they are only morphs.


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: June 23rd, 2017, 5:34 am 

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I agree with both of you. But for me the subspecies is also important due to geographic location. Specifically in L. zonata.

craig


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: June 23rd, 2017, 9:54 am 
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Brian Hubbs wrote:
"For me, a subspecies is a population within a population that has some significant differences from other populations within the population."

BAM...you nailed it, but I would add that the significant difference consists of characteristics that are peculiar to that subspecies and are found everywhere it is found. This is different from morphs, which are not the dominant characteristic of the subspecies. IE...banded cal kings, striped cal kings, and aberrant cal kings. None of those constitutes a subspecies, they are only morphs.


Let me first take a side road. It's about your use of the term 'population'. To my mind, a species or subspecies may hold many populations. Only if there is no barrier which disables contact, you could say that the taxon (ssp/sp) is a population, but often these barriers exist. They can be of recent nature (e.g. anthropogenic habitat fragmentation) or older (sea level rise reducing a single land mass to a number of islands).

Note that not all taxonomists want to cancel the use of the subspecies level.

Other than that, maybe we agree, but let me put what I assume to be the original definition. Subspecies are basically geographical varieties. Their particular characteristics differ from other subspecies in a discrete way (in contrast to cases of clinal variation, where the variation occurs bit-by-bit along a continuous gradient) . These 'significant differences' do not have to be apparent in every single specimen - some may look like the typical specimens of a different subspecies.

Brian's morph definition is OK to me too.

And now where at least Brian will disagree... The distinctive characteristics can show themselves at different levels. They can be external/morphological, but also rather internal (cf. phylogenetic clades without reproductive isolation). More often than not, the two are linked, as the external morphology goes hand in hand with molecular diversification, caused by some level of restricted gene flow (= imperfect separation in contrast to all specimens being able to breed with each other in one big soup of genes).


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: June 23rd, 2017, 10:56 am 
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"These 'significant differences' do not have to be apparent in every single specimen - some may look like the typical specimens of a different subspecies."

:lol: OK, I will disagree a little...the distinct characteristic of a subspecies will ALWAYS be externally present within every individual of that subspecies. The only place it will breakdown is within the intergrade zones between subspecies ranges. Your statement included part of the definition of an intergrade...where individuals could look like another subspecies. If an individual, let's say a cal king...looks a little like a desert king (splendida), it is an intergrade, not a pure cal king, and it will NOT be found within the range of pure cal kings...


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: June 24th, 2017, 5:24 am 
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Brian Hubbs wrote:
"These 'significant differences' do not have to be apparent in every single specimen - some may look like the typical specimens of a different subspecies."

:lol: OK, I will disagree a little...the distinct characteristic of a subspecies will ALWAYS be externally present within every individual of that subspecies. The only place it will breakdown is within the intergrade zones between subspecies ranges. Your statement included part of the definition of an intergrade...where individuals could look like another subspecies. If an individual, let's say a cal king...looks a little like a desert king (splendida), it is an intergrade, not a pure cal king, and it will NOT be found within the range of pure cal kings...


Well, that's simply not true for all subspecies, species,...


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: June 24th, 2017, 2:12 pm 
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It is from my experience with king and milk snake subspecies...and I've probably seen more in diverse places than anyone...

You know, I wrote a very big and detailed book on common kings...showing all the intergrade zones and many of the intergrade "looks". You should check it out sometime. :lol:

Arguing with me on kingsnake subspecies is just going to frustrate you. It would be like me trying to tell you everything about Belgian frogs and salamanders when I've never been there...


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: June 25th, 2017, 12:59 am 
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I believe we were discussing the general concept, not its application to a single taxon/group. Unless you want to allow definitions to differ between taxa and continents, knowledge of certain specific taxa or experience in a certain part of the world are of limited value.

