Phylogenomics of Snakes


Reduced representation genome sequencing has ushered in new methods for understanding how life evolved on earth. These methods utilise genetic data in the form of dozens, hundreds or even thousands of loci to estimate phylogenetic relationships. This approach, often termed phylogenomic analysis, has the potential to resolve controversial evolutionary relationships, particularly among ancient, rapid radiations. Among vertebrates, phylogenomic analyses are increasingly applied to an iconic group of reptiles, snakes. Phylogenomic analyses of snakes have begun to shed light on long‐standing questions including relationships among snake families, their origin among squamate reptiles and putative causes of speciation within recent radiations. In addition, these methods may even be used to obtain genetic data from archival museum specimens. This emerging approach for understanding snake evolution will be improved by whole genome sequencing initiatives that include a diverse group of snake species.

Key Concepts

  • Snakes are important study systems for human physiology and medicine.
  • Snakes are important predators in ecosystems/important to maintaining ecosystem health.
  • Robust phylogenetic hypotheses are necessary to understand snake evolution.
  • Genome‐wide data offer unprecedented opportunities to resolve snake phylogeny and the tree of life.
  • Phylogenomic analyses of snakes will aid biologists and medical researchers worldwide.

Keywords: evolutionary trees; phylogenetic inference; herpetology; serpentes; genomics

Figure 1. Number of articles using the terms ‘phylogenomic’ and ‘snakes’ since 1995. These estimates were obtained using filtered Google Scholar searches in early 2017.
Figure 2. Graphical representation of methods used to acquire phylogenomic data sets from snakes. All methods require obtaining genetic samples from snake tissues/cells (a) and subsequent DNA (deoxyribonucleic acid) extraction (b). Genomic DNAs are then processed to reduce the size of the genome and generate data sets that can be compared in phylogenetic contexts. Three primary methods for generating phylogenomics data sets are (1) using oligonucleotide primers and polymerase chain reaction amplification (c), (2) restriction enzyme digestion (RADseq; d) and (3) targeted sequence capture (e). For illustrative purposes, in (d) we have depicted the use of the HaeIII endonuclease (restriction enzyme), which has a 4‐nucleotide recognition site of GGCC.
Figure 3. Phylogeny of snake families analysed by Streicher and Wiens (; modified from their Figure 4A) demonstrating the application of phylogenomic methods across snakes. Families with more than one species in the phylogeny have been collapsed. See text for description of different methodologies. Coding refers to the methodology of Schott et al.. A question mark indicates a branch (placement of uropletids + cylindrophiids) that the likelihood and species‐tree (multispecies coalescent) analyses of Streicher and Wiens disagreed upon. An asterisk indicates that scolecophidians are not recovered as monophyletic in all analyses.


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Further Reading

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Pyron RA (2016) Novel approaches for phylogenetic inference from morphological data and total‐evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians). Systematic Biology 66: 38–56.

Reid NM, Hird SM, Brown JM, et al. (2013) Poor fit to the multispecies coalescent is widely detectable in empirical data. Systematic Biology 63: 322–333.

Streicher JW, Schulte JA II and Wiens JJ (2016) How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards. Systematic Biology 65: 128–145.

Zheng Y and Wiens JJ (2016) Combining phylogenomic and supermatrix approaches, and a time‐calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Molecular Phylogenetics and Evolution 94: 537–547.

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How to Cite close
Streicher, Jeffrey W, and Ruane, Sara(Feb 2018) Phylogenomics of Snakes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0027476]