You thought the milksnake changes were bad?

Dedicated exclusively to field herping.

Moderator: Scott Waters

Post Reply
User avatar
Bryan Hamilton
Posts: 1234
Joined: June 10th, 2010, 9:49 pm

You thought the milksnake changes were bad?

Post by Bryan Hamilton »

Thirty-nine species!

Abstract
A study of DNA sequence variation in the plethodontid salamander Batrachoseps attenuatus by Martínez-Solano et al. (2007) revealed more species than acknowledged by the authors. They sequenced 677 base pairs of the cytochrome-b mitochondrial gene in 178 individuals from 123 populations of the currently recognized species B. attenuatus from throughout most of its known range in southwestern Oregon and northern and central California. Their data show that the common ancestor of the species diverged into five clades during the late Miocene Epoch, an estimated 9.2–5.5 mya, with subsequent divergences producing at least 39 living lineages that replace each other geographically. These groups have been diverging independently from each other throughout the Pleistocene Epoch and many of them have probably reached the species level of divergence.

Highton, R., 2014. Detecting cryptic species in phylogeographic studies: Speciation in the California Slender Salamander, Batrachoseps attenuatus. Molecular Phylogenetics and Evolution 71, 127-141.
User avatar
dery
Posts: 1779
Joined: October 1st, 2011, 12:01 pm
Location: huntsville

Re: You thought the milksnake changes were bad?

Post by dery »

Yikes. I already suck at caudata taxonomy.
User avatar
Sam Sweet
Posts: 233
Joined: June 7th, 2010, 5:49 pm

Re: You thought the milksnake changes were bad?

Post by Sam Sweet »

This topic is already live in the California chapter forum.
User avatar
dery
Posts: 1779
Joined: October 1st, 2011, 12:01 pm
Location: huntsville

Re: You thought the milksnake changes were bad?

Post by dery »

I don't visit the callie forum much. When it comes to US Chapters, I usually stick to the places I've herped.
User avatar
Soopaman
Posts: 924
Joined: March 18th, 2012, 7:34 pm
Location: Houston, Texas

Re: You thought the milksnake changes were bad?

Post by Soopaman »

Ridiculous, both of them. Regardless of whether it may be "correct" or not, depending on how you wish to run taxonomy, I fail to see how splitting hairs on species can possibly help to further the scientific endeavor and benefit the human race. We were all fine, and would have been fine with the way they were classified.
User avatar
Soopaman
Posts: 924
Joined: March 18th, 2012, 7:34 pm
Location: Houston, Texas

Re: You thought the milksnake changes were bad?

Post by Soopaman »

John Vanek wrote:
Without reading the paper in question, you have no idea whether it is splitting hairs or very correct. Some DNA studies are junk, and some are excellent.

DNA studies often identify cryptic species, which may need conservation help. A species cannot be targeted for conservation until it is identified.
In my opinion, as a non-biologist, regardless of what evolutionary/DNA linkage is, if you have an animal that looks alike throughout its range and you decide to split it into multiple species, you're splitting hairs. The only reason (again, my opinion) that something needs its own species designation is if it can't naturally breed and produce viable offspring with whatever you're comparing it to.

In regards to conservation, I'm probably not the best person to judge. If you've got two "species" with their own special batch of mitochondrial DNA that fill the same ecological niche and can interbreed with each other, then why do you need to have special conservation cases for each one? They do the same thing, look the same, and breed with each other like they're the same, why should we treat them like they're different because they evolved differently? The environment needed something to fill the niche and the both evolved and filled it.
User avatar
Soopaman
Posts: 924
Joined: March 18th, 2012, 7:34 pm
Location: Houston, Texas

Re: You thought the milksnake changes were bad?

Post by Soopaman »

John Vanek wrote:
There are great questions.

It's likely that animals with distinct lineages likely do not do exactly the same thing, breed with each other, or act to fill the same niche. If they did, they likely wouldn't be distinct genetically.

Here's a good example:

Northern and Southern Black Racers look the same. What's different about them is the morphology of the spines on their hemepenes. Should internal anatomy be treated the same as color pattern? If not, why? If so, think of DNA as much smaller internal anatomy.
"Likely that they do not" is not a sufficient backing for any argument. The genetic distinction of mitochondrial DNA is, as you should know, entirely different from the rest of the genome. How close are the nuclear genomes of the milk snakes and salamanders that are being argued about here? Nearly identical.


