The Phylogeny Explorer Project

Another short break from the SVP 2018 abstracts…

I just came across a new volunteer led evolution website
The Phylogeny Explorer Project is a navigable, online encyclopedia of the entire evolutionary tree of life. Navigate the cladogram, from root to tips, and see ancestral lineages branching like a a tree. Search for specific clades or species, and interact with the nodes at each branch to find out more information, including pictures, parent or child clades, and reference material.”

According to Wikipedia:
Creator and Founder Aron-Ra (= L Aron Nelson) “is an atheist activist, former president of the Atheist Alliance of America, and the host of the Ra-Men Podcast, He is also the former Texas state-director of American Atheists. Ra is a critic of creationism, and promotes the teaching of science in Texas schools.” 

According to the Phylogeny Explorer Project website:
“Aron Ra is the creator and founder of the Phylogeny Explorer. He is a science educator, author, international speaker, and he has been a political activist, and Texas State and US National Leader for American Atheists. 

“Building the Phylogeny Explorer is a massive project that is volunteer led, widely international, and is comprised of individuals of various vocational and educational backgrounds, all bringing their own skills, insights, and creativity.”

At present
the website is seeking donors and volunteers. There is also a Forum section and the rules state:

  1. Join an existing debate or create your own.
  2. Be Respectful.
  3. Anyone using hateful or vulgar speech will be booted.
  4. And remember, “If you can’t show it, then you don’t know it!” – AronRa

When you sign up to register to see the cladograms you will see this paragraph:
“Only a select group of people are allowed to access the Explorer at this time. Please join the Facebook group if you would like to get involved with the project. Public access will be granted when the Explorer reaches Beta. You may register, however access is only granted to those with a valid reference code or prior permission from a project administrator. All registrations must be reviewed and approved by an admin before access is granted.”

On YouTube
AronRa currently has 190,000+ subscribers and 558 videos. Here is his homepage. The primary video on that homepage Phylogeny Challenge (7 years ago) includes previously produced websites devoted to evolution including:

  1. Mikko’s Phylogeny Archive (last update 2016): http://www.helsinki.fi/~mhaaramo/
  2. Palaeos.com: http://palaeos.com/evolution/
  3. Arizona Tree of Life Web Project: http://www.tolweb.org/tree/

Aron-Ra notes, two of the above websites (1 and 2) are “unfunded private ventures.”

According to Wikipedia
The Tree of Life Web Project: “This collaborative peer reviewed project began in 1995, and is written by biologists from around the world. The site has not been updated since 2011, however the pages are still accessible. 

“The pages are linked hierarchically, in the form of the branching evolutionary tree of life, organized cladistically.[1] Each page contains information about one particular group of organisms and is organized according to a branched tree-like form, thus showing hypothetical relationships between different groups of organisms.

“From 1996-2011, over 300 biologists from around the globe added taxa web pages into the phylogeny browser.”

All of these websites preceded ReptileEvolutiion.com.

Unfortunately,
Aron-Ra’s seven-year-old video follows this history of online evolution projects with a dismissal of trait-based phylogenies in favor of gene-based phylogenies (which cannot include fossil taxa and often fail over large phylogenetic distances) and he employs supra-generic taxa (many of which become invalid when taxa are added). Bottom line: Aron-Ra seems to be more of a journalist than a scientist because he reports on new findings without testing them. It is better to test new data. That’s why scientist announce discoveries; so they will be either confirmed or refuted by other workers.

Moving on to more recent online videos of the Phylogeny Project:

  1. A one hour audio interview with Aron-Ra (2017): https://www.youtube.com/watch?v=OIFPqe03hVE
  2. A Scott Reeves reply to The Phylogeny Challenge, who states, “the challenge in the Phylogeny Challenge is misdirected at creationists. It should actually be directed at evolutionists, because the phylogenetic tree is THEIR hypothesis.” https://www.youtube.com/watch?v=b-EfJlCvrqI

You might remember,
four years ago, and after Darren Naish’s critique of ReptileEvolution.com, Aron-Ra posted a YouTube video calling PterosaurHeresies.Wordpress.com and ReptileEvolution.com: BS without testing the presented hypotheses and suggested taxa. Hopefully the last four years of adding taxa and nesting enigmas have modified his view.

