which new sceloporus species is this one?

[Paul White]

According to my field guide, it's undulatus I think but then, my guide was written before the current split and I'm not sure which species the NE New Mexico undulatus got put into. Found in harding county NM. One of several.



edit: I dug up an old thread I started bout the undulatus split and the boundary line isn't clear where I found this--could be virgiatus (sp) I think, or consobrinus. How would I tell?

[herpseeker1978]

I think they are Sceloporus tristichus but will have to check my guide in the morning. I would strongly recommend getting this book: Lizards of the American Southwest: A Photographic Field Guide
http://www.amazon.com/Lizards-American- ... 1933855355

Josh

[ThamnElegans24]

Herpseeker1978, Was that book writen by Jesus and signed by Leonardo da Vinci, because $899.99 to $3,511.03 seems a little steep for a fieldguide.

[herpseeker1978]

Holy crap! I didn't even look at the price! Here is a better link: http://www.mapstore.utah.gov/bn100.html

Josh

[ThamnElegans24]

Now that's much better.

[Paul White]

Now that I unpacked my copy of it (was sitlli n the trunk) I'd go with tristichus too, but only based on size--this was *much* bigger than consobrinus is around here. The rest of the diagnostic traits I didn't get a good enough look at to say with any confidence. Couldn't tell you if his throat was solid or formed two distinct patches or if it had small granular scales on the back thighs or not

[Ribbit]

You can download a PDF of the article that split up Sceloporus undulatus from the CNAH website at: http://www.naherpetology.org/pdf_files/132.pdf. At least, I think that 2002 article is still the baseline for the currently accepted taxonomy (someone please correct me if I’m out of date).

John

[ChrisNM]

based upon distribution maps of the current split and our close proximity to TX, I was going to side with consobrinus. Unfortunately, the one Scelop I was able to get for photos was not an adult and I'd not brought back to camp for keying out based upon Lizards of the American Southwest. FWIW, Mills Canyon is virtually on the Mora/Harding County lines, with Mora having tristichus and Harding having consobrinus. We could all default to paalexan's response and just label it was Sceloporus sp.

Wouldn't be virgatus. They are, thus far, restricted to the boot heel of NM, Hidalgo County.

[Paul White]

It looked like consobrinus, kind of, but like, built to maybe 1/5th over scale, at least compared to the ones here.

The new range map I saw int he last thread showed lots of what had been undulatus switched to virgatus, including some NM populations? I'll have to recheck when I'm off work (I'm being bad and goldbricking a bit my first day back at the office).

[paalexan]

Rather than Sceloporus sp., I'd go with Sceloporus undulatus.

If we follow Leaché's (2002) split of Sceloporus undulatus we'd have to sequence mitochondrial DNA to tell which species this is (geographically, it's in a sampling hole between three of the putative species). However, there's an interesting recent (2009) paper from Leaché:

http://www.cnah.org/pdf_files/1363.pdf

If you don't want to read the whole thing, just look at Figure 1. You've got a mitochondrial tree on the left, a nuclear tree on the right. These give different results. Leaché's mitochondrial species are apparently not cohesive genetic entities when you look at the nuclear genome (i.e., most of the genome). There's other interesting stuff in the paper, but if we restrict our focus to the taxonomic question the take-home message is that Leaché's (2002) split of Sceloporus undulatus does not hold up when additional sources of information are included.

Which is the long way of saying that this is Sceloporus undulatus.

Patrick

[Paul White]

I can't keep up with all this taxonomic shit anymore That lizard does not care what species it is, it cares that there's a lot of food and females near that spot.

