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Squamate papers (fossil and living)

From: Ben Creisler

A number of recent non-dino papers about squamates may be of interest:

A special issue of Palaeobiodiversity and Palaeoenvironments devoted
to fossil squamates and lissamphibians is in open access (free pdfs)
through February 2014.


This issue includes a number of papers already mentioned in advance
publication on the DML.
Of particular note for squamates are:

Randall L. Nydam (2013)
Squamates from the Jurassic and Cretaceous of North America.
Palaeobiodiversity and Palaeoenvironments 93(4): 535-565


Jean-Claude Rage (2013)
Mesozoic and Cenozoic squamates of Europe.
Palaeobiodiversity and Palaeoenvironments 93(4): 517-534

Recent snake articles that may also be of interest:

R. Graham Reynolds, Matthew L. Niemiller & Liam J. Revell [2013]
Toward a Tree-of-Life for the boas and pythons: Multilocus
species-level phylogeny with unprecedented taxon sampling.
Molecular Phylogenetics and Evolution (advance online publication)
doi: http://dx.doi.org/10.1016/j.ympev.2013.11.011

Snakes in the families Boidae and Pythonidae constitute some of the
most spectacular reptiles and comprise an enormous diversity of
morphology, behavior, and ecology. While many species of boas and
pythons are familiar, taxonomy and evolutionary relationships within
these families remain contentious and fluid. A major effort in
evolutionary and conservation biology is to assemble a comprehensive
Tree-of-Life, or a macro-scale phylogenetic hypothesis, for all known
life on Earth. No previously published study has produced a
species-level molecular phylogeny for more than 61% of boa species or
65% of python species. Using both novel and previously published
sequence data, we have produced a species-level phylogeny for 84.5% of
boid species and 82.5% of pythonid species, contextualized within a
larger phylogeny of henophidian snakes. We obtained new sequence data
for three boid, one pythonid, and two tropidophiid taxa which have
never previously been included in a molecular study, in addition to
generating novel sequences for seven genes across an additional 12
taxa. We compiled an 11-gene dataset for 127 taxa, consisting of the
mitochondrial genes CYTB, 12S, and 16S, and the nuclear genes bdnf,
bmp2, c-mos, gpr35, rag1, ntf3, odc, and slc30a1, totaling up to 7561
base pairs per taxon. We analyzed this dataset using both maximum
likelihood and Bayesian inference and recovered a well-supported
phylogeny for these species. We found significant evidence of
discordance between taxonomy and evolutionary relationships in the
genera Tropidophis, Morelia, Liasis, and Leiopython, and we found
support for elevating two previously suggested boid species. We
suggest a revised taxonomy for the boas (13 genera, 58 species) and
pythons (8 genera, 40 species), review relationships between our study
and the many other molecular phylogenetic studies of henophidian
snakes, and present a taxonomic database and alignment which may be
easily used and built upon by other researchers.

We present a multilocus phylogeny of the boas and pythons.
We achieved >80% species coverage for both boas and pythons.
We found taxonomic discordance in Tropidophis, Morelia, Liasis, and Leiopython.
We found support for elevating two previously suggested boid species.
We suggest a revised taxonomy for the boas and pythons.

Todd A. Castoe, A. P. Jason de Koning, Kathryn T. Hall, Daren C. Card,
Drew R. Schield, Matthew K. Fujita, Robert P. Ruggiero, Jack F.
Degner, Juan M. Daza, Wanjun Gu, Jacobo Reyes-Velasco, Kyle J. Shaney,
Jill M. Castoe, Samuel E. Fox, Alex W. Poole, Daniel Polanco, Jason
Dobry, Michael W. Vandewege, Qing Li, Ryan K. Schott, Aurélie Kapusta,
Patrick Minx, Cédric Feschotte, Peter Uetz, David A. Ray, Federico G.
Hoffmann, Robert Bogden, Eric N. Smith, Belinda S. W. Chang, Freek J.
Vonk, Nicholas R. Casewell, Christiaan V. Henkel, Michael K.
Richardson, Stephen P. Mackessy, Anne M. Bronikowsi, Mark Yandell,
Wesley C. Warren, Stephen M. Secor, and David D. Pollock (2013)

The Burmese python genome reveals the molecular basis for extreme
adaptation in snakes.
Proceedings of the National Academy of Sciences (advance online publication)


The molecular basis of morphological and physiological adaptations in
snakes is largely unknown. Here, we study these phenotypes using the
genome of the Burmese python (Python molurus bivittatus), a model for
extreme phenotypic plasticity and metabolic adaptation. We discovered
massive rapid changes in gene expression that coordinate major changes
in organ size and function after feeding. Many significantly
responsive genes are associated with metabolism, development, and
mammalian diseases. A striking number of genes experienced positive
selection in ancestral snakes. Such genes were related to metabolism,
development, lungs, eyes, heart, kidney, and skeletal structure—all
highly modified features in snakes. Snake phenotypic novelty seems to
be driven by the system-wide coordination of protein adaptation, gene
expression, and changes in genome structure.