And you can't think of DNA as internal anatomy in that regard. If the hemipenes in the southern and northern black racers are different enough to cause them to be unable to breed with each other (I really don't know if that's the case or not), then they are two distinct species as there will be no mixing of the nuclear or mitochondrial DNA (not that mitochondrial DNA mixes, as it's passed on from the Oocyte, if I recall correctly). However, if they can, there's no reason they shouldn't be considered the same species provided this occurs naturally and the offspring are viable. The mitochondrial DNA shows where they came from, not necessarily where they are today.
Furthermore, if you'd like to use that argument, my internal anatomy, my DNA is different from yours by a fractional amount. One of my ancestors was a Cherokee Indian, are we two different species?
User avatar
Soopaman
Posts: 924
Joined: March 18th, 2012, 7:34 pm
Location: Houston, Texas

Re: You thought the milksnake changes were bad?

Post by Soopaman »

I think you may have missed my point somewhere in there.

What I was trying to say, and apparently we agree on, is that if there is no breeding occurring, they are different species. I don't really have much of a problem with the morphology being the same, but I do have issues with mitochondrial DNA lineages being used to split things into different species. Maybe it's a good use for subspecies. Bottom line for me is that if they won't breed with each other, they're not the same species. Everything else is irrelevant, though generally, and what sparks a lot of the arguments, is that things that look alike usually breed.
If all 39 salamanders and 500 milk snakes (or whatever they have, this is hyperbole) won't breed, then by all means call them different things.

And in regards to the birds, I believe that's behavioral divergence, yes? It's interesting, there's certain RNA regulation in regards to the songs of some birds (I can't remember the details of what bird or birds it is, or were studied on) but essentially there's RNA that suppresses and activates genes in response to specific bird songs. Pretty impressive mechanisms, and it'd be neat to know if there isn't some sort of molecular divergence in those two meadowlarks. What that sort of study can tell in the greater scheme of things or benefit mankind, I cannot fathom, but it would be interesting none-the-less.

Overall, the molecular studies and the splitting of species really seems very frivolous, to me, as there really isn't any (that I can see) overarching goal that can be a benefit to man, other than having a really nice categorical index of things, one that someone will likely try to reshuffle in another century or millennium.
User avatar
Jeroen Speybroeck
Posts: 826
Joined: June 29th, 2011, 1:56 am
Location: Belgium
Contact:

Re: You thought the milksnake changes were bad?

Post by Jeroen Speybroeck »

Soopaman wrote:Overall, the molecular studies and the splitting of species really seems very frivolous, to me, as there really isn't any (that I can see) overarching goal that can be a benefit to man, other than having a really nice categorical index of things, one that someone will likely try to reshuffle in another century or millennium.
I'm not going to repeat all I wrote on the other thread, but just briefly this.

Imho, mtDNA alone should never be used as sufficient evidence for species level splits. There are too many confounding mechanisms at work.

Inter-fertility does not always work because speciation is a dynamic process. Thus, we need to be a little bit more flexible than the static original biological species concept. Reproductive isolation (to at least some degree) and restricted gene flow need to be established, or else I won't take it.
User avatar
Brian Hubbs
Posts: 4735
Joined: June 7th, 2010, 11:41 am
Location: "Buy My Books"-land

Re: You thought the milksnake changes were bad?

Post by Brian Hubbs »

Well, that cancels out the new U.S. milk species and the getula split...what else can we dismantle with your view?
User avatar
Cole Grover
Posts: 746
Joined: June 8th, 2010, 10:06 am
Location: Montana

Re: You thought the milksnake changes were bad?

Post by Cole Grover »

Brian Hubbs wrote:Well, that cancels out the new U.S. milk species and the getula split...what else can we dismantle with your view?
And the recent Pantherophis obsoletus group splits, too...
User avatar
BDSkinner
Posts: 231
Joined: February 15th, 2011, 8:03 am
Location: Boone, NC

Re: You thought the milksnake changes were bad?

Post by BDSkinner »

That many species seems overkill at first glance. I have yet to read the paper though. What I do know is that salamanders really confound our species concepts. Those uni-sexual ambystomids have very interesting processes and come from a few different lineages with mtDNA from species outside of their range and their relatives ranges. How? Why will a Eurycea wilderae from the southern appalachians breed with a Eurycea bislineata from Long Island, NY? Some weird things are at work.

There's a lot to take into consideration to figure this all out. I do think it is a trend to run sequences and go "Oh! That's different!". Also, I was under the impression that mtDNA gathered changes in its code slower than nuclear DNA. If that's the case, that shows a longer separation of individuals and populations, right? I never got that deep in my studies to answer that. It would add support to their separation.

I also find myself asking, what does it really matter? We are trying to understand our world in every aspect to continue its long life, how does this species complex rank in that regard? That, I also don't know.


