SquaMates

The fifth episode of the SquaMates podcast—with cool new papers, and a special surprise. The show is hosted by Mark D. Scherz, Gabriel Ugueto, and Ethan Kocak, and this week we’re joined by guest host, #HERper Helen Plylar!

In this fifth episode, we talk about amphibian genome size evolution, the speciation of dusky salamanders (Desmognathus), and the Great Anolis Debate. We talk with Helen about her experience as a #HERper, and our main topic of discussion is her research on heat ‘vision’ in snakes.

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

Works in Frogress:

Mark has a new book:

Andreone, F., Crottini, A., Rosa, G.M., Rakotoarison, A., Scherz, M.D. & Raselimanana, A.P. (2018) Les Amphibiens du Nord de Madagascar. Association Vahatra, Antananarivo, Madagascar, 355 pp.

and two new papers:

Sentís, M., Chang, Y., Scherz, M.D., Prötzel, D. & Glaw, F. (2018) Rising from the ashes: resurrection of the Malagasy chameleons Furcifer monoceras and Furcifer voeltzkowi (Squamata: Chamaeleonidae), based on micro-CT analyses and external morphology. Zootaxa, 4483(3):549–566. 10.11646/zootaxa.4483.3.7

Rasolonjatovo, S.M., Scherz, M.D., Raselimanana, A.P. & Vences, M. (2018) Tadpole predation by Mantidactylus bellyi Mocquard, 1895 with brief description of the site and morphological measurements of the specimen. Herpetology Notes, 11:747–750. [pdf]

Gabriel is being featured in an exhibition in Albuquerque, New Mexico:

Museum’s Unique Fossil Collection & Paleoart Exhibit open for Paleontologists Convention in Albuquerque

Ethan is doing Skinktober

And True or Poo?, a sequel to Does it Fart?, written by Dani Rabaiotti (@DaniRabaiotti) and Nick Caruso (@PlethodoNick) and illustrated by our own Ethan Kocak, is out!

Breaking Newts References:

Jones, K.S. & Weisrock, D.W. (in press) Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders. Evolution. 10.1111/evo.13606

Liedtke, H.C., Gower, D.J., Wilkinson, M. & Gomez-Mestre, I. (in press) Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate. Nature Ecology & Evolution. 10.1038/s41559-018-0674-4

Nori, J., Villalobos, F. & Loyola, R. (in press) Global priority areas for amphibian research. Journal of Biogeography. 10.1111/jbi.13435

Nori, J. & Loyola, R. (2015) On the Worrying Fate of Data Deficient Amphibians. PLoS ONE, 10, e0125055. 10.1371/journal.pone.0125055

Data deficiency and the plight of the unknown – a blog post by Mark on the Nori & Loyola (2015) paper when it first came out.

Amado, T.F., Bidau, C.J. & Olalla-Tárraga, M.Á. (in press) Geographic variation of body size in New World anurans: energy and water in a balance. Ecography. 10.1111/ecog.03889 — check out @amadotalita on twitter!

The great Anolis debate:

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, 573-586. 10.11646/zootaxa.4461.4.7

in response to

Poe, S., Nieto-montes de oca, A., Torres-carvajal, O., De Queiroz, K., Velasco, J.A., Truett, B., Gray, L.N., Ryan, M.J., Köhler, G., Ayala-varela, F. & Latella, I. (2017) A phylogenetic, biogeographic, and taxonomic study of all extant species of Anolis (Squamata; Iguanidae). Systematic Biology, 66, 663–697. 10.1093/sysbio/syx029

and

Poe, S. (2013). 1986 Redux: New genera of anoles (Squamata: Dactyloidae) are unwarranted. Zootaxa, 3626(2), 295–299.

in response to

Nicholson, K.E., Crother, B.I., Guyer, C. & Savage, J.M. (2012) It is time for a new classification of anoles (Squamata: Dactyloidae). Zootaxa, 3477, 108.

and so on, and so forth.

