SquaMates Ep. 2: Attack of the Genomes

SquaMatesThemselves New Episodes July 22, 2018 | 0

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The much-anticipated second episode of the SquaMates podcast, hosted by Mark D. Scherz, Gabriel Ugueto, and Ethan Kocak, here for your ears at last!

The this second episode, we give an overview of some of the biggest new research in herpetology since the start of 2018, and the topic of the week is axolotls and their enormous genomes. The featured #HERper is Prof. Marvalee Wake!

Episode notes sometimes get clipped on your device or by your podcast provider; for full (extensive) notes, go to http://www.squamatespod.com

General notes on the episode (preliminary corrections, clarifications):

We always have to record episodes a few weeks in advance, because of our busy schedules, and as a result, we might have missed some interesting advances that have just emerged. We will always endeavour to cover the best of these in the following episode! This may sometimes break down the illusion of being a current podcast, but we promise we are trying to keep everything as timely as possible!

Since recording, the two accepted papers mentioned by Mark have been published, and you can read about them and access the PDFs at http://www.markscherz.com/archives/3827

On JMIH (Joint Meeting of Ichthyologists and Herpetologists): Our episode was recorded before the story of Dick Vogt’s inappropriate slides had emerged. We would like to make it clear that we believe there is no place for the sexualisation of female researchers (or any other dehumanising practices in research, for that matter), and we were pleased that the Herpetologists’ League has signed onto the JMIH code of conduct, and approve especially the decision to form committees addressing inclusivity, diversity, and professionalism, which, as we highlighted in the first episode, has been a long-standing issue in herpetology.

Note also that Mark was incorrect; JMIH 2019 will be in Snowbird, Utah.

Our twitter poll on how to pronounce ‘anole’ (https://twitter.com/SquaMatesPod/status/1012344498683342848) received 680 votes, of which 59.3% (corrected for 95 people who wanted to see the results) agreed with Mark and Ethan that the correct pronunciation is without a sharp ‘e’ (ah/uh-noll), 24.4% agreed with Gabriel that it should have a sharp ‘e’ (ah/uh-no-lee), and 16.2% wanted to circumvent the issue by using the Latin name, Anolis, meaning that a whopping 75.5% of tweeps think Gabriel is wrong. But he has decided that this is the hill that he will fight and die on, and who are we to deny him that desire?

Breaking Newts References:

Xing, L., Stanley, E.L., Bai, M. & Blackburn, D.C. (2018) The earliest direct evidence of frogs in wet tropical forests from Cretaceous Burmese amber. Scientific Reports, 8, 8770. 10.1038/s41598-018-26848-w — This paper was discussed in more detail in Episode 67 of the TetZooPodcats: http://tetzoo.com/podcast/2018/6/21/episode-67-stupid-successful-frog

Simões, T.R., Caldwell, M.W., Talanda, M., Bernardi, M., Palci, A., Vernygora, O., Bernardini, F., Mancini, L. & Nydam, R.L. (2018) The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps. Nature, 557, 706–709. 10.1038/s41586-018-0093-3 — This paper was discussed at length in an interview with the first author in Episode 92 of Palaeocast: http://www.palaeocast.com/squamate-origins/

O’Hanlon, S.J., Rieux, A., Farrer, R.A., Rosa, G.M., Waldman, B., Bataille, A., Kosch, T.A., Murray, K.A., Brankovics, B., Fumagalli, M., Martin, M.D., Wales, N., Alvarado-Rybak, M., Bates, K.A., Berger, L., Böll, S., Brookes, L., Clare, F., Courtois, E.A., Cunningham, A.A., Doherty-Bone, T.M., Ghosh, P., Gower, D.J., Hintz, W.E., Höglund, J., Jenkinson, T.S., Lin, C.-F., Laurila, A., Loyau, A., Martel, A., Meurling, S., Miaud, C., Minting, P., Pasmans, F., Schmeller, D.S., Schmidt, B.R., Shelton, J.M.G., Skerratt, L.F., Smith, F., Soto-Azat, C., Spagnoletti, M., Tessa, G., Toledo, L.F., Valenzuela-Sanchez, A., Verster, R., Vörös, J., Webb, R.J., Wierzbicki, C., Wombwell, E., Zamudio, K.R., Aanensen, D.M., James, T.Y., Gilbert, M.T.P., Weldon, C., Bosch, J., Balloux, F., Garner, T.W.J. & Fisher, M.C. (2018) Recent Asian origin of chytrid fungi causing global amphibian declines. Science, 360, 621–627. 10.1126/science.aar1965 — Not with love or money was it possible to find out which species of frog carried the oldest isolate of chytrid found in this study, because Science has somehow misplaced the supplemental materials of the article. Sorry! But it was probably a Bombina, and almost certainly was not a salamander.

