Tag: phylogeography

Hi everyone. I recently received and have to determine what to do with the following paper (editor’s note, for background, see this recent post):

Nicholson, K.E., Crother, B.I., Guyer, C., & Savage, J.M. 2018. Translating a clade based classification into one that is valid under the international code of zoological nomenclature: the case of the lizards of the family Dactyloidae (Order Squamata). Zootaxa 4461 (4): 573–586. DOI:10.11646/zootaxa.4461.4.7

As an administrator and bureaucrat at Wikispecies I have to decide how to proceed with this group of reptiles. I have made a tentative start here but please realize this is a simple start easily undone.

I recall the last time this came up, in 2012. I joined the discussion at the time. However, despite my comments at the time, I did not follow splitting the genus up then. In the end, my view is for stability and consensus. By stability, I mean the actual meaning of stability under the ICZN code, which does not apply here. But consensus could.

Why is this paper different? Well, first up, last time it was a PhyloCode paper and as such is relatively easy to ignore, as it does not submit to the rules of nomenclature. However, this time it is an ICZN compliant paper so you cannot ignore it. As stated many times, names are to considered as valid on publication or refuted–there is no ignore. So the above paper may be refuted, but not ignored.

Last time, many argued that the genus is monophyletic. This is not really an argument against splitting. It’s a position statement. The order Testudines is also monophyletic, should every turtle species (275 living species) all go back into the genus Testudo? The current genera or lack of them present are only a reference to the history of research. It does not mean it is the most suitable arrangement.

More importantly is diagnosibility. Can the new proposed genera and their inherent species be adequately diagnosed? This is a more important question.

Note that a genus with some 500 species is generally considered too big. Many writers over the years have deemed between 100-200 species about the maximum size wanted. However, this does still need to address the previous point on diagnosibility.

Another point people brought up last time was stability. Well, stability actually refers to the mononomial and whether a name can be replaced by a forgotten name. It is used as a reason to reverse priority. This is the code purpose of stability. Note that the combination first up does not have to be stable, and second is a taxonomic decision, not a nomenclatural one. Hence outside the code.

So what I am after: Basically I want to see through any commentary if the people who work on anole’s are likely to use this new nomenclature. If they are, I will adopt it at Wikispecies. That will require the moving and reorganisation of some 550 pages. I do not take that on lightly. Hence I am asking you, the people who work on anoles, first. My decision will be based on the answers I get. I do not work on anoles. I am a turtle and tortoise specialist. But I do have a job to do at Wikispecies.

For your information, I have discussed this briefly with Peter Uetz at Reptile Database also. He also was not sure what to do, but remembered the last time it came up here. So I am reaching out to all of you on this issue. I am after consensus, not stability. As I said, stability does not apply here. But I will say that to reject the nomenclatural proposals of Nicholson et al. (2018) does require a refutation. They have presented to science in good faith in a very good journal, Zootaxa. We cannot ignore this and as a taxonomist, I will not.

In advance, I thank everyone for their comments. I think this issue needs to be openly debated.

JMIH 2018: Does the Bluefields Anole (A. opalinus) Contain a Cryptic Species?

By Chris Thawley

On July 14, 2018

In New Research

Kiyomi Johnson (L) and Marina Carbi (R) presenting their poster, “Speciation and Phylogeography of Anolis opalinus on Jamaica,” at JMIH 2018.

Caribbean anoles have been studied extensively, with researchers examining their evolution, ecology, physiology, morphology, and behavior in many different contexts. In some respects, they are one of the best known groups of organisms in the world. But are there still unique species “hidden” within the diversity of anoles we already know? Some papers suggest just that. In 2002, Jackman et al. examined the mitochondrial DNA of Jamaican anoles and found evidence that several species contained deeply diverged clades, indicating the potential presence of cryptic species.

