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Franc Gubenšek - One of the best experts on this subject based on the ideXlab platform.
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Ammodytoxin C gene helps to elucidate the irregular structure of Crotalinae group II phospholipase A2, genes
European journal of biochemistry, 2017Co-Authors: Franc Gubenšek, Dušan KordišAbstract:Ammodytoxin C is a presynaptically neurotoxic phospholipase A2 (PLA2) expressed in the venom glands of Vipera ammodytes (subfamily Viperinae). The gene spans more than 4 kb and consists of five exons and four introns characteristic of group II phospholipase A2 genes. The first exon encodes the 5' untranslated region, the second exon encodes most of the signal peptide, while exons 3-5 encode three parts of the mature protein. Comparison of the Crotalinae and Viperinae PLA2 genes has shown that Crotalinae PLA2 retain the first intron in their mRNAs. The apparent cause of this retention is a deletion of 40 bp in the first exon of PLA2 genes of the subfamily Crotalinae, which prevents splicing of the first intron. Analysis of the secondary structure of the pre-mRNA of the ammodytoxin C gene has shown that the first exon is able to form an intra-exon hairpin which is absent in Crotalinae PLA2 pre-mRNAs. Our results indicate that this intra-exon hairpin structure is essential for the splicing of the retained first intron. Contrary to the predictions of the neutral theory of molecular evolution, the introns of all known snake venom PLA2 genes are conserved up to 90%, that is considerably more than the exons. Consequently it is proposed that highly conserved introns, in multigene families, which evolve under positive Darwinian selection, may have an important role in enabling homologous recombination.
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The Bov-B lines found in Vipera ammodytes toxic PLA2 genes are widespread in snake genomes.
Toxicon : official journal of the International Society on Toxinology, 1998Co-Authors: Dušan Kordiš, Franc GubenšekAbstract:Abstract In the fourth intron of two toxic Vipera ammodytes PLA2 genes a Ruminantia specific 5′-truncated Bov-B LINE element was identified. Southern blot analysis of Bov-B LINE distribution in vertebrates shows that, apart from the Ruminantia, it is limited to Viperidae snakes (V. ammodytes, Vipera palaestinae, Echis coloratus, Bothrops alternatus, Trimeresurus flavoviridis and Trimeresurus gramineus). The copy number of the 3′ end of Bov-B LINE in the V. ammodytes genome is between 62 000 and 75 000. At orthologous positions in other snake PLA2 genes the Bov-B LINE element is absent, indicating that its retrotransposition in the V. ammodytes PLA2 gene locus has occurred quite recently, about 5 Myr ago. The amplification of Bov-B LINEs in snakes may have occurred before the divergence of the Viperinae and Crotalinae subfamilies. Due to its wide distribution in Viperidae snakes it should be a valuable phylogenetic marker. The neighbour-joining phylogenetic tree shows two clusters of truncated Bov-B LINE, a Bovidae and a snake cluster, indicating an early horizontal transfer of this transposable element.
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Bov‐B Long Interspersed Repeated DNA (LINE) Sequences are Present in Vipera Ammodytes Phospholipase A2 Genes and in Genomes of Viperidae Snakes
European journal of biochemistry, 1997Co-Authors: Dušan Kordiš, Franc GubenšekAbstract:Ammodytin L is a myotoxic Ser49 phospholipase A2 (PLA2) homologue, which is tissue-specifically expressed in the venom glands of Vipera ammodytes. The complete DNA sequence of the gene and its 5′ and 3′ flanking regions has been determined. The gene consists of five exons separated by four introns. Comparative analysis of the ammodytin L and ammodytoxin C genes shows that all intron and flanking sequences are considerably more conserved (93–97%) than the mature protein-coding exons. The pattern of nucleotide substitutions in protein-coding exons is not random but occurs preferentially on the first and the second positions of codons, which suggests positive Darwinian evolution for a new function. An Ruminantia specific ART-2 retroposon, recently recognised as a S′-truncated Bov-B long interspersed repeated DNA (LINE) sequence, was identified in the fourth intron of both genes. This result suggests that ammodytin L and ammodytoxin C genes are derived by duplication of a common ancestral gene. The phylogenetic distribution of Bov-B LINE among vertebrate classes shows that, besides the Ruminantia, it is limited to Viperidae snakes (Vipera ammodytes, Vipera palaestinae, Echis coloratus, Bothrops alternatus, Trimeresurus flavoviridis and Trimeresurus gramineus). The copy number of the 3′ end of Bov-B LINE in the Vipera ammodytes genome is between 62000 and 75000. The absence of Bov-B LINE at orthologous positions in other snake PLA2 genes indicates that its retrotransposition in the V. ammodytes PLA2 gene locus has occurred quite recently, about 5 My ago. The amplification of Bov-B LINEs in snakes may have occurred before the divergence of the Viperinae and Crotalinae subfamilies. Due to its wide distribution in Viperidae snakes it may be a valuable phylogenetic marker. The neighbor-joining phylogenetic tree shows two clusters of truncated Bov-B LINE, a Bovidae and a snake cluster, indicating an early horizontal transfer of this transposable element.