[ritt]

paalexan: The different results between the nuclear and mitochondrial datasets simply shows something that has been shown time and again: gene flow among distinct species (which could be ongoing or could be historic). Due to hybridization between some of the species, mitochondrial haplotypes have introgressed into the other species, resulting in the pattern of a few samples from near the boundaries that appear to be in the 'wrong' clade on the nuclear tree: these are samples that have introgressed mitochondrial DNA. This could have occurred thousands of years ago and may or may not be ongoing. Avoiding the debate on a strict biological species concept or a more relaxed BSC that allows some level of gene flow, this does not mean that these are not distinct species. Leache actually has some pretty good evidence that they are different species. However, it is clear that the mitochondrial clades are not perfect representations of the species boundaries, which is something that pops up all over the place. As such, its necessary to conduct more thorough sampling, combining nuclear data with morphological data to figure out exactly where the boundaries between the species are. Regardless, its definitely not the case that the species boundaries from the mtDNA don't hold up, actually with the exception of those few samples from near the boundaries they hold up quite well (particularly considering how 'slow' nuclear DNA evolution is relative to vertebrate mtDNA evolution). Don't get concerned by woodi being embedded within undulatus in the nuclear tree, I can go into it in more detail if you want, but this is the result of what is called incomplete lineage sorting, and this sort of pattern is well documented based on empirical and simulated data, and should be expected in recently diverged species, particularly if they have large population sizes (such as undulatus).

Its been awhile since I read the recent Leache paper, but I think the biggest problem I have with it, beyond the small sample sizes, is that on Fig. 1, the clade boundaries are drawn based on the mtDNA clades, whereas it is clear from the nuclear data that some of the samples called one species are a different species (e.g. cMS is undulatus, even though it has consobrinus mtDNA (which actually makes a lot of sense, the Mississippi River and the Mississippi Alluvial plain, where Sceloporus are largely absent, are the break between those two species. Similarly tCO is consobrinus, cwAZ is tristichus).



Paul: I'd call it Sceloporus consobrinus, but make a note that it is close to the boundary with S. cowlesi and S. tristichus, and may (or may not) have some intergradation / mixed ancestry.

-Eric

[paalexan]

paalexan: The different results between the nuclear and mitochondrial datasets simply shows something that has been shown time and again: gene flow among distinct species (which could be ongoing or could be historic). Due to hybridization between some of the species, mitochondrial haplotypes have introgressed into the other species, resulting in the pattern of a few samples from near the boundaries that appear to be in the 'wrong' clade on the nuclear tree: these are samples that have introgressed mitochondrial DNA. This could have occurred thousands of years ago and may or may not be ongoing. Avoiding the debate on a strict biological species concept or a more relaxed BSC that allows some level of gene flow, this does not mean that these are not distinct species. Leache actually has some pretty good evidence that they are different species.

Rather than "avoiding the debate", I think you're assuming a very particular position in that debate. If we (rather naïvely) take Leaché's results at face value, around 20% of the individuals in Sceloporus undulatus sensu lato are introgressed between the various segregate species. This suggests a very high rate of gene flow for us to consider these separate species.

However, it is clear that the mitochondrial clades are not perfect representations of the species boundaries, which is something that pops up all over the place. As such, its necessary to conduct more thorough sampling, combining nuclear data with morphological data to figure out exactly where the boundaries between the species are. Regardless, its definitely not the case that the species boundaries from the mtDNA don't hold up, actually with the exception of those few samples from near the boundaries they hold up quite well (particularly considering how 'slow' nuclear DNA evolution is relative to vertebrate mtDNA evolution).

Well, I disagree. I consider mtDNA-only studies a non-starter when it comes to delimiting species (the data aren't relevant to the question). Once it's been further established, as it is in the 2009 paper, that mitochondrial and nuclear results show substantial incongruence, personally I consider the mtDNA-delimited species defunct.

Also, regarding Sceloporus woodi--I am curious why you would attribute the nuclear placement to incomplete lineage sorting. I'm familiar with the phenomenon, but it seems improbable in a 29-locus concatenated data set. Under conditions that would allow ILS, independent loci should give conflicting results, rather than converging on an "incorrect" (with respect to the species tree) tree. Further, attributing the placement of any particular terminal in a tree to ILS requires that we have some other, better source of data that indicates that the observed placement is incorrect. Otherwise, all we can say is that the placement of a terminal might be due to ILS (as might be the placements of every last other terminal!).