Poll on AnoleAnnals suggests people don’t want to the adopt the alternative taxonomy

Pyron, R.A., Burbrink, F.T. & Wiens, J.J. (2013) A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology, 13, 93. 10.1186/1471-2148-13-93 (Mark mistakenly referred to this as the ‘Pyron and Wiens paper’)

#HERpers and main discussion

Read an interview with Helen Bond Plylar!

Read the Wikipedia page about Infrared ‘Vision’ in snakes

Questions from lizardners shoutouts

@llewelly

Alex Hall, @allopatry

Nicholas Sly, @nickslybirdguy

Natalia Maass, @NatDoesScience

Follow the show and the hosts on social media!

SquaMates: website • twitter • instagram • facebook

Mark D. Scherz: website • twitter • instagram • tumblr • facebook • researchgate

Gabriel Ugueto: website • twitter • instagram • facebook • artwork prints

Ethan Kocak: website • twitter • tumblr • facebook

Helen Bond Plylar: twitter

The post SquaMates Ep. 5: The Pythons Strike Back first appeared on SquaMates.

The fourth episode of the SquaMates podcast! You wanted more snake genomes? You got them! You wanted more controversy? Double dose! This show is rife with bad puns and brilliant science, hosted by Mark D. Scherz, Gabriel Ugueto, and Ethan Kocak!

In this fourth episode, we revisit the Toxicofera, whinge about how busy we all are, mourn the loss of priceless collections, and bring you some hot new science from the last month! These breaking newts include some new snake genomes, some shockingly complicated methods, and a strong message of STAHP SENDING SALAMANDERS OVERSEAS! Our main discussion is a free-form conversation about the way we think about invasive species, and how it is often based on gut feelings, rather than evidence (which discuss without mentioning any primary literature). The featured #HERper is Rose Marie Antoinette Blommers-Schlösser, whose work did wonders for researchers studying Madagascar’s amphibians.

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

Missedsnakes References:

Koch, N.M. & Gauthier, J.A. (2018) Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. PloS ONE, 13, e0202729. 10.1371/journal.pone.0202729

Works in Froggress

True or Poo is coming out soon—pre-order it now!

Breaking Newts References:

Wikimedia Campaign to upload photos of the Museu Nacional, Rio de Janeiro. Or upload your photos here. Or send them to [email protected], [email protected], or [email protected].

Miralles, A., Marin, J., Markus, D., Herrel, A., Hedges, S.B. & Vidal, N. (in press) Molecular evidence for the paraphyly of Scolecophidia and its evolutionary implications. Journal of Evolutionary Biology. 10.1111/jeb.13373

Opazo, J.C. & Zavala, K. (2018) Phylogenetic evidence for independent origins of GDF1 and GDF3 genes in anurans and mammals. Scientific Reports, 8, 13595. 10.1038/s41598-018-31954-w

Shibata, H., Chijiwa, T., Oda-Ueda, N., Nakamura, H., Yamaguchi, K., Hattori, S., Matsubara, K., Matsuda, Y., Yamashita, A. & Isomoto, A. (2018) The habu genome reveals accelerated evolution of venom protein genes. Scientific Reports, 8, 11300. 10.1038/s41598-018-28749-4

Burbrink, F.T. & Gehara, M. (2018) The biogeography of deep time phylogenetic reticulation. Systematic Biology, 67, 743–755. 10.1093/sysbio/syy019

Li, J.-T., Gao, Y.-D., Xie, L., Deng, C., Shi, P., Guan, M.-L., Huang, S., Ren, J.-L., Wu, D.-D. & Ding, L. (2018) Comparative genomic investigation of high-elevation adaptation in ectothermic snakes. Proceedings of the National Academy of Sciences of the USA, 201805348. 10.1073/pnas.1805348115

Sun, A.X., Londono, R., Hudnall, M.L., Tuan, R.S. & Lozito, T.P. (2018) Differences in neural stem cell identity and differentiation capacity drive divergent regenerative outcomes in lizards and salamanders. Proceedings of the National Academy of Sciences of the USA, 201803780. 10.1073/pnas.1803780115

*This paper was discussed in the news segment of Episode 42 of the Common Descent Podcast

McGlothlin, J.W., Kobiela, M.E., Wright, H.V., Mahler, D.L., Kolbe, J.J., Losos, J.B. & Brodie III, E.D. (2018) Adaptive radiation along a deeply conserved genetic line of least resistance in Anolis lizards. Evolution Letters, 2, 310–322. 10.1002/evl3.72

*This extremely complicated paper is summarised on the Evolution Letters editor’s blog.