Voyles, j., Woodhams, D.C., Saenz, V., Byrne, A.Q., Perez, R., Rios-Sotelo, G., Ryan, M.J., Bletz, M.C., Sobell, F.A., McLetchie, S., Reinert, L., Rosenblum, E.B., Rollins-Smith, L.A., Ibáñez, R., Ray, J.M., Griffith, E.J., Ross, H. & Richards-Zawacki, C.L. (2018) Shifts in disease dynamics in a tropical amphibian assemblage are not due to pathogen attenuation. Science, 359, 1517–1519. 10.1126/science.aao4806

Woinarski, J.C.Z., Murphy, B.P., Palmer, R., Legge, S.M., Dickman, C.R., Doherty, T.S., Edwards, G., Nankivell, A., Read, J.L. & Stokeld, D. (2018) How many reptiles are killed by cats in Australia? Wildlife Research, 45, 247–266. 10.1071/WR17160 — Keep your cats indoors!!! It is perfectly possible to keep a cat happy and healthy without it having to go outside except on a lead. There is loads of literature online about this, but you can start here: https://www.vetwest.com.au/pet-library/indoor-cats-keep-your-feline-happy

Arteaga, A., Salazar-Valenzuela, D., Mebert, K., Peñafiel, N., Aguiar, G., Sánchez-Nivicela, J.C., Pyron, R.A., Colston, T.J., Cisneros-Heredia, D.F., Yánez-Muñoz, M.H., Venegas, P.J., Guayasamin, J.M. & Torres-Carvajal, O. (2018) Systematics of South American snail-eating snakes (Serpentes, Dipsadini), with the description of five new species from Ecuador and Peru. ZooKeys, 766, 79–147. 10.3897/zookeys.766.24523 — See this article on Mongabay about the selling of the names to buy up forest to protect, and save the species: https://news.mongabay.com/2018/06/scientists-find-new-snail-eating-snakes-auction-naming-rights-to-save-them/. • This paper was featured in Episode 31 of Herpetological Highlights: https://herphighlights.podbean.com/e/031-from-tortoise-brutality-to-snail-eating-snakes/. • We failed to talk about naming new species after people—we will do this in a future episode

Weinell, J.L. & Brown, R.M. (2018) Discovery of an old, archipelago-wide, endemic radiation of Philippine snakes. Molecular Phylogenetics and Evolution, 119, 133–150. 10.1016/j.ympev.2017.11.004

#HERpers

More information about Prof. Marvalee H. Wake:

https://scholar.google.com/citations?user=x20bM6cAAAAJ&hl=en&oi=ao

https://en.wikipedia.org/wiki/Marvalee_Wake

Publications discussed:

Wake, D.B., Roth, G. & Wake, M.H. (1983) On the problem of stasis in organismal evolution. Journal of Theoretical Biology, 101, 211–224. — The Wikipedia page on Punctuated equilibrium is really good: https://en.wikipedia.org/wiki/Punctuated_equilibrium

Wake, M.H. (1977) The reproductive biology of caecilians: an evolutionary perspective. In: Taylor, D.H. & Guttman, S.I. (Eds.) The reproductive biology of amphibians. Springer, Boston, MA, USA. — This paper has has 124 citations, not 600 as stated in the episode (yet!).

Wake, M.H. (1993) Evolution of oviductal gestation in amphibians. The Journal of Experimental Zoology, 266, 394–413. [pdf]

Estes, R. & Wake, M.H. (1972) The first fossil record of caecilian amphibians. Nature, 239, 228–231. 10.1038/239228b0

A few mistakes made in the episode:

• Maternal dermatotrophy was originally discovered in part by Wilkinson & Nussbaum (1998 J. Nat. Hist. 32:1403) and in described in much more detail in Kupfer et al. (2006 Nature 440:926)—what was known to Prof. Wake at the time of her studies was Matrotrophy, which involves the consumption of the lining of the oviduct lining, not the external skin, and she contributed significantly to knowledge on that topic in the paper Wake, M. H. & Dickie, R. (1998) Oviduct structure and function and reproductive modes in amphibians. Journal of Experimental Zoology, 282:477–506, but it seems to have been originally described by… Dr. Hampton Wildman Parker. Of course. Parker did everything first, it seems.

• Mark got super confused explaining the oviductal gestation paper: Nectophrynoides are live-bearing frogs. Salamandra atra are live-bearing salamanders. Dermophis are live-bearing caecilians. Duh.

Main discussion

In this episode, we have done our best to cover a little bit about the genomes of axolotls, but we have actually only barely touched on just how incredible the genomes of these and other salamanders are, or how much we already know about them. This was necessary given the format and length of the podcast, but there is a huge amount of great literature out there that we did not manage to touch on! This may come up in future episodes, but otherwise, we encourage you to read more about these genomes yourselves!