You should deem yourself lucky that in your beloved Lampropeltis every single specimen of each subspecies displays the diagnostic phenotypic traits. I merely pointed out that in many cases (excl. Lampros, just to be sure, sure, sure you're understanding me) a small percentage within a subspecies displays more 'general' traits (or looks like those of a different subspecies). These specimens are usually rare, but they still belong to the same subspecies as those in their population with the more subspecies-specific traits.

---
<nonsense>
As you know, I'm too much of an elitist money-grabbing scientist to care for books entitled "Harmful snakes of a tiny part of the universe". Furthermore, your books are afraid to cross a national border. In this day and age, who can believe it... :P :lol:
If you want to broaden your horizon and see what subspecies are outside of Hubbsland, my book offers ample illustration and is available on Amazon. :mrgreen: :crazyeyes:
</nonsense>


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: June 25th, 2017, 8:30 am 
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Does Amazon cross international borders? :lol: My books are sold on Amazon...

I guess I would need to see examples of which you speak. My criteria is not limited to Lampros, but my expertise is limited to the U.S. (a tiny part of the world that uses 90% of the world's resources...).


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: July 4th, 2017, 11:44 am 
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One of the problems is species are kind of fluid in some groups to begin with. Bear with me while I pontificate.

If memory serves, there is a small greenish warbler(?) that has a range that circumnavigates the Mediterranean. However, it gets slightly larger and yellower as it does so. At the point where the smallest bird breeds, the largest version of itself also breeds, but they don't interbreed and are considered the same species.

There are a number of North American Warblers the readily interbreed with each other, where they both occur. It is occasionally put out that they should be lumped together. Maybe at one point they were separated/ disjunct populations of the same species that now are now no longer isolated.

For telling the difference between Hybrid and "OK" American oystercatchers, birders have what they call the Jehl scale. Because American and Black oystercatchers hybridize, a certain number of "Americans" have too much black on them to be considered "real" Americans. Maybe some birds great, great, great grandpa bird got drunk one night and ...well you know.... So by scoring the bird on a scale of points, a bird can be classified as "pure" enough to be counted, or a mutt. Maybe it's just that birders are so tightly wound that they feel they have to classify every thing they see :roll:

One more.....(if I remember correctly)

It has recently been determined that the Sage grouse (which is larger than the rest of the population, but is otherwise phenotypically the same) that occurs up near Bishop, California, is genetically more distinct from the rest of the population than the Gunnison Sage grouse is. The Gunnison was of course split out and is phenotypically more distinct. However, since it looks the same, nobody wants to split the larger grouse into a new species.

OK. Back to herps...

If genetically things can't be told apart, even though they look different, maybe we should use "phases" instead of subspecies..? Just a thought. Back to FunkyRes's thought on T. elegans, I see a fair number most years when I go up north, on the eastern side of the Sierras. Most of the ones I see could be classified as intergrades between mountain and wandering, but you can find ones that look perfectly good to the subspecies in the same area. Since they seem to hybridize so readily, maybe it's just better to do away with the whole subspecies thing.

Another species that has always sort of confounded me is the Glossy, Arizona elegans(specifically Mojave and Desert). The descriptions of the subspecies, unless I've misremembered, list a range of number of blotches to "tell" the subspecies apart. Unfortunately, there is a large overlap in the number of blotches in the "subspecies". So if I find a snake that has a number of blotches that could be good for either one, what do you call it?? Do you go based on range, and if you're in what may be a totally made up intergrade range to begin with, do you just not use the subspecies level(what I usually end up doing)....?

Since we don't have comprehensive genetic studies for most herps, range maps are only as good as a guestimate anyway, and herps aren't necessarily the most selective mate choosers when it come to subspecies, we'll always be in the same boat for any herps who's subspecies ranges meet.

-nightdriver


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: July 4th, 2017, 1:35 pm 
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I can't speak for bird scientists, but the definition of a herp subspecies intergrade zone is where you can find individuals that are either in-betweens or favor one or the other of the parent subspecies. So, if you find a garter that looks just like a Mtn Garter right next to one that looks like an intergrade, you are in an INTERGRADE zone...