Unfortunately,
like Dr. Naish, Aron-Ra is brilliant, but pulls his knowledge of reptile clades from the academic literature. Both trust genetic data over trait data. Both trust the authority of the PhD over the process of testing for one’s self (a basic tenet of science). Neither has tested candidate taxa suggested by the large reptile tree, nor have they tested the claims of the academic literature with wide gamut cladograms of their own. It is easy enough to do, but does take time.

If I can do this, anyone can, because this is real science.
No doubt both Dr. Naish, Aron-Ra are competent workers, but their decisions to (ironically) put their faith in the academic literature and genes, rather than test results for themselves using trait-based analyses, puts them in the same faith-based camp that they profess to rally against. And that’s just because, like you and me, they, too, are human. It is so much easier to read and accept. I would have had the same prejudices and inclinations had I not tested things for myself. It’s been an eye-opening journey, one that I hope you, too, will tackle during your lifetime.

With regard to The Phylyogeny Explorer Project, I say to Aron-Ra:
Don’t rely on volunteers. Don’t ask for donations. Do the work yourself. You will be rewarded by what you find, as I have. You already understand the reward of telling others about what you read… now sit down with MacClade and PAUP and discover for yourself what is and is not true about what you have read.

References
PEP websites:

  1. https://phylogenyexplorerproject.com  at present there is a home page, with intro, intro to the creator and founder, Aron-Ra, links to a Forum, Contact and Donate links. Not sure if there are any cladograms on the site yet, or if they are available only after a registration process (which I did not attempt). You don’t have to register to glean data from ReptileEvolutiion.com. The third PEP video below shows several linking cladograms.

PEP videos:

  1. Chiroptera by Robert England: https://www.youtube.com/watch?v=fz5IXluLXSI
  2. Arfel Tayona Evolution Presentation Part 1: https://www.youtube.com/watch?v=-G3KIGB_lsc&feature=youtu.be
  3. At TetZooCon (2018): https://www.youtube.com/watch?v=vU7difOTyvk

In this last video Aron-Ra discusses the online resource www.fossilworks.org, a paleobiology database which I use often. It includes no illustrations, but does include 378,000+ taxa and 67,000+ references contributed by 493 scientists. A quick look at “Cosesaurus” reveals no references to anything I have had published in the peer-reviewed academic literature. So we know how that goes.

Aron-Ra also discusses the online resource evogeneao.com, which is new to me. They say: “Our mission is to promote the teaching of evolution by emphasizing its greatest lesson: LIFE ON EARTH IS ONE BIG EXTENDED FAMILY!” The site includes a list of three recommended books. and two Doug Larson cartoons among many others. Key to the site is a large evolutionary tree in which one can find the last common ancestor of included taxa, like Gooseneck barnacle and American robin.

Third on Aron-Ra’s list, the online resource eol.org, the encyclopedia of life. He notes it contains every extant taxa, but no fossils. Even so it includes over 1.3 million pages, 3.8 million images and has 93,00+ members.

Fourth on Aron-Ra’s list is onezoom.org According to that website their fractal “Tree of Life Explorer” is, “An interactive map of the evolutionary relationships between 2,123,183 species of life on our planet. Each leaf on the tree represents a species and the branches show how they are connected through evolution.” It lists only recent species.

Fifth on Aron-Ra’s list is timetree.org. TimeTree: The Timescale of Life permits one to enter two extant taxa (from a list of 97,000) and the website determines how long ago they shared a last common ancestor, along with solar luminosity, carbon dioxide levels and oxygen levels. BTW, their estimated time of divergence for the archosauromorph bird, Corvus, and the lepidosauromorph lizard, Varanus, is 280 mya, a wee bit shy of Gephyrostegus at 310 mya or Silvanerpeton at 335 mya.

Sixth on Aron-Ra’s list is Palaeos.com (listed above). Workers formerly associated with this site now work on the PEP site. Unfortunagely some pages at Palaeos.com no longer work as “the site is currently undergoing a major overhaul.”

Apparently ReptileEvolution.com is still not on Aron-Ra’s ‘good’ list.

 

A molecule study that includes ratfish and rats

Here’s a molecule study (Irisarri et al. (10 co-authors)
that includes select members of the Gnathostomata (jawed vertebrates going back to ratfish). Their abstract reports, “Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial.”