-Brad
User avatar
Jeroen Speybroeck
Posts: 826
Joined: June 29th, 2011, 1:56 am
Location: Belgium
Contact:

Re: You thought the milksnake changes were bad?

Post by Jeroen Speybroeck »

Brian Hubbs wrote:what else can we dismantle with your view?
As much as you like ;)
Seriously though, I'm not up to speed with all the literature on N American herps and it's probably of little use to talk you about the Hyla arborea complex, the Bufo viridis complex, Triturus cristatus superspecies, Emys trinacris etc. Like I said, I think European scientists might be a little more conservative(?).
User avatar
Brian Hubbs
Posts: 4735
Joined: June 7th, 2010, 11:41 am
Location: "Buy My Books"-land

Re: You thought the milksnake changes were bad?

Post by Brian Hubbs »

Image

Image

:lol: :lol: :lol:
User avatar
Jeroen Speybroeck
Posts: 826
Joined: June 29th, 2011, 1:56 am
Location: Belgium
Contact:

Re: You thought the milksnake changes were bad?

Post by Jeroen Speybroeck »

Image
WW**
Posts: 240
Joined: June 7th, 2010, 6:32 am

Re: You thought the milksnake changes were bad?

Post by WW** »

Brian Hubbs wrote:
Image
Congratulations to America on their epic victory in the SuperBowl and World Series against… errr… themselves!

:lol: :lol: :lol:

:P
User avatar
The Jake-Man
Posts: 224
Joined: June 25th, 2012, 4:08 pm
Location: Lebanon Pennsylvania

Re: You thought the milksnake changes were bad?

Post by The Jake-Man »

Though I don't pretend to know much about mtDNA sequencing, but I have always thought that animals with very small dispersal distances, like salamanders, that can be completely geographically isolated from reproducing with other populations would experience some kind of radiative speciation over time. I wonder how many new species we would have if this method were applied to Plethodon and Desmognathus in the Appalachians.
User avatar
klawnskale
Posts: 1211
Joined: June 7th, 2010, 7:09 pm

Re: You thought the milksnake changes were bad?

Post by klawnskale »

But now look at a Western and Eastern Meadowlark:
Much more similar in appearance, but completely different species that cannot and will not interbreed.

John: According to information I gathered from the Cornell Ornithology Lab, Eastern and Western Meadowlarks will occasionally interbreed at the edge of their ranges when there is a scarcity of potential mates available . They have been able to breed them in captivity but the clutch sizes are small and the eggs do not hatch. There are so many variables and exceptions within the science of biology that practicing academicians in the disciplines of physics and mathematics at times denounce it as not being a legitimate science. Ofcourse, this is just the opinions of a select group of individuals, and we are well aware of the universal trait of opinions...
User avatar
cbernz
Posts: 547
Joined: March 16th, 2011, 12:28 pm
Location: New Jersey
Contact:

Re: You thought the milksnake changes were bad?

Post by cbernz »

Brian Hubbs wrote:Image
Number of countries on this map the average American can identify: 0
User avatar
Sam Sweet
Posts: 233
Joined: June 7th, 2010, 5:49 pm

Re: You thought the milksnake changes were bad?

Post by Sam Sweet »

Is there anyone else who is slightly embarrassed to admit to knowing Hubbs?
https://www.youtube.com/watch?v=Cey35bBWXls
User avatar
Jeroen Speybroeck
Posts: 826
Joined: June 29th, 2011, 1:56 am
Location: Belgium
Contact:

Re: You thought the milksnake changes were bad?

Post by Jeroen Speybroeck »

Sam Sweet wrote:Is there anyone else who is slightly embarrassed to admit to knowing Hubbs?
Who is Hubbs?
User avatar
klawnskale
Posts: 1211
Joined: June 7th, 2010, 7:09 pm

Re: You thought the milksnake changes were bad?

Post by klawnskale »

Sam Sweet wrote:Is there anyone else who is slightly embarrassed to admit to knowing Hubbs?
https://www.youtube.com/watch?v=Cey35bBWXls
Never mind that trait about him. Just ask him about "barking spiders".
User avatar
Brian Hubbs
Posts: 4735
Joined: June 7th, 2010, 11:41 am
Location: "Buy My Books"-land

Re: You thought the milksnake changes were bad?

Post by Brian Hubbs »

Well, I thought the jokes were funny... :roll:
I even thought Jeroen's American joke was funny...some people are just too uptight and politically correct...
Let's see, Budapest is the capital of...uh, wow, I'm really Hungry right now...time to eat.

Anyway, I'm really starting to feel like Jeroen is part of the family now... :shock:

http://www.youtube.com/watch?v=6e-3dfQK7w4

http://www.youtube.com/watch?v=nBSTzZejCFE
User avatar
Don Becker
Posts: 3312
Joined: June 7th, 2010, 4:21 am
Location: Iowa
Contact:

Re: You thought the milksnake changes were bad?