I don't know why this concept is so hard for some to grasp... :o


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: July 4th, 2017, 10:57 pm 
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In the case of the garters it's not hard to grasp.... at least for me. But, if the progeny of two intergrades(or an intergrade and a "pure" subspecies individual) phenotypically fall into what is considered the norm for either of the individual subspecies, would they still not be intergrades regardless of what they look like?

I'm good with calling most of the garter snakes I see intergrades. The intergrade zone on the eastern side of the Sierras has to be somewhere in the neighborhood of 100 miles wide . In the case of glossys, unless you find two snakes that are on the extreme of the blotch count(both high and low) in the same spot, you wouldn't know you were in an intergrade zone. Even then I wouldn't be so sure, because of words in the descriptions such as "usually have ".... many blotches.

I think somebody wrote a book on Kings I've been wanting to get.... ;)

-nightdriver


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: July 5th, 2017, 5:40 am 
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nightdriver wrote:
One of the problems is species are kind of fluid in some groups to begin with.

Sure. Biota don't care about our obsession to sort things into categories by less than waterproof criteria.

nightdriver wrote:
If genetically things can't be told apart, even though they look different, maybe we should use "phases" instead of subspecies..?

Or morphs. However, it they have some level of discrete distribution, we'll usely be able to find molecular differences too.

nightdriver wrote:
Back to FunkyRes's thought on T. elegans, I see a fair number most years when I go up north, on the eastern side of the Sierras. Most of the ones I see could be classified as intergrades between mountain and wandering, but you can find ones that look perfectly good to the subspecies in the same area. Since they seem to hybridize so readily, maybe it's just better to do away with the whole subspecies thing.

That's not hybridization, as it's within the same species. In theory, all subspecies interbreed readily, so then you'd get rid of all subspecies. You could, but you'd loose a label for intraspecific substructure and variability.

nightdriver wrote:
if the progeny of two intergrades(or an intergrade and a "pure" subspecies individual) phenotypically fall into what is considered the norm for either of the individual subspecies, would they still not be intergrades regardless of what they look like?

Yes. It's (or should be...) about evolutionary distinctness/distance, not about looks.

nightdriver wrote:
The intergrade zone on the eastern side of the Sierras has to be somewhere in the neighborhood of 100 miles wide.

Based on looks, I suppose.


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: July 5th, 2017, 8:56 am 
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A lay person’s thoughts on modern herp taxonomy:

I can empathize with all parties and their positions, but since my formal zoological training was “long ago in a galaxy far away”, my thoughts now are merely opinions.

Although interested in all aspects of herpetology as a young man, I particularly was obsessed with ratsnakes, particularly North American animals.

As a kid, I consumed info on species and subspecies, especially the “obsoleta” group. The 1958 Conant field guide was the “bible”.
I couldn’t wait to see, in person, subspecies like “Gulf Hammock Ratsnakes ( Elaphe obsoleta williamsi)”, “Deckert’s Ratsnakes ( Elaphe obsoleta deckerti )”, “Everglades Ratsnakes ( Elaphe obsoleta rossalleni )”, “Black Ratsnakes ( Elaphe obsoleta obsoleta )”, “Gray Ratsnakes ( Elaphe obsoleta spiloides)”, “Texas Ratsnakes ( Elaphe obsoleta lindheimeri )”, Baird’s Ratsnakes ( Elaphe obsoleta bairdi )”, and, of course, Yellow Ratsnakes ( Elaphe obsoleta quadrivittata )”.

By the time I personally found these in the wild, 1971, “Deckert’s” and “Gulf Hammock” were no longer considered subspecies, and rightly so. The “type” examples of these in the wild and the way they looked were way too limited in range and a product of hasty judgments for herpetologists to publish or perish.

“Baird’s” now had been elevated to species level.

I was crushed because the too that vanished looked so different in the book! Emotionally I was disappointed, but couldn’t ignore the logic of science.