Snakes possess many extreme morphological and physiological
adaptations. Identification of the molecular basis of these traits can
provide novel understanding for vertebrate biology and medicine. Here,
we study snake biology using the genome sequence of the Burmese python
(Python molurus bivittatus), a model of extreme physiological and
metabolic adaptation. We compare the python and king cobra genomes
along with genomic samples from other snakes and perform transcriptome
analysis to gain insights into the extreme phenotypes of the python.
We discovered rapid and massive transcriptional responses in multiple
organ systems that occur on feeding and coordinate major changes in
organ size and function. Intriguingly, the homologs of these genes in
humans are associated with metabolism, development, and pathology. We
also found that many snake metabolic genes have undergone positive
selection, which together with the rapid evolution of mitochondrial
proteins, provides evidence for extensive adaptive redesign of snake
metabolic pathways. Additional evidence for molecular adaptation and
gene family expansions and contractions is associated with major
physiological and phenotypic adaptations in snakes; genes involved are
related to cell cycle, development, lungs, eyes, heart, intestine, and
skeletal structure, including GRB2-associated binding protein 1, SSH,
WNT16, and bone morphogenetic protein 7. Finally, changes in
repetitive DNA content, guanine-cytosine isochore structure, and
nucleotide substitution rates indicate major shifts in the structure
and evolution of snake genomes compared with other amniotes.
Phenotypic and physiological novelty in snakes seems to be driven by
system-wide coordination of protein adaptation, gene expression, and
changes in the structure of the genome.

News story:


Freek J. Vonk, Nicholas R. Casewell, Christiaan V. Henkel, Alysha M.
Heimberg, Hans J. Jansen, Ryan J. R. McCleary, Harald M. E. Kerkkamp,
Rutger A. Vos, Isabel Guerreiro, Juan J. Calvete, Wolfgang Wüster,
Anthony E. Woods, Jessica M. Logan, Robert A. Harrison, Todd A.
Castoe, A. P. Jason de Koning, David D. Pollock, Mark Yandell, Diego
Calderon, Camila Renjifo, Rachel B. Currier, David Salgado, Davinia
Pla, Libia Sanz, Asad S. Hyder, José M. C. Ribeiro, Jan W. Arntzen,
Guido E. E. J. M. van den Thillart, Marten Boetzer, Walter Pirovano,
Ron P. Dirks, Herman P. Spaink, Denis Duboule, Edwina McGlinn, R.
Manjunatha Kini, and Michael K. Richardson (2013)
The king cobra genome reveals dynamic gene evolution and adaptation in
the snake venom system.
Proceedings of the National Academy of Sciences (advance online publication)

NOTE: This article is in open access with a free pdf.

Snakes are limbless predators, and many species use venom to help
overpower relatively large, agile prey. Snake venoms are complex
protein mixtures encoded by several multilocus gene families that
function synergistically to cause incapacitation. To examine venom
evolution, we sequenced and interrogated the genome of a venomous
snake, the king cobra (Ophiophagus hannah), and compared it, together
with our unique transcriptome, microRNA, and proteome datasets from
this species, with data from other vertebrates. In contrast to the
platypus, the only other venomous vertebrate with a sequenced genome,
we find that snake toxin genes evolve through several distinct
co-option mechanisms and exhibit surprisingly variable levels of gene
duplication and directional selection that correlate with their
functional importance in prey capture. The enigmatic accessory venom
gland shows a very different pattern of toxin gene expression from the
main venom gland and seems to have recruited toxin-like lectin genes
repeatedly for new nontoxic functions. In addition, tissue-specific
microRNA analyses suggested the co-option of core genetic regulatory
components of the venom secretory system from a pancreatic origin.
Although the king cobra is limbless, we recovered coding sequences for
all Hox genes involved in amniote limb development, with the exception
of Hoxd12. Our results provide a unique view of the origin and
evolution of snake venom and reveal multiple genome-level adaptive
responses to natural selection in this complex biological weapon
system. More generally, they provide insight into mechanisms of
protein evolution under strong selection.