References:

Nowoshilow, S., Schloissnig, S., Fei, J.-F., Dahl, A., Pang, A.W.C., Pippel, M., Winkler, S., Hastie, A.R., Young, G., Roscito, J.G., Falcon, F., Knapp, D., Powell, S., Cruz, A., Cao, H., Habermann, B., Hiller, M., Tanaka, E.M. & Myers, E.W. (2018) The axolotl genome and the evolution of key tissue formation regulators. Nature, 554, 50. 10.1038/nature25458

Humphrey, R.R. (1967) Albino axolotls from an albino tiger salamander through hybridization. Journal of Heredity, 58, 95–101. 10.1093/oxfordjournals.jhered.a107572

de Both, N.J. (1968) Transplantation of axolotl heads. Science, 162, 460–461. 10.1126/science.162.3852.460

Keinath, M.C., Timoshevskaya, N., Timoshevskiy, V.A., Voss, S.R. & Smith, J.J. (preprint) Miniscule differences between the sex chromosomes in the giant genome of a salamander, Ambystoma mexicanum. bioRxiv, 10.1101/354092

Elewa, A., Wang, H., Talavera-López, C., Joven, A., Brito, G., Kumar, A., Hameed, L.S., Penrad-Mobayed, M., Yao, Z., Zamani, N., Abbas, Y., Abdullayev, I., Sandberg, R., Grabherr, M., Andersson, B. & Simon, A. (2017) Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration. Nature Communications, 8, 2286. 10.1038/s41467-017-01964-9

A few clarifications:

Humboldt brought the first dead specimens of Ambystoma mexicanum to Europe in 1804, which were placed in the natural history museum in Paris. Living specimens were brought to Europe and bred in laboratories from 1864 onwards. Anyone with an interest in Alexander von Humboldt should read The Invention of Nature, by Andrea Wulf—an excellent biography on Alexander von Humboldt: https://www.goodreads.com/book/show/23995249-the-invention-of-nature

Briefly mentioned and further reading

Daza, J.D., Stanley, E.L., Wagner, P., Bauer, A.M. & Grimaldi, D.A. (2016) Mid-Cretaceous amber fossils illuminate the past diversity of tropical lizards. Science Advances, 2, e1501080. 10.1126/sciadv.1501080

Xing, L., O’Connor, J.K., McKellar, R.C., Chiappe, L.M., Bai, M., Tseng, K., Zhang, J., Yang, H., Fang, J. & Li, G. (2018) A flattened enantiornithine in mid-Cretaceous Burmese amber: morphology and preservation. Science Bulletin, 63, 235–243. 10.1016/j.scib.2018.01.019

Xing, L., McKellar, R.C., Xu, X., Li, G., Bai, M., Persons, W.S.I., Miyashita, T., Benton, M.J., Zhang, J., Wolfe, A.P., Yi, Q., Tsing, K., Ran, H. & Currie, P.J. (2016) A feathered dinosaur tail with primitive plumage trapped in mid-Cretaceous amber. Current Biology, 26, 3352–3360. 10.1016/j.cub.2016.10.008

Losos, J.B., Jackman, T.R., Larson, A., de Queiroz, K. & Rodríguez-Schettino, L. (1998) Contingency and determinism in replicated adaptive radiations of island lizards. Science, 279, 2115–2118. 10.1126/science.279.5359.2115

Additional material

Awful rendering of Atelopus hoogmoedi: https://frogoftheweek.wordpress.com/2016/04/10/fotw3/ —I mean, honestly.

Axolotl song: https://www.youtube.com/watch?v=MxA0QVGVEJw

Genome size database: http://genomesize.com/

TALEN information: https://www.youtube.com/watch?v=BwEiNySbBLY&t=4s (sorry, there’s not a lot out there on this)

CRISPR information: https://www.youtube.com/watch?v=UfA_jAKV29g • https://www.youtube.com/watch?v=1BXYSGepx7Q • https://www.youtube.com/watch?v=k99bMtg4zRk

Evo-devo song: https://www.youtube.com/watch?v=ydqReeTV_vk

Giant bullfrog tadpole: @afro_herper, https://twitter.com/Afro_Herper/status/1007064141549457408

Ethan’s Blackmudpuppy comic! http://www.blackmudpuppy.com

Shout-outs

Dr. Darren Naish (@tetzoo) and John Conway (@thejohnconway), and the Tetrapod Zoology podcast http://www.tetzoo.com/

Tom Major (@Thomas_Major) and Ben Marshall (@Ben_M_Marshall), and the Herpetological Highlights (@HerpHighlights) podcast https://herphighlights.podbean.com/