Fitzpatrick, L.D., Pasmans, F., Martel, A. & Cunningham, A.A. (2018) Epidemiological tracing of Batrachochytrium salamandrivorans identifies widespread infection and associated mortalities in private amphibian collections. Scientific Reports, 8, 13845. 10.1038/s41598-018-31800-z

#HERper further reading:

Wikipedia: Rose Marie Antoinette Blommers-Schlösser

Blommers-Schlösser, R.M.A. & Blanc, C.P. (1991) Amphibiens (première partie). Faune de Madagascar, 75, 1–397. [can be purchased here]

Blommers-Schlösser, R.M.A. & Blanc, C.P. (1993) Amphibiens (duexième partie). Faune de Madagascar, 75, 385–530. [can be purchased here]

Blommers-Schlösser, R.M.A. (1975) Observations on the larval development of some Malagasy frogs, with notes on their ecology and biology (Anura: Dyscophinae, Scaphiophryninae, and Cophylinae). Beaufortia, 24, 7–26. [pdf available here]

Shout-outs

llewelly: @llewelly (sorry about the epic fail at answering your question!)

Jakob Vinther: @macroevolut — the deliverer of the fossil colour talk that Mark mentioned in Works in Froggress.

Emma Sherratt: @DrEmSherratt — the deliverer of arguably the best talk at Evolution 2018.

Germán Orizaola: @GOrizaola — works on the treefrogs in Chernobyl

Colin Donihue: @colindonihue

Hey @TomBodett, I heard you ask @Faith_Salie on @waitwait for a pic of my leafblower setup. Here ya go!

— Colin Donihue (@colindonihue) July 28, 2018

Follow the show and the hosts on social media!

SquaMates: website • twitter • instagram • facebook

Mark D. Scherz: website • twitter • instagram • tumblr • facebook • researchgate

Gabriel Ugueto: website • twitter • instagram • facebook • artwork prints

Ethan Kocak: website • twitter • tumblr • facebook

The post SquaMates Ep. 4: A Newt Hope first appeared on SquaMates.

The third episode of the SquaMates podcast—bigger, better, and much, much longer than ever before! The show is rife with bad puns and brilliant science, and hosted by Mark D. Scherz, Gabriel Ugueto, and Ethan Kocak!

In this third episode, an unplanned drinking game is introduced, as well as a new section title! We talk about cobras, leafblowers, synapomorphic skull loss among stem Serpentes, and the ridiculous diversity of the Gymnophthghshmhalmidae, before diving into our main topic (by popular demand): the Toxicofera, and the age-old question, ‘just what is venom, anyway?’ and ‘why is my hand falling off?’ The featured #HERpers are a trifecta of amazing Victorian-Edwardian women, whose fates differed dramatically, but who helped light the way for women in herpetology.

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

Missedsnakes References:

Smith, J.J., Timoshevskaya, N., Timoshevskiy, V.A., Keinath, M.C., Hardy, D. & Voss, S.R. (2018) A Chromosome-Scale Assembly of the Enormous (32 Gb) Axolotl Genome. bioRxiv, 10.1101/373548

Works in Frogress:

Mark’s blogpost about the new geckos and frogs he described

New books illustrated by Gabriel and Ethan: ‘So you think you know about… Dinosaurs’

Breaking Newts References:

Wüster, W., Chirio, L., Trape, J.-F., Ineich, I., Jackson, K., Greenbaum, E., Barron, C., Kusamba, C., Nagy, Z.T., Storey, R., Hall, C., Wüster, C.E., Barlow, A. & Broadley, D.G. (2018) Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae). Zootaxa, 4455, 68–98. 10.11646/zootaxa.4455.1.3