Enter Marina Carbi and Kiyomi Johnson, two public high school students with a drive to dig into the biological sciences and a budding curiosity about all things Anolis. Ms. Carbi, a recent high school graduate, and Ms. Johnson, a rising senior at Fiorello H. LaGuardia public high school, began an internship specifically for high school students at the American Museum of Natural History. Working with Dr. Ed Myers, they set out to investigate the phylogenetic diversity in A. opalinus, the Bluefields anole, by sequencing a combination of mitochondrial and nuclear DNA from a series of 22 specimens of Jamaican anoles.

Mss. Carbi and Johnson found that both the mitochondrial data and combined species tree support the existence of a cryptic species within what is currently considered A. opalinus. Populations of the Bluefields anole found in the Blue Mountains area are monophyletic and sister to A. valencienni, indicating a potentially deep divergence from A. opalinus. Todd Jackman, whose initial work inspired this research, dropped by to check out Kiyomi and Marina’s follow up to his paper and was impressed. “Hopefully, they can go to Jamaica themselves,” Todd remarked, before adding as an aside, “I’m glad that their results match ours.”

The authors presented strong evidence that A. opalinus contains a cryptic species. Pic via Twitter.

Looking forward, Ms. Carbi has plans to attend Cornell University in the future, while Ms. Johnson is completing her high school degree. Both expressed interest in continuing to work in biology, with Ms. Carbi noting that she was excited to have had the opportunity to interact with researchers from Cornell at JMIH. The Society for the Study of Amphibians and Reptiles provided support for Mss. Johnson and Carbi to attend the meeting. More extensive sequencing is ongoing in order to further elucidate the phylogeography of what is currently known as Anolis opalinus. Stay tuned!

JMIH 2016: Phylogeography and Population structure of Anolis cristatellus

By Kristin Winchell

On July 9, 2016

In New Research

Quynh Quach presenting her Master’s thesis work at JMIH.

Quynh Quach, a master’s student from the Revell Lab at U. Mass. Boston, presented her thesis research on “Phylogeography and Population Structure of Anolis cristatellus on the island of Vieques.” Before Quynh joined the Revell lab, former post-doc Graham Reynolds and former Losos lab undergraduate Tanner Strickland looked at the phylogeography of Anolis cristatellus across Puerto Rico and the Virgin Islands using mitochondrial DNA (in review). Tanner’s work revealed that there was a mitochondrial break on the island of Vieques, just off the coast of Puerto Rico. The mitochondrial data suggested that there were two genetically different groups of A. cristatellus, one on the East and one on the West of Vieques. The only problem was, as we know, mtDNA patterns are not always supported by nuclear whole-genome DNA patterns. In addition, Tanner’s dataset only consisted of 9 samples from Vieques.

When Quynh joined the lab, she wanted to know more about this pattern. Would this division be supported by nuclear genome analyses? Were these lineages anthropogenically introduced? If not, what was the origin of these groups – historical allopatry followed by secondary contact or isolation by distance? So she set out to answer these questions by collecting 300 tail tips from across the island of Vieques, extracting and sequencing both mtDNA and nuclear DNA.

The mtDNA variation shows a strong geographic pattern.

Quynh first constructed a mitochondrial phylogeny to verify the pattern observed by Tanner and Graham. The mtDNA analysis confirmed that there are 2 mtDNA clades on Vieques with strong geographic patterns. The island-wide pattern of mtDNA variation was not what we would expect if anthropogenic introduction were the cause since this would be unlikely to show such a clear East-West pattern with the small contact zone in the middle. So then how did this pattern arise?

Analysis with K=2 shows two clear groups associated with the East and West.

To answer that question, Quynh next looked at nuclear DNA using RADseq. She sequenced 48 individuals: 5 from Virgin Islands, 6 from Puerto Rico, and 37 from Vieques, then de novo assembled the genome and called 16,808 SNP’s. She ran STRUCTURE and DAPC analyses on this data and found that the Virgin Island samples form 1 cluster and Puerto Rico and Vieques form a second cluster with 4.1% divergence between the groups. But she wondered, what if we look at just Vieques and specify K=2? When she did this with DAPC and saw a clear geographic pattern similar to what she found with the mtDNA. Finally, she tested whether this represented isolation by distance. She found that there was significantly reduced gene flow between geographically distant individuals, supporting this hypothesis as the most likely cause of the variation.

