Tag: evolution

Dan Nicholson at SICB 2020

Evolution has long thought to be a slow process, taking thousands if not millions of years. Recently, there has been a paradigm shift in how scientists think about evolution. We now know that we can observe evolution on a contemporary timescale, observable to the human eye. Dan Nicholson, a Ph.D. Candidate at Queen Mary University of London in Rob Knell’s lab, is working with Mike Logan and others to observe the effects of habitat change on the evolutionary ecology of Anolis apletophallus.

Dan and his team transplanted anoles from the mainland of Panama to several islands around Barro Colorado Island in July of 2017. Before release, they recorded the anoles’ morphological characteristics, including hindlimb and forelimb length, toe pad size, and head depth, and well as characteristics of their perch location, including height and width. Tracking changes in these characteristics can detect natural selection at work. At SICB 2019, Dan reported the results of the first generation of island anoles.

At SICB 2020, Dan included the trends of the second generation of island anoles. The preliminary results indicate the island anoles have continued to use wider perches than the mainland anoles. However, the majority of the island anole morphological traits now align with the mainland anoles. The exception is that hindlimb length of the island anoles decreased, while the mainland anoles hindlimb length has increased.

Some potential causes of these results, Dan speculates, include genetic drift due to the small population size. The islands started with a robust number of anoles, but over the two years of this study, their numbers have rapidly dwindled. Another possibility is the island anoles are aligning with the mainland anoles morphologically due to gene flow. In the future, Dan wants to further analyze the preliminary results from a population angle, looking at changes in groups of traits instead of individual traits.

You can learn more about Dan’s research by following him on twitter.

SICB 2019: Does a Tropical Anole Evolve When Colonizing a Novel Habitat?

By Chris Thawley

On January 7, 2019

In New Research

Anolis apletophallus from Panama, a well-studied species from the Panama mainland.

Over the past 15 to 20 years, the study of evolution has undergone something of a paradigm shift. Whereas scientists used to believe that evolution in most animals was a slow process, only observable over longer timescales, we now know that evolution is fast. Meaningful change can occur in many types of traits, including morphology and physiology, in just a handful of generations of a given organism. With this shift in our understanding, many biologists have begun conducting experiments which attempt to observe evolutionary processes in action, and shed light on how evolutionary mechanisms play out in the real world.

Dan Nicholson, a student in Rob Knell’s lab at Queen Mary University of London, worked with Mike Logan and a team of researchers to do just this in a tropical anole, Anolis apletophallus. Dan and his colleagues caught over 400 individual anoles from the mainland and introduced them to a novel environment: four small, anole-free islands formed when the Panama Canal was created. Two of these islands were similar to mainland habitats, while two had wider types of vegetation. Prior to placement on these islands, Dan measured a suite of characters of these individuals, including perch height, size, leg length, head, and toe morphology, enabling him to observe any changes in the distribution of these traits over time.

After leaving the anoles on their new tropical island homes for a year, Dan returned to recapture the survivors and measure both them and their offspring. By comparing the traits of the surviving lizards and their young with those of the population founders, Dan could observe changes in traits as well as measure natural selection on them. At SICB 2019, Dan reported that he found that anoles on islands with wider vegetation did indeed use these broader perches and that anoles also perched closer to the ground. Correspondingly, he found that toe pad size decreased and that hindlimb lengths were longer on some islands, potentially allowing lizards to better exploit lower, broader perches.

Anoles on all islands also showed a reduction in head depth. The reason is unclear, but Dan is looking into whether differences in competition or the prey community are potentially driving this pattern. Finally, measuring selection was very difficult and analyses proved problematic, though in some cases selection estimates do seem to match with observed changes in morphological characters. Dan and his team are hoping that adding data from another generation of anoles will clarify these effects, so stay tuned!

Keep track of the latest from Dan on Twitter: @DanJNicholson

Natural Selection on Morphology in a Tropical Lizard After a Rapid Shift in Habitat Structure NICHOLSON, DJ*; LOGAN, ML; COX, C; CHUNG, A; DEGON, Z; DUBOIS, M; NEEL, L; CURLIS, JD; MCMILLAN, WO; GARNER, T; KNELL, RJ; Queen Mary University London

Nomenclature of Dactyloidae: Revisit and Opinions Wanted

By Scott Thomson

On October 1, 2018

In All Posts, New Research

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.

Is There a Crisis in Anolis Taxonomy? Part 2

By Levi Gray

On October 10, 2016

In All Posts, Research Methods

In a (somewhat) recent blog post entitled “Is there a crisis in Anolis taxonomy?”, Julian Velasco invited discussion on a perceived decline in the number of new anole taxonomists. While it was a fun look at the dynamics of anole taxonomy over time, I couldn’t help but feel like there is a more pressing taxonomic crisis going on right now, and it affects many of the researchers that frequent this blog.