Donihue, C.M., Herrel, A., Fabre, A.-C., Kamath, A., Geneva, A.J., Schoener, T.W., Kolbe, J.J. & Losos, J.B. (2018) Hurricane-induced selection on the morphology of an island lizard. Nature, 560, 88–91. 10.1038/s41586-018-0352-3

*hilarious video here

Xing, L., Caldwell, M.W., Chen, R., Nydam, R.L., Palci, A., Simões, T.R., McKellar, R.C., Lee, M.S.Y., Liu, Y., Shi, H., Wang, K. & Bai, M. (2018) A mid-Cretaceous embryonic-to-neonate snake in amber from Myanmar. Science Advances, 4, eaat5042. 10.1126/sciadv.aat5042

Perry, B.W., Card, D.C., McGlothlin, J.W., Pasquesi, G.I.M., Adams, R.H., Schield, D.R., Hales, N.R., Corbin, A.B., Demuth, J.P., Hoffmann, F.G., Vandewege, M.W., Schott, R.K., Bhattacharyya, N., Chang, B.S.W., Casewell, N.R., Whiteley, G., Reyes-Velasco, J., Mackessy, S.P., Gamble, T., Storey, K.B., Biggar, K.K., Passow, C.N., Kuo, C.-H., McGaugh, S.E., Bronikowski, A.M., de Koning, J., Edwards, S.V., Pfrender, M.E., Minx, P., Brodie, I.I.I.E.D., Brodie, J.E.D., Warren, W.C. & Castoe, T.A. (in press) Molecular adaptations for sensing and securing prey and insight into amniote genome diversity from the garter snake genome. Genome Biology and Evolution, accepted, evy157. 10.1093/gbe/evy157

Edwards, R.J., Tuipulotu, D.E., Amos, T.G., O’Meally, D., Richardson, M.F., Russell, T.L., Vallinoto, M., Carneiro, M., Ferrand, N., Wilkins, M.R., Sequeira, F., Rollins, L.A., Holmes, E.C., Shine, R. & White, P.A. (in press) Draft genome assembly of the invasive cane toad, Rhinella marina. GigaScience, giy095. 10.1093/gigascience/giy095

Pasquesi, G.I.M., Adams, R.H., Card, D.C., Schield, D.R., Corbin, A.B., Perry, B.W., Reyes-Velasco, J., Ruggiero, R.P., Vandewege, M.W., Shortt, J.A. & Castoe, T.A. (2018) Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nature Communications, 9, 2774. 10.1038/s41467-018-05279-1

Portik, D.M., Bell, R.C., Blackburn, D.C., Bauer, A.M., Barratt, C.D., Branch, W.R., Burger, M., Channing, A., Colston, T.J., Conradie, W., Dehling, J.M., Drewes, R.C., Ernst, R., Greenbaum, E., Gvoždík, V., Harvey, J., Hillers, A., Hirschfeld, M., Jongsma, G., Kielgast, J., Kouete, M.T., Lawson, L.P., Leaché, A.D., Loader, S.P., Lötters, S., van der Meijden, A., Menegon, M., Müller, S., Nagy, Z.T., Ofori-Boateng, C., Ohler, A., Papenfuss, T.J., Rößler, D., Sinsch, U., Rödel, M.-O., Veith, M., Vindum, J., Zassi-Boulou, A.-G. & McGuire, J.A. (2018) Sexual dichromatism drives diversification within a major radiation of African amphibians. bioRxiv, 10.1101/372250

Moravec, J., Šmíd, J., Štundl, J. & Lehr, E. (2018) Systematics of Neotropical microteiid lizards (Gymnophthalmidae, Cercosaurinae), with the description of a new genus and species from the Andean montane forests. ZooKeys, 774, 10.3897/zookeys.774.25332

#HERper further reading:

Dr Doris Mable Cochran:

Wikipedia

Smithsonian Institution Archives

A lovely and incredibly in-depth piece on this by Dr Leslie M.B. (full name unknown) 

Dr Bertha Lutz:

Wikipedia

Feminism, Fascism, and Frogs: The Case of Bertha Lutz at the United Nations

Get to Know a Brazilian – Bertha Lutz

Enrica Calabresi:

Wikipedia

Toxicofera citations:

Fry, B.G., Vidal, N., Norman, J.A., Vonk, F.J., Scheib, H., Ramjan, S.F., Kuruppu, S., Fung, K., Hedges, S.B., Richardson, M.K., Hodgson, W.C., Ignjatovic, V., Summerhayes, R. & Kochva, E. (2005) Early evolution of the venom system in lizards and snakes. Nature, 439, 584–588. 10.1038/nature04328

Vidal, N. & Hedges, S.B. (2005) The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes. Comptes Rendus Biologies, 328, 1000–1008. 10.1016/j.crvi.2005.10.001

Hargreaves, A.D., Swain, M.T., Logan, D.W. & Mulley, J.F. (2014) Testing the Toxicofera: Comparative transcriptomics casts doubt on the single, early evolution of the reptile venom system. Toxicon, 92, 140–156. 10.1016/j.toxicon.2014.10.004

Losos, J.B., Hillis, D.M. & Greene, H.W. (2012) Who Speaks with a Forked Tongue? Science, 338, 1428–1429. 10.1126/science.1232455 [pdf]

Gauthier, J.A., Kearney, M., Maisano, J.A., Rieppel, O. & Behlke, A.D.B. (2012) Assembling the squamate tree of life: perspectives from the phenotype and the fossil record. Bulletin of the Peabody Museum of Natural History, 53, 3–308. 10.3374/014.053.0101

Fry, B.G., Casewell, N.R., Wüster, W., Vidal, N., Young, B. & Jackson, T.N.W. (2012) The structural and functional diversification of the Toxicofera reptile venom system. Toxicon, 60, 434–448. 10.1016/j.toxicon.2012.02.013

*This paper received a few replies… see the doi link and read those to formulate your own opinions.

Irisarri, I., Baurain, D., Brinkmann, H., Delsuc, F., Sire, J.-Y., Kupfer, A., Petersen, J., Jarek, M., Meyer, A., Vences, M. & Philippe, H. (2017) Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nature Ecology and Evolution, 1, 1370–1378. 10.1038/s41559-017-0240-5

Streicher, J.W. & Wiens, J.J. (2017) Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families. Biology Letters, 13, 20170393. 10.1098/rsbl.2017.0393

Reeder, T.W., Townsend, T.M., Mulcahy, D.G., Noonan, B.P., Wood, P.L., Jr., Sites, J.W., Jr. & Wiens, J.J. (2015) Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa. PLoS ONE, 10, e0118199. 10.1371/journal.pone.0118199

Koludarov, I., Jackson, T.N.W., op den Brouw, B., Dobson, J., Dashevsky, D., Arbuckle, K., Clemente, C.J., Stockdale, E.J., Cochran, C., Debono, J., Stephens, C., Panagides, N., Li, B., Roy Manchadi, M.-L., Violette, A., Fourmy, R., Hendrikx, I., Nouwens, A., Clements, J., Martelli, P., Kwok, H.F. & Fry, B.G. (2017) Enter the dragon: the dynamic and multifunctional evolution of Anguimorpha lizard venoms. Toxins, 9, 242. 10.3390/toxins9080242

*we fucked up: this was published on the 8th of August 2017, NOT 2018! Oops.

Questions from Lizardners References

Reynolds, R.G., Niemiller, M.L. & Revell, L.J. (2014) Toward a Tree-of-Life for the boas and pythons: Multilocus species-level phylogeny with unprecedented taxon sampling. Molecular Phylogenetics and Evolution, 71, 201–213. 10.1016/j.ympev.2013.11.011

Cieri, R.L., Craven, B.A., Schachner, E.R. & Farmer, C.G. (2014) New insight into the evolution of the vertebrate respiratory system and the discovery of unidirectional airflow in iguana lungs. Proceedings of the National Academy of Sciences, 111, 17218–17223. 10.1073/pnas.1405088111

Tetrapod Zoology: Skinks, Skinks, Skinks!

Tetrapod Zoology: Sandfishes and kin: of sand-swimming, placentation, and limb and digit reduction (skinks part III)

Tetrapod Zoology: Worm Lizards: Lifestyles of the limbless

Shout-outs

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

Julian Rossi @JulianJRossi

Dr Owen Davies @DrOwenDavies

Nicholas Sly @NickSlyBirdGuy

Sarah McAnulty @SarahMackAttack

Follow the show and the hosts on social media!