The taxonomy of “obsoleta” was stable until 2000, when Burbrink et al and then Utiger et al. presented ideas that changed everything and brought back the genus, “Pantherophis”. These studies were received badly because study sample sizes were limited and based solely on mitochondrial DNA, ignoring much morphology.

As a concerned lay person, I wasn’t crushed, yet; I just took the position that this will be refined, possibly not accepted, but merged with morphological traits. I balked at the idea that I wouldn’t be able to tell in the field what species of now “obsoletus” (the correct gender matching to Pantherophis) without a lab test. What will every science teacher, hunter, fisher person, park ranger, nature center lecturer, etc., tell the general public when they ask, “what snake is that?”

I finally had to admit that my whole reaction was emotional and ignorant of the genetic tale of systematics.

Time passed, sample sizes increased, more “ologists” got into the science of genes laying out our evolutionary past, and morphology started to align with this way of looking at lifes developments. It started to make sense to a lay person. After all, I always accepted Ernst Haeckel’s 19th century concept "ontogeny recapitulates phylogeny".


Back to my obsession, ratsnakes:
I started looking at the divisions of three “obsoletus” species through a herper’s eyes, which still is primarily founded on morphology, and started to see the logic.

As an example, from personal observation, 60 years of herping, I recalled that my “Black Ratsnake” finds in northern Alabama, Tennessee, Kentucky, Indiana, Ohio, and Illinois all showed blotches and had lighter ventrals; east of the Appalachians, often the blackest “Black Ratsnakes”, showed subtle stripes, especially as you approached the Atlantic coast; and those I’d found in Missouri and eastern Kansas seemed to have more bulk and more red between the scales.

None of these traits would be strong enough for a morphology division, but add the genetic info… HMMMM

Now when I considered the geological history of North America, where areas that were covered by continental glaciers virtually had no snakes, along with alpine glaciers in the southern mountains increasing the genetic barrier between Eastern Ratsnakes and Gray Ratsnakes, and combined with Mississippi River becoming a virtual cove of the Gulf of Mexico, BAM!
The genetic markers coincide with the geological barriers.

Maybe those lab jelly jockies were on to it!

Looking at it through this lens, latitudinal migration, as well as altitudinal migration, after glaciation makes more sense.
Today, again as a lay person, I have no problem with current three species and I prefer to call the old subspecies just “variants”.

The “deli-cup” world is not a good source for arguing these concepts on many levels, but primarily because animals are more often than not, the result of employing human selection rather than natural selection. That said, it was from my emersion into this world that finally pushed me, as a lay person, into more acceptance of the three species concept. Color, pattern, etc separates the old eastern subspecies. Not much in the way of scale meristics.

Take out color and pattern: The propagation of mutants and sports in the deli-cup world gave us large populations of leucistic animals, and I would challenge anyone to definitively identify a leucistic “Black Ratsnake” from eastern Virginia from a central Florida “Yellow Ratsnake”.

Just an opinion.


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: July 5th, 2017, 9:48 am 
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In the case of the garters it's not hard to grasp.... at least for me. But, if the progeny of two intergrades(or an intergrade and a "pure" subspecies individual) phenotypically fall into what is considered the norm for either of the individual subspecies, would they still not be intergrades regardless of what they look like?


Yes, they would...that's what I was saying...An intergrade will not show up within the pure range of the parent subspecies, but can look like either of the parent subspecies in the intergrade zone.

Quote:
I think somebody wrote a book on Kings I've been wanting to get.... ;)


Well....?


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: July 5th, 2017, 9:56 am 
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Well said, Bill...but I only have one problem with the Ratsnakes...I think the Yellow Ratsnake still deserves a subspecific designation simply based on the extreme color difference from the Black Ratsnake. also, if the Gray Ratsnake is still lumped with the TX, I think that should be changed too. I am not up to speed on the current classifications of these though...cause...uh...I'm more of a Lampro guy... :lol:


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: July 5th, 2017, 12:29 pm 
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FunkyRes wrote:
So - just because genetics may not be able to distinguish between two populations at the DNA level, if there are distinct enough differences then I would say subspecies level designation is valid and important because it gives us a taxonomic way to note those differences that may be an indication the population is headed for speciation.