I fear too many species of Anolis are being described based on questionable evidence. While this problem is not unique to anoles (a common term for it is “taxonomic inflation”; Isaac et al. 2004), a number of recently described anole species may be the result of overzealous taxonomic splitting. I will give some examples below and then briefly discuss two lines of evidence that I believe are often used to divide species inappropriately. Before I do so, it’s worth stating up front that I’ll focus on the work of Dr. Gunther Köhler and colleagues. This shouldn’t be surprising, as Dr. Köhler is the most prolific living describer of anole species. The following criticisms should not be seen as personal, as Köhler is not unique on any of the points I discuss below. But with many cryptic species described or resurrected over the past 10-15 years, his work has the largest impact on anole taxonomy and the science that depends on it.

I’ll start with the revision of the Anolis tropidonotus complex published in Mesoamerican Herpetology (Köhler et al. 2016). Below I provide a quick breakdown of the paper. I hope that others will contribute their own views on this work in the comments. The A. tropidonotus group is one that I am well-acquainted with, having spent months of field time collecting individuals across the distribution of the group. Köhler et al. (2016) raise a subspecies (A. tropidonotus spilorhipis) to species status while describing two new species, A. wilsoni and A. mccraniei. Unfortunately, the data presented–morphology and DNA–do not appear to strongly support the recognition of any new species level taxa. I argue that the inference of four species within A. tropidonotus sensu lato should require stronger evidence than that presented.

The authors sequenced 16S mitochondrial DNA for molecular analyses and present a consensus tree from Bayesian analyses of these data. This tree recovers four well-supported and geographically circumscribed mtDNA haplotype clades that correspond with the four new species. A table following the tree reveals the genetic distances between putatively new species topped out at 4.5%. This level of mitochondrial divergence is significantly less than intraspecific variation observed in other anoles (Malhotra & Thorpe 2000; Thorpe & Stenson 2003; Ng & Glor 2011). Moreover, Köhler et al.’s (2016) sampling map reflects sparse sampling of molecular data.

Based on Figure 3, morphology (other than perhaps hemipenes, which I discuss below) does not provide any support for delimitation of those populations characterized by distinct mtDNA haplotypes. The dewlap differences reported are slight and appear to fall within the type of variation observed within and among other populations of species in this group (see photos at the top of this post for an example of two spilorhipis males that came from the same locality; photos courtesy Luke Mahler). Bottom line–we see several populations with mitochondrial haplotypes that cluster together geographically with little to no morphological evidence for divergence.

The phylogenetic and morphological patterns displayed in Köhler et al. (2016) are consistent with patchy sampling of a widespread and continuously distributed species with potentially locally-adapted populations. The authors cite “the high degree of genetic distinctiveness… as evidence for a lack of gene flow, and conclude that these four lineages represent species-level units” (Köhler et al. 2016). This assumption is questionable, as researchers have long known of the pitfalls of using mtDNA to determine gene flow (Avise et al. 1983; Avise et al. 1984; Funk & Omland 2003) and supporting evidence from morphology is lacking. The different hemipenial types represent the strongest evidence for recognizing the lineages mtDNA haplotype groups. Below I will discuss the utility of those traits for species delimitation.

Finally, the authors did not compare their purported new tropidonotus-like species to Anolis wampuensis, a morphologically indistinguishable (McCranie & Kohler 2015) form that is potentially codistributed with the new species A. mccraniei. This should have been done to avoid the possibility that A. wampuensis is conspecific with one of the newly named forms.

Another example of taxonomic inflation in Anolis is from a 2014 monograph in Zootaxa (Köhler et al. 2014).

Resolving Phylogenetic Uncertainty in Anoles Using Treescape

By Michelle Kendall

On July 5, 2016

In All Posts, Lizards in an Evolutionary Tree

It’s an all-too-common situation: you would like to infer a phylogeny for a set of organisms, you try a few different methods and you end up with many different trees. Even with the most careful choice of software, settings, tree priors, and the most beautifully converged Bayesian posterior likelihood, you may find that the maximum clade credibility (MCC) tree has low posterior support for certain deep clades.

Anole MCC tree with posterior supports, from Geneva et al. [1]

Tree inference is very complicated, particularly for species trees, and is hampered by factors which include the vast size of tree space, conflicting signals from different genetic loci, confusing signals from convergent evolution, and non-tree-like evolution (recombination, hybridisation, etc.). Geneva et al. experienced just this sort of difficulty when they performed a comprehensive Bayesian phylogenetic analysis of the distichus group of trunk ecomorph anoles [1]. Their MCC tree is reproduced here, and the posterior support values show uncertainty in the branching structure of various deep clades. There are many combinations of ways to resolve these uncertain splits. We wanted to see which alternative trees were supported by the data.