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bov b long interspersed repeated dna line sequences are present in vipera ammodytes phospholipase a2 genes and in genomes of viperidae snakes
FEBS Journal, 1997Co-Authors: Dušan Kordiš, Franc GubenšekAbstract:Ammodytin L is a myotoxic Ser49 phospholipase A2 (PLA2) homologue, which is tissue-specifically expressed in the venom glands of Vipera ammodytes. The complete DNA sequence of the gene and its 5′ and 3′ flanking regions has been determined. The gene consists of five exons separated by four introns. Comparative analysis of the ammodytin L and ammodytoxin C genes shows that all intron and flanking sequences are considerably more conserved (93–97%) than the mature protein-coding exons. The pattern of nucleotide substitutions in protein-coding exons is not random but occurs preferentially on the first and the second positions of codons, which suggests positive Darwinian evolution for a new function. An Ruminantia specific ART-2 retroposon, recently recognised as a S′-truncated Bov-B long interspersed repeated DNA (LINE) sequence, was identified in the fourth intron of both genes. This result suggests that ammodytin L and ammodytoxin C genes are derived by duplication of a common ancestral gene. The phylogenetic distribution of Bov-B LINE among vertebrate classes shows that, besides the Ruminantia, it is limited to Viperidae snakes (Vipera ammodytes, Vipera palaestinae, Echis coloratus, Bothrops alternatus, Trimeresurus flavoviridis and Trimeresurus gramineus). The copy number of the 3′ end of Bov-B LINE in the Vipera ammodytes genome is between 62000 and 75000. The absence of Bov-B LINE at orthologous positions in other snake PLA2 genes indicates that its retrotransposition in the V. ammodytes PLA2 gene locus has occurred quite recently, about 5 My ago. The amplification of Bov-B LINEs in snakes may have occurred before the divergence of the Viperinae and Crotalinae subfamilies. Due to its wide distribution in Viperidae snakes it may be a valuable phylogenetic marker. The neighbor-joining phylogenetic tree shows two clusters of truncated Bov-B LINE, a Bovidae and a snake cluster, indicating an early horizontal transfer of this transposable element.
Dušan Kordiš - One of the best experts on this subject based on the ideXlab platform.
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Ammodytoxin C gene helps to elucidate the irregular structure of Crotalinae group II phospholipase A2, genes
European journal of biochemistry, 2017Co-Authors: Franc Gubenšek, Dušan KordišAbstract:Ammodytoxin C is a presynaptically neurotoxic phospholipase A2 (PLA2) expressed in the venom glands of Vipera ammodytes (subfamily Viperinae). The gene spans more than 4 kb and consists of five exons and four introns characteristic of group II phospholipase A2 genes. The first exon encodes the 5' untranslated region, the second exon encodes most of the signal peptide, while exons 3-5 encode three parts of the mature protein. Comparison of the Crotalinae and Viperinae PLA2 genes has shown that Crotalinae PLA2 retain the first intron in their mRNAs. The apparent cause of this retention is a deletion of 40 bp in the first exon of PLA2 genes of the subfamily Crotalinae, which prevents splicing of the first intron. Analysis of the secondary structure of the pre-mRNA of the ammodytoxin C gene has shown that the first exon is able to form an intra-exon hairpin which is absent in Crotalinae PLA2 pre-mRNAs. Our results indicate that this intra-exon hairpin structure is essential for the splicing of the retained first intron. Contrary to the predictions of the neutral theory of molecular evolution, the introns of all known snake venom PLA2 genes are conserved up to 90%, that is considerably more than the exons. Consequently it is proposed that highly conserved introns, in multigene families, which evolve under positive Darwinian selection, may have an important role in enabling homologous recombination.
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The Bov-B lines found in Vipera ammodytes toxic PLA2 genes are widespread in snake genomes.