T. elegans complex is a good example.

I do not consider Coast Range to be a valid subspecies, I think they are Mountain Garters that sometimes (usually) have a red phase. Some sub-populations of Coast Range don't. I do however consider Wandering Garter to be a valid subspecies. Not only does it look different, but its natural history is different too.

However for making entries into the database, I would enter Coast Range as Coast Range because to my knowledge there is not yet a peer reviewed accepted paper invalidating it as a species, so I go with what science currently suggests.

But as far as lab scientists who want to do away with subspecies, I strongly disagree. I think they are an important designation in studying the process by which sexually reproducing species evolve.

Thoughts?


Actually, there are several recent examples (some in the US), where people choose to designate subspecies instead of full species. There are different reasonings for why they still include the subspecies rank, but the general consensus is that there should be a new criteria to designate the subspecies designation. I fall close to the phylogenetic/integrative camp when it comes to species concepts, but I don't necessarily have a problem with subspecies like some do. However, I think that most of the subspecies of North American herps should be re-evaluated under more serious analysis. Whether or not the subspecies is eliminated by synonymy/elevation to full species status, or conserved, should probably be done on a case-by-case basis.

Here's two examples of where the subspecies designation is validated, both go into detail on why the subspecies name has contemporary merit:

Sackett, L.C., Seglund, A.E., Guralnick, R.P., Mazzella, M.N., Wagner, D.M., Busch, J.D. & Martin, A.P. (2014) Evidence for two subspecies of Gunnison's prairie dogs (Cynomys gunnisoni), and the general importance of the subspecies concept. Biological Conservation, 174, 1–11.

Torstrom, S. M., Pangle, K. L., & Swanson, B. J. (2014). Shedding subspecies: the influence of genetics on reptile subspecies taxonomy. Molecular Phylogenetics and Evolution, 76, 134-143.

~

Also, color pattern is a murky character when it comes to morphology. In some groups, it can be extremely useful for diagnosing species of snakes, but in other cases, it can create a lot of confusion. It's just one aspect of a snake's phenotype, there are several other aspects of morphology that can lead to much cleaner diagnosis. When these characters (like scalation, hemipenal morphology, viscera) are added into the equation, it can dramatically change the results. Such analyses were applied to the Thamnophis couchii complex which gives us the current taxonomy we have now, which as far as I know, has largely been stable and corroborated with some molecular evidence as well.

Here's a great example using strictly morphological data (ie. no DNA gestapo agents) on Leaf-nosed Snakes, which suggests that the previously described subspecies for Phyllorhynchus decurtatus are invalid.

Gardner, S. A., & Mendelson III, J. R. (2004). Taxonomy and geographic variation in the leaf-nosed snake Phyllorhynchus decurtatus (Squamata: Colubridae). Journal of Herpetology, 38(2), 187-196.

This study on garter snakes from the midwest shows how variable they can be, even in "intergrade zones"

Mooi, R. D., Wiens, J. P., & Casper, G. S. (2011). Extreme color variation within populations of the Common Gartersnake, Thamnophis sirtalis, in central North America, with implications for subspecies status. Copeia, 2011(2), 187-200.


If you want more case studies or examples, holler :thumb:


– Justin


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 Post subject: Re: What is a species subspecies? Layman thoughts...
PostPosted: July 5th, 2017, 7:34 pm 
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I'll try to read all those references.....someday. Especially that leaf-nosed paper.

Loving the input. :beer:

-nightdriver


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PostPosted: July 6th, 2017, 3:59 pm 
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Color variation is not the same as intergrades between subspecies. There are 74 morphs of naturally occurring cal kings, but they are all pure cal kings. There are different color morphs of milk snakes too. but it takes more than color variation to make an intergrade. There are patterns to be considered, and scale counts, etc. I'm jus' sayin'...


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