SquaMates: website • twitter • instagram • facebook

Mark D. Scherz: website • twitter • instagram • tumblr • facebook • researchgate

Gabriel Ugueto: website • twitter • instagram • facebook • artwork prints

Ethan Kocak: website • twitter • tumblr • facebook

The post SquaMates Ep. 3: Revenge of the Toxicofera first appeared on SquaMates.

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/

Kirsten Hecht: @hellbenderhecht

Dr. Owen Davies: @drowendavies

Zach Miller: @zmiller1902

Follow the show and the hosts on social media!

SquaMates: website • twitter • instagram • facebook

Mark D. Scherz: website • twitter • instagram • tumblr • facebook • researchgate

Gabriel Ugueto: website • twitter • instagram • facebook • artwork prints

Ethan Kocak: website • twitter • tumblr • facebook

The post SquaMates Ep. 2: Attack of the Genomes first appeared on SquaMates.

It’s finally here! The first episode of SquaMates, the totally serious herpetology podcast, hosted by Mark D. Scherz, Gabriel Ugueto, and Ethan Kocak!

In this first episode, we introduce you to the show and its format, then cover all of herpetological history, and then discuss all reptiles and amphibians ever.

Show References:

Caruso, N. & Rabaiotti, D. (2018) Does it fart? The definitive field guide to animal flatulence. Quercus, 144 pp.

Cope, E.D. (1895) The classification of the Ophidia. Transactions of the American Philosophical Society, 18, 186–219.

Duellman, W.E. & Trueb, L. (1986) Biology of Amphibians. John Hopkins University Press, Baltimore.

Feng, Y.-J., Blackburn, D.C., Liang, D., Hillis, D.M., Wake, D.B., Cannatella, D.C. & Zhang, P. (2017) Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary. Proceedings of the national Academy of Sciences of the USA, 114, E5864–E5870. 10.1073/pnas.1704632114

Irisarri, I., Baurain, D., Brinkmann, H., Delsuc, F., Sire, J.-Y., Kupfer, A., Petersen, J., Jarek, M., Meyer, A., Vences, M. & Philippe, H. (2017) Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nature Ecology and Evolution, 1, 13709–1378. 10.1038/s41559-017-0240-5

Trueb, L. (1968) Cranial Osteology of the Hylid Frog, Smilisca baudini. University of Kansas Publications, Museum of Natural History, 18, 11–35.

Trueb, L. (1973) Bones, frogs, and evolution. In: Vial, J.L. (Ed.) Evolutionary biology of the anurans: Contemporary research on major problems. University of Missouri Press, USA, pp. 65–132.

Trueb, L. (1993) Patterns of Diversity in the Lissamphibian Skull. In: Hanken, J. & Hall, B.K. (Eds.) The Skull, Volume 2: Patterns of Structural and Systematic Diversity. University of Chicago Press, Chicago IL, USA, pp. 255–343.

Wollenberg Valero, K.C., Garcia-Porta, J., Rodríguez, A., Arias, M., Shah, A., Randrianiaina, R.D., Brown, J.L., Glaw, F., Amat, F., Künzel, S., Metzler, D., Isokpehi, R.D. & Vences, M. (2017) Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases. Nature Communications, 8, 15213. 10.1038/ncomms15213

Yan, F., Lü, J., Zhang, B., Yuan, Z., Wei, G., Mi, X., Zou, D., Xu, W., Chen, S., Wang, J., Xie, F., Wu, M., Xiao, H., Liang, Z., Jin, J., Wu, S., Xu, C., Tapley, B., Turvey, S.T., Papenfuss, T.J., Cunningham, A.A., Murphy, R.W., Zhang, Y. & Che, J. (2018) The Chinese giant salamander exemplifies the hidden extinction of cryptic species. Current Biology, 28, R590–R592. 10.1016/j.cub.2018.04.004

The post SquaMates Ep. 1: The Fishopod Menace first appeared on SquaMates.