At least they are on the right track, with a wide gamut study. The LRT covers very few fish, but a long list tetrapods. Evidently the LRT was not on their radar. (sigh)

“We tested a new bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost-effective. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.”

Importance? Unfortunately you have to be a believer, because their RNA interrelationships can and cannot be verified by a competing analysis of traits (explained in detail below).

“Gene jackknifing of genomic data corroborates the robustness of our tree.”

Unfortunately, genomic data produces several false positives when compared to phenomic data.

Here we’ll compare results
to the large reptile tree (LRT, 1187 taxa), which goes back nearly as far in a morphological study and employs fossil taxa. I have often said that molecules produce false positives over large phylogenetic distances. Here that statement proves to be both true and false, depending on the node.

The LRT includes only bony vertebrates,
so sharks, rays and ratfish are not included as taxa in the LRT. Lungfish and most teleosts are also not included.

Where the Irisarri et al. tree matches the LRT:
Both trees:

  1. separate ray fin fish from lobe fin fish
  2. separate tetrapods from lobe fin fish
  3. separate amniotes from amphibians (only living taxa are tested)
  4. separate caecilians from salamanders + frogs
  5. separate turtles, mammals, archosaurs and lepidosaurs
  6. nest birds with crocs
  7. nest Sphenodon with squamates
  8. nest all mammals with other mammals, turtles with turtles, birds with birds, etc. etc.
  9. nest placental mammals with other placental mammals, apart from non-placental mammals
  10. nest palaegnath birds with palaeognath birds, apart from neognath birds
  11. nest placental mammals splitting from Monodelphis

Where the Irisarri et al. tree does not match the LRT:
The Isirarri et al. tree:

  1. separates mammal reptiles from all other reptiles
  2. separates turtles from lepidosaurs, instead nesting turtles with birds and crocs
  3. separates iguanids from Sphenodon, instead nesting iguanids and Elgaria (alligator lizard) with snakes
  4. separates geckos from snakes, instead nesting geckos with skinks
  5. separates the finch (Taeniopygia guttatafrom the chicken and turkey, instead nesting the finch as the basalmost neognath

The LRT:

  1. nests mammals with birds and crocs, not lepidosaurs
  2. nests turtles with lizards, not archosaurs
  3. nests geckos with snakes, not skinks
  4. nests iguanids at the base of all squamates, therefore closer to Sphenodon
  5. nests Elgaria with Cryptolacerta (Eocene) and Ophisaurus (extant, not tested by Irisarri et al)

You might remember
molecules brought us the clade Afrotheria, a clade that includes elephants, aardvarks and golden moles, among a larger list of unrelated taxa

At present a certain amount of faith
attends gene sequencing, a hope that similar genes will translate to the appearance of similar body parts and proportions. Often that faith is rewarded. Other times, it is not. While DNA testing has proven its validity within genera (in crime labs and ancestry searches), the possibility of a ‘false positive’ using gene sequencing over larger phylogenetic distances occurs too often.

Ultimately
if you want to see how evolution works in tetrapods, molecules work for some nodes, not for others, and excludes fossil taxa. For more consistent results that deliver gradual accumulations of traits in derived taxa, using every sort of tetrapod taxa (including fossils), try morphology. It’s the benchmark against which molecules succeed sometimes and fail other times. I cannot yet unravel the pattern of false positives vs. verified positives.

Perhaps the worst aspect of DNA analysis:
it is correct often enough that some well-meaning scientist consider it flawless. At present only one person on the planet has produced a competing trait analysis that shows DNA analysis is flawed…sometimes.

References
Irisarri I et al. 2017. Phylotranscriptomic consolidation of the jawed vertebrate time tree. Nature ecology & evolution 1: 1370–1378. doi:10.1038/s41559-017-0240-5

Things I didn’t know about phylogenetic analyses based on DNA molecules.

In my never ending quest to understand reptile phylogeny
I was fortunate to read Scotland et al. (2003) and Jenner (2004). Thankfully the latter rebutted the former. Scotland et al. are all plant scientists, so bear in mind, they deal with far fewer ‘moving parts’ in the taxa they study.

Scott et al. (2004) wrote: “We present the view that rigorous and critical anatomical studies of fewer morphological characters, in the context of molecular phylogenies, is a more fruitful approach to integrating the strengths of morphological data with those of sequence data. This approach is preferable to compiling larger data matrices of increasingly ambiguous and problematic morphological characters.