Patrick

[ritt]

First off, Paul, sorry for hijacking your thread a bit here.

By avoiding the debate I meant to try to avoid a debate on whether gene flow needs to be completely ceased for things to be considered different species. Regardless, trying to say 20% of the samples have introgressed mtDNA is, as you put it, naive, though I'd argue "naive" is an understatement. Rather, such a value is misleading and ignorant of the sampling strategy and the purpose of the study. Leache was targeting samples near the mt clade boundaries, looking for incongruences between mt and nuc clades. So of course he found a relatively high rate of it, he was specifically looking for it. I'd be willing to bet if you took a random sampling of the sample number of undulatus complex lizards from across their distribution, you wouldn't get a number anywhere near that high (of course that still wouldn't be a good estimate of introgression, but it would be better than the 20% suggestion). Further, just because there are occurrences of 'wrong' mt haplotypes at present, from this study there is no way to say if this is the result of retention of mt haplotypes from historic hybridization, or if hybridization is ongoing (not that I doubt the lineages are hybridizing now, but that is not a question that can be answered from the available data).

I consider mtDNA-only studies a non-starter when it comes to delimiting species (the data aren't relevant to the question).

In what way are they not relevant? Any single locus study is far from ideal, be it based on a mtDNA or nucDNA, but I don't see how mt data are irrelevant to the question of species delimitation. There are clades of highly divergent mitochondrial haplotypes in these guys (and loads of other groups). How did these divergent clades arise? Most likely they, at some point in the past, occurred in isolated pockets without gene flow among them, that then spread to the current distribution. While these were likely associated with bottlenecks that accelerated the loss of other mt haplotypes (thus resulting in the single clade for each species), but the point is they were almost certainly isolated at some point. I have yet to hear an argument that isolated populations will not speciate given sufficient time in isolation. I'm not saying that studies should be based solely on mtDNA data, in fact I don't feel taxonomic revisions should be suggested based solely on mtDNA, but multiple nuclear loci and / or morphology (preferably both) need to be considered for taxonomic changes. But, what I am saying is mtDNA is relevant to species delimitation. Not sufficient for elevation of species in my opinion, but certainly relevant.

mitochondrial and nuclear results show substantial incongruence

As I stated above, the only reason such high incongruence was observed is Leache was specifically targeting samples from near the clade boundaries. Drop out those 3 samples from near the boundaries, then all the sudden the only congruences are at the deeper levels. The clades within the undulatus complex are the same except for those 3 samples from near the mt clade boundaries.

regarding Sceloporus woodi...

I'm not sure if you have access to the supplemental, but there is a supplemental figure with all the individual gene genealogies. Incomplete lineage sorting is all over the place. This is to be expected with nuclear loci at this level, particularly for critters like Sceloporus that have massive effective population sizes. It takes around 4 +/- 2 N generations for any given locus to sort to reciprocal monophyly. That N generations is the standard coalescent branch length, basically to convert that to years you take the effective population size (Ne) and multiply it by the generation time. Now Ne is very tough to accurately estimate, but say you've got an effective population size of 100,000 individuals. If the generation time was 2 years, it would take an average of 800,000 years for a locus to sort to monophyly. Given that there's almost certainly way more than 100,000 Scelops out there that are reproductively active and part of the Ne, you can imagine it takes a super long time. The strong support for its particular placement in the concatenated tree is a bit odd, but by concatenating them you're assuming they all share the same signal (i.e. that the topology is the same for each locus), which is clearly not the case here when you look at the gene trees. So the concatenated tree isn't really useful, I've been looking at the BUCKy trees in Fig. 5, which basically looks for concordance among the gene trees, and doesn't assume that they've got the same topology. The different placement in the concatenated tree might be due to strong signal at some loci showing that relationship (which drove the pattern), and weaker signal at other loci, or something along those lines. But getting back to my original point, if you look at the gene trees in the supplemental, there is a ton of incomplete lineage sorting.