Toxicon : official journal of the International Society on Toxinology, 1998Co-Authors: Dušan Kordiš, Franc GubenšekAbstract:Abstract In the fourth intron of two toxic Vipera ammodytes PLA2 genes a Ruminantia specific 5′-truncated Bov-B LINE element was identified. Southern blot analysis of Bov-B LINE distribution in vertebrates shows that, apart from the Ruminantia, it is limited to Viperidae snakes (V. ammodytes, Vipera palaestinae, Echis coloratus, Bothrops alternatus, Trimeresurus flavoviridis and Trimeresurus gramineus). The copy number of the 3′ end of Bov-B LINE in the V. ammodytes genome is between 62 000 and 75 000. At orthologous positions in other snake PLA2 genes the Bov-B LINE element is absent, indicating that its retrotransposition in the V. ammodytes PLA2 gene locus has occurred quite recently, about 5 Myr ago. The amplification of Bov-B LINEs in snakes may have occurred before the divergence of the Viperinae and Crotalinae subfamilies. Due to its wide distribution in Viperidae snakes it should be a valuable phylogenetic marker. The neighbour-joining phylogenetic tree shows two clusters of truncated Bov-B LINE, a Bovidae and a snake cluster, indicating an early horizontal transfer of this transposable element.
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Bov‐B Long Interspersed Repeated DNA (LINE) Sequences are Present in Vipera Ammodytes Phospholipase A2 Genes and in Genomes of Viperidae Snakes
European journal of biochemistry, 1997Co-Authors: Dušan Kordiš, Franc GubenšekAbstract:Ammodytin L is a myotoxic Ser49 phospholipase A2 (PLA2) homologue, which is tissue-specifically expressed in the venom glands of Vipera ammodytes. The complete DNA sequence of the gene and its 5′ and 3′ flanking regions has been determined. The gene consists of five exons separated by four introns. Comparative analysis of the ammodytin L and ammodytoxin C genes shows that all intron and flanking sequences are considerably more conserved (93–97%) than the mature protein-coding exons. The pattern of nucleotide substitutions in protein-coding exons is not random but occurs preferentially on the first and the second positions of codons, which suggests positive Darwinian evolution for a new function. An Ruminantia specific ART-2 retroposon, recently recognised as a S′-truncated Bov-B long interspersed repeated DNA (LINE) sequence, was identified in the fourth intron of both genes. This result suggests that ammodytin L and ammodytoxin C genes are derived by duplication of a common ancestral gene. The phylogenetic distribution of Bov-B LINE among vertebrate classes shows that, besides the Ruminantia, it is limited to Viperidae snakes (Vipera ammodytes, Vipera palaestinae, Echis coloratus, Bothrops alternatus, Trimeresurus flavoviridis and Trimeresurus gramineus). The copy number of the 3′ end of Bov-B LINE in the Vipera ammodytes genome is between 62000 and 75000. The absence of Bov-B LINE at orthologous positions in other snake PLA2 genes indicates that its retrotransposition in the V. ammodytes PLA2 gene locus has occurred quite recently, about 5 My ago. The amplification of Bov-B LINEs in snakes may have occurred before the divergence of the Viperinae and Crotalinae subfamilies. Due to its wide distribution in Viperidae snakes it may be a valuable phylogenetic marker. The neighbor-joining phylogenetic tree shows two clusters of truncated Bov-B LINE, a Bovidae and a snake cluster, indicating an early horizontal transfer of this transposable element.
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bov b long interspersed repeated dna line sequences are present in vipera ammodytes phospholipase a2 genes and in genomes of viperidae snakes
FEBS Journal, 1997Co-Authors: Dušan Kordiš, Franc GubenšekAbstract:Ammodytin L is a myotoxic Ser49 phospholipase A2 (PLA2) homologue, which is tissue-specifically expressed in the venom glands of Vipera ammodytes. The complete DNA sequence of the gene and its 5′ and 3′ flanking regions has been determined. The gene consists of five exons separated by four introns. Comparative analysis of the ammodytin L and ammodytoxin C genes shows that all intron and flanking sequences are considerably more conserved (93–97%) than the mature protein-coding exons. The pattern of nucleotide substitutions in protein-coding exons is not random but occurs preferentially on the first and the second positions of codons, which suggests positive Darwinian evolution for a new function. An Ruminantia specific ART-2 retroposon, recently recognised as a S′-truncated Bov-B long interspersed repeated DNA (LINE) sequence, was identified in the fourth intron of both genes. This result suggests that ammodytin L and ammodytoxin C genes are derived by duplication of a common ancestral gene. The phylogenetic distribution of Bov-B LINE among vertebrate classes shows that, besides the Ruminantia, it is limited to Viperidae snakes (Vipera ammodytes, Vipera palaestinae, Echis coloratus, Bothrops alternatus, Trimeresurus flavoviridis and Trimeresurus gramineus). The copy number of the 3′ end of Bov-B LINE in the Vipera ammodytes genome is between 62000 and 75000. The absence of Bov-B LINE at orthologous positions in other snake PLA2 genes indicates that its retrotransposition in the V. ammodytes PLA2 gene locus has occurred quite recently, about 5 My ago. The amplification of Bov-B LINEs in snakes may have occurred before the divergence of the Viperinae and Crotalinae subfamilies. Due to its wide distribution in Viperidae snakes it may be a valuable phylogenetic marker. The neighbor-joining phylogenetic tree shows two clusters of truncated Bov-B LINE, a Bovidae and a snake cluster, indicating an early horizontal transfer of this transposable element.