“In conclusion, problems surrounding character coding of morphological data reduce the number of unambiguous morphological characters for analysis. The crucial issue for morphology is that the already small number of morphological characters is further compromised by ambiguous homology assessment.

“DNA is much simpler. There is no ambiguity that the unit of comparison is the nucleotide and that adenine, guanine, cytosine, and thymine represent different versions of the same entity.
 
“Hillis and Wiens (2000) stated that dense taxon sampling is the greatest advantage of morphological data, citing recent simulation studies demonstrating the importance of taxon sampling for accurate phylogeny estimates (Hillis, 1996, 1998; Graybeal, 1998). For example, in one simulation study, Graybeal (1998) demonstrated that under some conditions phylogenetic accuracy was improved as the number of taxa increased, but not when more characters were added.”
There it is!. That’s what I’ve been saying!
Here’s the main problem with too few characters
according to Scotland et al. 2003):

“Another important issue relative to increased taxon sampling, in the context of morphological data, relates to the potential decreased number of unambiguous charactersas more taxa are added to a study. Characters that were discrete [in smaller studies] are no longer discrete when additional taxa were added.”
What the large reptile tree tells us:
Discrete characters are fine (they were Larry Martin’s favorite subject). But they’re not important in the scheme of things. What is important, as we’ve always heard, is the suite of characters present in each taxon. Let’s face it, sister taxa share all the characters that lump them together, except for the few that split them apart. And that happens again and again at every one of the 415 nodes in the large reptile tree.

A raft of clarity from Jenner 2004.
Jenner argued against Scotland et al. (2003) like this: “Scotland et al. (2003) evaluated the role of morphology in phylogeny reconstruction, and concluded that morphological evidence offers no hope to resolve phylogeny at any taxonomic level. Consequently, they advocated a very restricted role for morphology in phylogenetics, mainly by mapping selected morphological characters onto molecular phylogenies. I critically examined the scientific basis for the arguments of Scotland et al. (2003), and found them to be unconvincing.”

This is most enlightening from Jenner 2004:
“Nucleotides are characters of relatively low complexity, and the character state space for nucleotides is much more restricted than for morphology. In certain circumstances this creates a considerable danger that the same nucleotide has evolved independently in the same position, and this realization has been an incentive to develop models of evolution that estimate the probability that the same nucleotides at a site are historically identical, and to explore the value of more complex molecular characters. In contrast, morphology generally presents a richer space of more complex characters, which allows a more fine-grained comparison of potential homology, and this may help explain why in certain cases morphology may be qualitatively superior to molecules when considered per character.

“Scotland et al. (2014, 541) claim that these problems of “subjectivity and interpretation” are absent from molecular data, because “areas of ambiguity [in sequence alignment] can be excluded.” As recent research shows, to choose this way of least resistance may be thoroughly misleading, and this short statement seriously underplays the degree of subjectivity and interpretation asocial ted with molecular phylogenetics.”

Jenner then discussed more than a decade of 18S rDNA studies that suggested bird/mammal affinities, which, of course, was in conflict with morphological studies and other molecular data. Jenner continued:

“After the 18S data was analysed in various different ways by different workers, they concluded that this was an example of different molecules giving significantly different estimates of phylogeny. However, a recent study by Xia et al. (2003) convincingly showed that the conflict between 18S data and the traditional and other molecular data was an artifact attributable to two main factors: misalignment of sequences, and inappropriate estimation of base frequency parameters.

“Crucial to the resolution of this paradox was the incorporation in the molecular data set of those regions of the 18S molecule that were most variable, and most difficult to align unambiguously. This study clearly showed that restricting the data set to only the least unambiguous sites might produce a thoroughly misleading phylogeny. The problem that ‘different workers will perceive and define characters in different ways’ is therefore certainly not limited to morphological data.”

Ater reading Jenner (2004), you won’t wonder about DNA studies anymore. They’re not perfect and may never be. They don’t work for fossil taxa (you knew that already) and they often come up with bizarre results.