-Eric

[paalexan]

First off, Paul, sorry for hijacking your thread a bit here.

By avoiding the debate I meant to try to avoid a debate on whether gene flow needs to be completely ceased for things to be considered different species. Regardless, trying to say 20% of the samples have introgressed mtDNA is, as you put it, naive, though I'd argue "naive" is an understatement. Rather, such a value is misleading and ignorant of the sampling strategy and the purpose of the study. Leache was targeting samples near the mt clade boundaries, looking for incongruences between mt and nuc clades. So of course he found a relatively high rate of it, he was specifically looking for it.

Well, not really. What he says in the paper is that samples were chosen to maximize geographic coverage, and that "some" specimens were sampled from mtDNA clade boundaries. Just take a look at the map; samples are pretty evenly distributed, not conspicuously concentrated at mtDNA clade boundaries.

That's kind of beside the point, though. I'm not going to argue that Leaché's data provide (or were intended to provide) robust estimates of introgression between these putative species. Instead, I think the important thing is that as far as we can tell from Leaché's 2009 data, there is a fair amount of introgression, and those data are all we have. So, it's not a good estimate, but it's what we've got to address the relevant question for species delimitation: Are the putative species genetically (or morphologically) discontinuous from each other?

I consider mtDNA-only studies a non-starter when it comes to delimiting species (the data aren't relevant to the question).

In what way are they not relevant? Any single locus study is far from ideal, be it based on a mtDNA or nucDNA, but I don't see how mt data are irrelevant to the question of species delimitation. There are clades of highly divergent mitochondrial haplotypes in these guys (and loads of other groups). How did these divergent clades arise? Most likely they, at some point in the past, occurred in isolated pockets without gene flow among them, that then spread to the current distribution. While these were likely associated with bottlenecks that accelerated the loss of other mt haplotypes (thus resulting in the single clade for each species), but the point is they were almost certainly isolated at some point.

There will be some set of hierarchical mtDNA relationships among any set of individuals. So, you sample a bunch of individuals from Sceloporus undulatus, yes, there will be mtDNA clades (which you can accurately recover to a greater or lesser degree depending on various aspects of the data and analyses). This isn't a novel empirical observation that tells you anything about the number of species involved. There will be some set of mtDNA clades whether it's one species, two species, etc.

It might be possible to use features of these clades to accurately determine the number of species. For instance, suppose you knew population sizes through time, dispersal rates, dates when areas were colonized, when mtDNA clades diverged, etc.; you might be able to create a useful modeled prediction of the characteristics that these mtDNA clades should be expected to have if the sampled individuals come from one vs. two vs. three (etc.) species, and test if the observed topology is significantly different from the expectations given one (or two, etc.) species. If all this were successfully done, you might have something workable in terms of single locus species delimitation (but, then, if you're just working with a single locus topology, where do the needed estimates of population genetic parameters come from?). So far as I am aware, no one has attempted or succeeded at such a method; in any case, Leaché's 2002 paper does not do this (his recent paper on Hemidactylus is a move in this general direction, although with multiple loci, but that analysis has the highly undesirable property that the number of species inferred is very sensitive to different guesses at values of the parameters involved--accurate estimates being critically important but unavailable!). Instead, he observes a set of mtDNA clades and infers that several of these are species. Analysis of the characteristics of those mtDNA clades is limited to observing that the mtDNA clades are geographically coherent, do not overlap, and are somewhat divergent, but we simply do not know what geographic pattern or level of divergence we should expect those mtDNA clades to have if Sceloporus undulatus sensu lato is a single species vs. two species, etc. We can't relate the observed pattern to what should be the case under various species delimitations in any meaningful sense.