Hussam Zaher - One of the best experts on this subject based on the ideXlab platform.
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Maximum likelihood species-level phylogeny of Colubroides.
2019Co-Authors: Hussam Zaher, Robert W. Murphy, Juan Camilo Arredondo, Roberta Graboski, Paulo Roberto Machado-filho, Kristin Mahlow, Giovanna G. Montingelli, Ana Bottallo Quadros, Nikolai L. Orlov, Mark WilkinsonAbstract:Families Xenodermidae, Pareidae, subfamily Viperinae. Skeleton of the complete tree is displayed on the left, with the area of the tree corresponding to the present figure highlighted in black. Colored squares on each node represent bootstrap and SHL values following the categories of combined clade support described in S2 Table and summarized on the upper left corner of the figure. Diamonds on each tip represent the percentage of data generated in this study for each terminal: white, 0%; light grey, between 1% and 50%; dark grey, between 50% and 99%; black, 100%.
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Maximum likelihood species-level phylogeny of Colubroides (continued).
2019Co-Authors: Hussam Zaher, Robert W. Murphy, Juan Camilo Arredondo, Roberta Graboski, Paulo Roberto Machado-filho, Kristin Mahlow, Giovanna G. Montingelli, Ana Bottallo Quadros, Nikolai L. Orlov, Mark WilkinsonAbstract:Family Viperidae, subfamilies Viperinae, Azemiopinae, Crotalinae.
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Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates.
Molecular phylogenetics and evolution, 2016Co-Authors: Laura R. V. Alencar, Tiago B. Quental, Felipe G. Grazziotin, Michael L. Alfaro, Marcio Martins, Mericien Venzon, Hussam ZaherAbstract:Abstract Snakes of the cosmopolitan family Viperidae comprise around 329 venomous species showing a striking heterogeneity in species richness among lineages. While the subfamily Azemiopinae comprises only two species, 70% of all viper species are arranged in the subfamily Crotalinae or the “pit vipers”. The radiation of the pit vipers was marked by the evolution of the heat-sensing pits, which has been suggested to be a key innovation for the successful diversification of the group. Additionally, only crotalines were able to successfully colonize the New World. Here, we present the most complete molecular phylogeny for the family to date that comprises sequences from nuclear and mitochondrial genes representing 79% of all living vipers. We also investigated the time of divergence between lineages, using six fossils to calibrate the tree, and explored the hypothesis that crotalines have undergone an explosive radiation. Our phylogenetic analyses retrieved high support values for the monophyly of the family Viperidae, subfamilies Viperinae and Crotalinae, and 22 out of 27 genera, as well as well-supported intergeneric relationships throughout the family. We were able to recover a strongly supported sister clade to the New World pit vipers that comprises Gloydius, Ovophis, Protobothrops and Trimeresurus gracilis. Our results agree in many aspects with other studies focusing on the phylogenetics of vipers, but we recover new relationships as well. Despite the addition of new sequences we were not able to resolve some of the poor supported relationships previously suggested. Time of divergence estimates suggested that vipers started to radiate around the late Paleocene to middle Eocene with subfamilies most likely dating back to the Eocene. The invasion of the New World might have taken place sometime close to the Oligocene/Miocene boundary. Diversification analyses suggested a shift in speciation rates during the radiation of a sub-clade of pit vipers where speciation rates rapidly increased but slowed down toward the present. Thus, the evolution of the loreal pits alone does not seem to explain their explosive speciation rates. We suggest that climatic and geological changes in Asia and the invasion of the New World may have also contributed to the speciation shift found in vipers.