References
Graybeal A 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Systematic Biology 48:9-17.
Hillis DM 1996. Inferring complex phylogenies. Nature 383:140- 141.
Hillis DM 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
Hillis DM and Wiens JJ 2000. Molecules versus morphology in systematics. Pp 1-19 in Phylogenetic analysis of morphological data (J. J. Wiens, ed.). Smithsonian Institution Press, Washington, D.C.
Jenner RA 2004. Value of morphological phylogenetics. Accepting Partnership by Submission? Morphological Phylogenetics in a Molecular Millennium. Systematic Biology 53333-359.
Scotland RW, Olmstead RG and  Bennett JR 2003. Phylogeny Reconstruction: The Role of Morphology. Systematic Biology 52:539-548.
Xia X, Xie Z and Kjer KM 2003. 18S ribosomal RNA and tetrapod phylogeny. Systematic Biology 52:283-295.

The reptile DNA problem: maybe this is the answer…

Q: How do you arrive at a family tree of reptiles?
1.
You can look at hundreds of taxa and score them for hundreds of characters and let maximum parsimony recover the family tree, as I did here. This is following in the paths of dozens of others who have created their own subsets of the reptile family tree with their own taxon and character lists. Because morphology is an expression of genetics, morphology is really the only genetics that counts. Morphology helps you survive in your niche and enhances secondary sexual characteristics to help you get laid to create replicants of your own naturally selected self.

or

2. You can look at the molecular DNA of several distinct specimens (all currently living) and let maximum parsimony recover a much more unfocused family tree leaving out hundreds of extinct taxa with no known living counterparts. Of course some of this DNA doesn’t express anything. Some of it jumps around the chromosomes. And DNA cannot be recovered from the vast majority of extinct taxa, so we’re left with huge ghost lineages, during which “things” happen (see below). Even the sex chromosomes are different between birds, mammals and lizards.

Male mammals have the XY combination while females have XX. Male birds carry what’s known as the ZZ pair and females have the ZW pair. The green anole X chromosome is a microchromosome. Yes, it’s nothing compared to having a skull, tail, four feet, five toes and relative constants like those when it comes to DNA.

BTW I freely admit to not knowing much about molecular studies except that they sometimes don’t replicate morph studies.

The DNA problems don’t end there…
We’re talking about reptiles here: DNA study results do not replicate morphological study results. Often DNA study results do not replicate other DNA study results. DNA is changing even when morphology does not (Hays 2008). This alone could be the reason for the discrepancy in DNA and morphology among reptiles (and not among mammals and humans involved in paternity suits).

Is this why reptile DNA studies don’t match morph studies?
A recent article on genetic sequencing of an anole lizard DNA reports, “We’ve now sequenced a lizard genome for the first time ever. The anoles shed light on non-coding sequences of genes. What they might be are the husks of special DNA sequences known as transposons. These can only be described as “jumping DNA”, able to actually move through the genomes and copy and paste themselves elsewhere. Transposons can give any genome that carries them great agility and resilience in dealing with unexpected environmental challenges.”

Lizard egg proteins
From the same article, “It appears that, as far as egg genes are concerned, reptiles are in a constant state of evolutionary flux, with the proteins revealing clear signs of rapid evolutionary change.”

The dorsal spines of Tuatara (Sphenodon).

Figure 1. The Tuatara (Sphenodon)

The Hays et al. 2008 abstract
“The tuatara of New Zealand is a unique reptile that coexisted with dinosaurs and has changed little morphologically from its Cretaceous relatives. Tuatara have very slow metabolic and growth rates, long generation times and slow rates of reproduction. This suggests that the species is likely to exhibit a very slow rate of molecular evolution. Our analysis of ancient and modern tuatara DNA shows that, surprisingly, tuatara have the highest rate of molecular change recorded in vertebrates. Our work also suggests that rates of neutral molecular and phenotypic evolution are decoupled.”

I take this to mean DNA genetic evolution is decoupled from morphological genetic evolution in the Lepidosauria (but not necessarily decoupled in other living things). With that hanging over our collective decision making processes, maybe morphological genetic studies should trump DNA genetic studies in non-mammalian reptiles.

Reptile DNA studies might be interesting, but let’s not hang our hats on them. Let’s stick with fossils and phylogenetic analysis. That covers all the bases down to the specimen.

As always, I encourage readers to see specimens, make observations and come to your own conclusions. Test. Test. And test again.

Evidence and support in the form of nexus, pdf and jpeg files will be sent to all who request additional data.

References
Hay JM, Subramanian S, Millar CD and Mohandesan E 2008. Rapid molecular evolution in a living fossil. Trends in Genetics, 24(3):106-109.