(As yet another parenthetical aside, suppose the mtDNA clades overlapped extensively. If non-overlapping mtDNA clades can be inferred to be distinct species, surely the opposite is true--overlapping mtDNA clades indicate interbreeding and extensive overlap would indicate we're not dealing with distinct species. In fact, Leaché uses this kind of reasoning in a study on mtDNA diversity in a contact zone between Sceloporus cowlesii and Sceloporus tristichus: http://faculty.washington.edu/leache/wo ... cology.pdf. He infers that co-occurrence of the respective mtDNA clades indicates hybridization between the putative species. What happens if we apply this reasoning uniformly is enlightening. If overlap between mtDNA clades of Sceloporus cowlesii and Sceloporus tristichus indicates interbreeding, so does overlap between mtDNA clades of Sceloporus consobrinus and Sceloporus olivaceus. If they're all species, we have no grounds for applying different standards. This leads to problematic conclusions, e.g., that Sceloporus olivaceus interbreeds extensively with both Sceloporus cowlesii and Sceloporus consobrinus. The overlap and thus inferred hybridization is so extensive that we would have to conclude that all three are conspecific. That Leaché will happily assume that co-occurrence = hybridization in some cases but not others indicates that he considers distinctions between, e.g., Sceloporus cowlesii and Sceloporus tristichus, to be of a fundamentally different kind, to which different analytical methods and expectations are applicable, than distinctions between, e.g., Sceloporus consobrinus and Sceloporus olivaceus. To me, it is obvious that the distinction involved is that between infraspecific taxa and species. Species don't interbreed when they co-occur. Subspecies do. I can only make sense of Leaché's reasoning in this context. The non-overlapping mtDNA-clades = species approach used by Leaché, Burbrink, et al., is not just inadequate, in that the patterns observed can not justify the conclusions drawn, but internally inconsistent. It requires that we infer the existence of multiple species by reasoning that can only be justified in an infraspecific context. We must assume that hybridization is determined simply by whether or not mtDNA clades co-occur. This is incoherent if members of the mtDNA clades belong to different species. It is only coherent if they belong to the same species.)

But, what I am saying is mtDNA is relevant to species delimitation. Not sufficient for elevation of species in my opinion, but certainly relevant.

On this point, I think I agree. I've been arguing that mtDNA alone (and this applies to other single loci as well, but in the herp world single locus analyses are all mitochondrial) is not relevant. It could be part of a more comprehensive set of data that would be informative, absolutely, but on its own, I don't think the observation of a particular set of mtDNA clades is relevant to inferring a number of species.

regarding Sceloporus woodi...

I'm not sure if you have access to the supplemental, but there is a supplemental figure with all the individual gene genealogies. Incomplete lineage sorting is all over the place.

Ah, OK, I haven't looked at the supplemental figures.

So the concatenated tree isn't really useful, I've been looking at the BUCKy trees in Fig. 5, which basically looks for concordance among the gene trees, and doesn't assume that they've got the same topology. The different placement in the concatenated tree might be due to strong signal at some loci showing that relationship (which drove the pattern), and weaker signal at other loci, or something along those lines. But getting back to my original point, if you look at the gene trees in the supplemental, there is a ton of incomplete lineage sorting.

I looked at the BUCKy trees a bit, too, but there are some problems with interpreting them relative to the entire 29-locus dataset that places Sceloporus woodi within Sceloporus undulatus; the BUCKy analyses are limited to the 8 loci with complete coverage, so I wonder to what extent the different topologies from concatenated ML/Bayesian analyses and BUCKy analyses are due to the different analytical methods or the different data matrices used. I guess staring at all the single locus analyses might clarify that, but I don't think I've got time at the moment for the rather tedious tree comparisons that would be involved...

Sorry, that was far too long.

Patrick

[Cole Grover]

Well stated, Patrick. I couldn't agree more.

-Cole