Fig 1.
Remarkable sequence conservation in distantly related toxins.
Sequence alignments of widely separated sea anemone and scorpion neurotoxins are depicted. Sampled locations of these toxins are indicated on the map. Identical positions in sequence alignments are shown in blue, while differing amino acids are shown in brown. Uniprot IDs of sequences are: 1) B1NWR0; 2) P01532; 3) P0C5F4; 4) P29187; 5) E2S062; 6) Q7YXD3; 7) D5HR48; 8) P01484 and 9) D5HR56.
Table 1.
Molecular evolution of centipede PFT, CAP and LDLA venom proteins.
Table 2.
Molecular evolution of scoloptoxins.
Fig 2.
Molecular evolution of venom in centipedes (A) and spiders (B).
A plot of site-specific ω against amino acid positions for various centipede and spider venom-encoding genes is presented in panel A and B, respectively. Significantly detected positively selected sites (model 8; Bayes Empirical Bayes approach) are presented as large red circles. The red horizontal line represents the line of neutrality: points above and below this line indicate positive and negative selection, respectively. A corresponding bar plot is provided, which shows the computed ω value for the respective toxin class. Bar plot color code: Panel A 1) Novel family (NF) 8; 2) NF 6; 3) NF 4; 4) NF 1; 5) β-PFT; 6) CAP; 7) LDLA; 8) SLPTX 1; 9) SLPTX 4; 10) SLPTX 5; 11) SLPTX 10; 12) SLPTX 11; 13) SLPTX 12; 14) SLPTX 13; 15) SLPTX 15; 16) SLPTX 16; 17) SLPTX 17; Panel B 1) lycotoxins; 2) latrotoxins; 3) magi-1 family; 4) Kunitz toxins; 5) Sphingomyelinase D; 6) Huwentoxin-1 family; 7) κ/ω-hexatoxins; 8) κ-hexatoxins; 9) ω-hexatoxins; 10) Superfamily E ICKs.
Table 3.
Molecular evolution of centipede novel putative toxin families.
Fig 3.
Molecular evolution of venom in Toxicofera lizards.
A plot of site-specific ω against amino acid positions for various Toxicofera lizard toxin types is presented. The red horizontal line represents the line of neutrality: points above and below this line indicate positive and negative selection, respectively. Bar plot color codes: 1) Phospholipase A2; 2) Nerve Growth Factors; 3) Natriuretic peptides and 4) CRiSPs; 5) Kallikreins; and 6) crotamines.
Fig 4.
Molecular evolution of venom in cnidarians (A) and scorpions (B).
A plot of site-specific ω against amino acid positions for various cnidarian and scorpion venom-encoding genes is presented in panel A and B, respectively. Significantly detected positively selected sites (model 8; Bayes Empirical Bayes approach) are presented as large red circles. The red horizontal line represents the line of neutrality: points above and below this line indicate positive and negative selection, respectively. A corresponding bar plot is provided, which shows the computed ω value for the respective toxin class. Bar-plot color code: Panel A 1) SCRiPs; 2) JFTs; 3) Hydralysins; 4) Aerolysin-related toxins in sea anemone; 5) Actinoporins; 6) KTx Type 1; 7) KTx Type 3; 8) NaTx; Panel B 1) Short KTx; 2) Long KTx; 3) Chloride; 4) β-NaTx; 5) α-NaTx; 6) ICK; 7) DDH; 8) Glycine-rich toxins; 9) Bradykinin Potentiating Peptides; 10) Anionic; 11) Antimicrobial peptide toxins.
Fig 5.
Molecular evolution of venom in coleoids.
A plot of site-specific ω against amino acid positions for various coleoid toxin types is presented. The red horizontal line represents the line of neutrality: points above and below this line indicate positive and negative selection, respectively. Bar plot color codes: 1) Serine Protease; 2) PLA2; 3) Pacifestin and 4) CAP.
Fig 6.
Molecular evolution of venom in advanced snakes (A) and cone snails (B).
A plot of site-specific ω against amino acid positions for various advanced snake and cone snail venom-encoding genes is presented. Significantly detected positively selected sites (model 8; Bayes Empirical Bayes approach) are presented as large red circles. The red horizontal line represents the line of neutrality: points above and below this line indicate positive and negative selection, respectively. A corresponding bar plot is provided, which shows the computed ω value for the respective toxin class. Bar-plot color code: Panel A 1) β-defensins; 2) Cytotoxins; 3) PII-Disintegrins; 4) Group I PLA2s; 5) Group II PLA2s; 6) Kallikreins; 7) Psammophis SVMPs; 8) Advanced snake SVMPs; 9) Serine Proteases; 10) Lectins; 11) κ-3FTxs; 12) Type III α-neurotoxins; 13) Type II α-neurotoxins; Type I α-neurotoxins; and 14) CRISPs. Panel B Conus marmoreus—> 1) Superfamily M; 2) Superfamily I2; 3) Superfamily T; 4) Superfamily O2; C. geographus—> 5) Superfamily O1; 6) Superfamily O2; 7) Superfamily O1; 8) Superfamily M; 9) Superfamily A; 10) Conkunitzin; 11) Conantokin; 12) Con-ikot-ikot.
Fig 7.
Schematic tree of life depicts the evolution of venom in animals, where blue, red and orange colored lines represent lineages that utilize venom for defense, predation or intraspecific needs, respectively.
Divergence times of lineages examined in this study (labels indicated in red) have been indicated. Pie charts depict the proportion of synonymous (dS), non-synonymous (dN) mutations and the number of significantly detected positively selected sites (#PS) in the venom-encoding genes of the respective lineage. Depicted phylogenetic relationships are based on Ref. [13].