Post by Don Becker »

WW** wrote:Congratulations to America on their epic victory in the SuperBowl and World Series against… errr… themselves!
Hey! We compete with like, one team from Canada for the World Series.
User avatar
klawnskale
Posts: 1211
Joined: June 7th, 2010, 7:09 pm

Re: You thought the milksnake changes were bad?

Post by klawnskale »

Brian Hubbs wrote:Well, I thought the jokes were funny... :roll:
I even thought Jeroen's American joke was funny...some people are just too uptight and politically correct...
Let's see, Budapest is the capital of...uh, wow, I'm really Hungry right now...time to eat.

Anyway, I'm really starting to feel like Jeroen is part of the family now... :shock:

http://www.youtube.com/watch?v=6e-3dfQK7w4

http://www.youtube.com/watch?v=nBSTzZejCFE
That's 'Flemish' to you, you Ugly American :mrgreen: :mrgreen:
User avatar
Owen
Posts: 1924
Joined: June 11th, 2010, 12:35 am
Location: San Jose', Northern Catcrapistan

Re: You thought the milksnake changes were bad?

Post by Owen »

Brian Hubbs wrote:Well, I thought the jokes were funny... :roll:
I even thought Jeroen's American joke was funny...some people are just too uptight and politically correct...
Let's see, Budapest is the capital of...uh, wow, I'm really Hungry right now...time to eat.

Anyway, I'm really starting to feel like Jeroen is part of the family now... :shock:

http://www.youtube.com/watch?v=6e-3dfQK7w4

http://www.youtube.com/watch?v=nBSTzZejCFE
I take it as good natured ribbing until it gets personal. After all, some of our most iconic music comes from Belgium:

User avatar
beemaster
Posts: 112
Joined: November 22nd, 2010, 4:09 pm
Location: SE Massachusetts

Re: You thought the milksnake changes were bad?

Post by beemaster »

WW** wrote:Congratulations to America on their epic victory in the SuperBowl and World Series against… errr… themselves!

:lol: :lol: :lol:

:P
To be fair, Canada did beat us in 1992 and 1993.

Go Red Sox!
User avatar
Fundad
Posts: 5721
Joined: June 7th, 2010, 7:11 am
Location: Los Angeles County
Contact:

Re: You thought the milksnake changes were bad?

Post by Fundad »

This is what a thread looks like when our good friend Hubbs joins it.

Image
User avatar
Soopaman
Posts: 924
Joined: March 18th, 2012, 7:34 pm
Location: Houston, Texas

Re: You thought the milksnake changes were bad?

Post by Soopaman »

Fundad wrote:This is what a thread looks like when our good friend Hubbs joins it.

Image

I thought that was depicting the result of the current taxonomy adjustments?
User avatar
Brian Hubbs
Posts: 4735
Joined: June 7th, 2010, 11:41 am
Location: "Buy My Books"-land

Re: You thought the milksnake changes were bad?

Post by Brian Hubbs »

Same thing...but without the Belgian jokes. :lol:
User avatar
Fieldnotes
Posts: 1474
Joined: June 7th, 2010, 6:12 pm
Location: Anaheim, California
Contact:

Re: You thought the milksnake changes were bad?

Post by Fieldnotes »

Five new species perhaps, but 39 no way. It appears from the brief viewing I saw of the document that every locality represents a new clade. The implication of accepting 39 new species would be horrible. A reevaluation of other Batrachoseps in the same fashion would show Black-bellied Slenders as containing 40 new species, Santa Lucia Mountain Slender with 20 new species, Gabilan Mountains Slender Salamander hiding 17 new species, so on and so on. Before you know it, there are 900 new species of Batrachoseps in California alone. Then, take this same testing and move it onto other herps of the world, before you know it the world gains 200x more species and all the new species are cryptic and only by using DNA can they be distinguished. :crazyeyes:
User avatar
Brian Hubbs
Posts: 4735
Joined: June 7th, 2010, 11:41 am
Location: "Buy My Books"-land

Re: You thought the milksnake changes were bad?

Post by Brian Hubbs »

Will: Are you trying to get us back on track?
User avatar
sjfriend
Posts: 257
Joined: February 20th, 2011, 1:38 pm
Location: Alaska

Re: You thought the milksnake changes were bad?

Post by sjfriend »

I always wondered why the other Bachs had such small ranges when the "Cali" had such a huge range but 39? I don't see how we'll be able to ID most of them. Oh well, now I'll have to go back to CA to fill in the new list.
Post Reply