Lastly, Quynh emphasized that it is important to consider multiple genetic markers and not just rely on mtDNA results. Had the group stopped at their original mitochondrial analysis, they would have reached a very different conclusion.

Evolution 2016: Genomic Insights into Anolis carolinensis Phylogeography

By Kristin Winchell

On June 19, 2016

In New Research

Anoles, in particular Anolis carolinensis, have long been considered an ideal group for studies investigating thermal physiology, reproductive endocrinology, and even regeneration. With the recent publication of the A. carolinensis genome (see AA posts on this here and here), the possibilities for new genomic studies in this new model species have significantly increased.

Joseph Manthey and co-authors used this new resource to clarify the phylogeographic relationships of A. carolinensis. Previous research on the phylogeography of A. carolinensis using both mitochondrial DNA and nuclear DNA showed that there were 5 clades. However, the relationships between these groups differed between the two approaches. Joseph looked at the genomes of 42 individuals from 26 localities across the native range to determine the true evolutionary relationship between regional groups and to shed light on the demographic histories of the groups. Manthey sequenced 500 loci using an anchored hybrid enrichment approach.

STRUCTURE analysis showed that the clusters had little admixture

Manthey et al. found that the genomic data predicted 5 genetic groups, in agreement with both the nuclear and mitochondrial analyses previously done. Their results also indicated that the 5 genetic clusters were distinct with little admixture. However, the relationships between groups did not agree with either the mitochondrial or nuclear trees, yet all nodes had extremely high support (93-100%)

Finally, Manthey commented on the likely timing of this diversification and associated demographic trends. Their results indicate that the initial split occurred during the late Miocene or early Pliocene and that the remaining diversification occurred during the Pleistocene. They also found that the most Southern population had a significant number of fixed genes while other populations did not. This suggests that this group was likely the oldest and most stable and supports an “out of Florida” hypothesis of diversification.

Evolution 2015 Recap

By Kristin Winchell

On July 9, 2015

In All Posts, New Research

Evolution 2015 is officially over and we have all sadly left beautiful Guarujá, Brazil. There were a lot of great talks and posters and a great representation of South American students and researchers. For coverage on the conference as a whole, check out #evol2015 on twitter! The herps were few and far between (I only saw 2 in my 16 days in Brazil!) but the posters and talks on herps were numerous. Unfortunately, anoles were poorly represented at Evolution this year with only three anole talks and a couple of others that briefly highlighted anoles. If you weren’t able to make it to Brazil, I’ve got the recap for you here.

click to read more about Travis Hagey's research

A glimpse at the variation in gecko toepads

Starting off in one of the first sessions was a talk by Travis Hagey titled “Independent Origins, Tempo, and Mode of Adhesive Performance Evolution Across Padded Lizards.” Although his talk was mostly about geckos, he did shine the spotlight on anoles for a few minutes. He focused on the phylogenetic pattern of toepad adhesion in pad-bearing lizards: geckos, skinks, and anoles. Specifically he looked at how clinging ability (measured as angular detachment – check out one of his videos showing this) varied within and among clades. Unsurprisingly, he found that anoles don’t cling nearly as well as geckos. He also demonstrated that gecko toepad diversification best followed a Brownian motion model with weak OU and anole toepad diversification was best fit by a strong Ornstein–Uhlenbeck process. In other words, gecko toepads diversified slowly over a very long period while anoles were quickly drawn towards an optimum over a short time-period. Travis concluded that these patterns explain why there is a large amount of diversity in gecko toepads but not in anole toepads.

Next up was Joel McGlothlin, who also gave a non-anole talk titled “Multiple origins of tetrodotoxin‐resistant sodium channels in squamates.”