In our recent paper [2] we present a method for handling phylogenetic uncertainty and incongruence. It takes a set of trees and “maps” them into a simple plot where similar trees are grouped together and more different trees are placed further apart. Where many similar trees are clustered together, contour lines indicate the density of points in that region. We began the development of our method theoretically, making sure we had designed a robust mathematical definition for tree distances which would correspond to biological intuition and lend itself to good quality map projections. Then, working closely with biologists, we fine-tuned our method for specific applications with real data and wrote the R package treescape [3] so that anyone can use it – there’s even a handy web app version which requires no knowledge of R.

treescape MDS plot: each point represents a tree, and proximity of points represents similarity of trees. 1000 trees are plotted here, many identical, so contour lines indicate density of points. Colours correspond to clusters of similar trees.

treescape MDS plot: each point represents a tree, and proximity of points represents similarity of trees. 1000 trees are plotted here, many of which are identical, so contour lines indicate the density of points. Colours correspond to clusters of similar trees.

When we applied our method to the trees from the analysis of Geneva et al. [4], we found that there were distinct “clusters” of equally likely tree topologies. It is reassuring that the MCC tree belongs to the largest of these clusters (highlighted on the plot by a yellow triangle), but clearly it cannot represent all of the likely tree shapes on its own. By taking a representative tree from each of the six or so tight clusters, we obtain a more thorough summary of the range of trees supported by the analysis. Such representative trees, taken from the geometric “centre” of each cluster, are credible summary trees with real branch lengths, unlike trees from other summary methods which can suffer from strange behaviour such as negative branch lengths.

We find that there are alternative placements of certain taxa, particularly the ocior, distichus, dominicensis2 clade, and (in our supplement) we explore some of the knock-on effects of using these different tree shapes when analysing the evolution of the anoles, specifically their geographical origins and transitions in their dewlap colour. For instance, we show here a representative tree from each of two different clusters on the map. The trees support ocior, distichus, and dominicensis2 being more closely related to anoles from the East of Hispaniola (the North paleo-island) or the South-West (the South paleo-island) respectively. Both evolutionary histories are supported by the data; in the absence of further research, there is no reason to exclude any of the alternative representative trees identified by our method.

Representative tree from top left cluster

Representative tree from top right cluster

[1] Geneva, A. J., Hilton, J., Noll, S. and Glor, R. E. (2015). Multilocus phylogenetic analyses of Hispaniolan and Bahamian trunk anoles (distichus species group). Molecular Phylogenetics and Evolution, 87:105-117.

[2] Kendall, M. and Colijn, C. (2016) Mapping phylogenetic trees to reveal distinct patterns of evolution. Molecular Biology and Evolution, first published online June 24, 2016. DOI: 10.1093/molbev/msw124

[3] Jombart T., Kendall M., Almagro-Garcia J., Colijn C. (2015). treescape: statistical exploration of landscapes of phylogenetic trees. R package version 1.9.17.

[4] Geneva A. J., Hilton J., Noll, S. and Glor, R. E. (2015). Data from: Multilocus phylogenetic analyses of Hispaniolan and Bahamian trunk anoles (distichus species group). Dryad Digital Repository.

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.”

Teaching With Anoles, Part 1

By mjohnson216

On August 20, 2011

In Education and Anoles

As the summer is ending and a new semester is beginning, your thoughts may have returned to teaching. I try to use a diversity of taxonomic groups in my lectures and labs, but of course, I find anoles to be useful examples for many topics in the classroom. In my Evolution course, taught each year to biology majors at Trinity University, I focus one laboratory module on anole evolution to teach my students to conduct phylogenetically-informed comparative analyses. Below, I’ll describe the approach I use in my course, and if you would like to see my materials, or adapt them for your own teaching, I’d be happy to share the lab handouts – just email me at michele.johnson[at]trinity.edu.

Many activities in my lecture and lab focus on creating and interpreting phylogenies, and one of my earliest lab sessions teaches students to use parsimony and similarity-based classification to build phylogenies from mammalian morphological traits.

Anole and Orchid Evolution–What Do They Have in Common?

By Jonathan Losos

On April 20, 2011

In All Posts

Figure 1 from Pauw (2006)

Anton Pauw of Stellenbosch University in South Africa writes:

“I am reading Lizards in an Evolutionary Tree and find it fascinating to see how many parallels there are with my one of my study systems, oil-secreting orchids. While the anoles have differentiated across a series of niches provided by a plant, the orchids have differentiated across a series of niches provided by an animal. The orchids segregate the body of the shared pollinator among them so that each places its pollen on a unique segment of the oil-collecting bee. Orchid speciation generally involves shifts between bee species (with placement site conserved), but some speciation also occurs through shift in pollen placement site within the bee , so that sister species occupy for example the first and second segment of the front leg respectively. Anyway, I thought that you too might find these parallels interesting, so I have attached two papers on the topic. I like the comparison of your Fig. 3.2 with Fig. 1 in the attached 2006 paper.”

The other paper is here. Incidentally, apparently no one has posted a picture of an anole sitting on an orchid on the internet.