Alain Mangin - One of the best experts on this subject based on the ideXlab platform.
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The snake hiss: potential acoustic mimicry in a viper-colubrid complex
Biological Journal of the Linnean Society, 2014Co-Authors: Fabien Aubret, Alain ManginAbstract:Examples of acoustic Batesian mimicry are scarce, in contrast to visual mimicry. Here we describe a potential case of acoustic mimicry of a venomous viper model by harmless viperine snakes (colubrid). Viperine snakes resemble vipers in size, shape, colour, pattern, and anti-predatory behaviours, including head flattening, false strikes, and hissing. We sought to investigate whether hissing evolved as part of, or separately to, the viper mimic syndrome. To do this, we recorded and analysed the hissing sounds of several individual asp vipers, viperine snakes, and grass snakes (a close relative of viperine snakes that hisses but does not mimic the asp viper). Frequencies consistently ranged from 40 to 12 000 Hz across species and individuals. All vipers (100%) and most viperine snakes (84%) produced inhalation hissing sounds, in comparison to only 25% of grass snakes. Inhalation hissing sounds lasted longer in vipers than in viperine snakes. The hissing-sound composition of grass snakes differed significantly from that of both asp vipers and viperine snakes; however, the hissing-sound composition between viperine snakes and asp vipers was not statistically distinguishable. Whilst grass snake hissing sounds were characterized by high frequencies (5000–10 000 Hz), both vipers and viperine snake hissing sounds were dominated by low frequencies (200–400 Hz). A principal component analysis revealed no overlap between grass snakes and vipers, but important overlaps between viperine snakes and vipers, and between viperine snakes and grass snakes. The likelihood that these overlaps respectively reflect natural selection for Batesian mimicry and phylogeny constraints is discussed.
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the snake hiss potential acoustic mimicry in a viper colubrid complex
Biological Journal of The Linnean Society, 2014Co-Authors: Fabien Aubret, Alain ManginAbstract:Examples of acoustic Batesian mimicry are scarce, in contrast to visual mimicry. Here we describe a potential case of acoustic mimicry of a venomous viper model by harmless viperine snakes (colubrid). Viperine snakes resemble vipers in size, shape, colour, pattern, and anti-predatory behaviours, including head flattening, false strikes, and hissing. We sought to investigate whether hissing evolved as part of, or separately to, the viper mimic syndrome. To do this, we recorded and analysed the hissing sounds of several individual asp vipers, viperine snakes, and grass snakes (a close relative of viperine snakes that hisses but does not mimic the asp viper). Frequencies consistently ranged from 40 to 12 000 Hz across species and individuals. All vipers (100%) and most viperine snakes (84%) produced inhalation hissing sounds, in comparison to only 25% of grass snakes. Inhalation hissing sounds lasted longer in vipers than in viperine snakes. The hissing-sound composition of grass snakes differed significantly from that of both asp vipers and viperine snakes; however, the hissing-sound composition between viperine snakes and asp vipers was not statistically distinguishable. Whilst grass snake hissing sounds were characterized by high frequencies (5000–10 000 Hz), both vipers and viperine snake hissing sounds were dominated by low frequencies (200–400 Hz). A principal component analysis revealed no overlap between grass snakes and vipers, but important overlaps between viperine snakes and vipers, and between viperine snakes and grass snakes. The likelihood that these overlaps respectively reflect natural selection for Batesian mimicry and phylogeny constraints is discussed. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 1107–1114.
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The snake hiss: potential acoustic mimicry in a viper–colubrid complex
Biological Journal of The Linnean Society, 2014Co-Authors: Fabien Aubret, Alain ManginAbstract:Examples of acoustic Batesian mimicry are scarce, in contrast to visual mimicry. Here we describe a potential case of acoustic mimicry of a venomous viper model by harmless viperine snakes (colubrid). Viperine snakes resemble vipers in size, shape, colour, pattern, and anti-predatory behaviours, including head flattening, false strikes, and hissing. We sought to investigate whether hissing evolved as part of, or separately to, the viper mimic syndrome. To do this, we recorded and analysed the hissing sounds of several individual asp vipers, viperine snakes, and grass snakes (a close relative of viperine snakes that hisses but does not mimic the asp viper). Frequencies consistently ranged from 40 to 12 000 Hz across species and individuals. All vipers (100%) and most viperine snakes (84%) produced inhalation hissing sounds, in comparison to only 25% of grass snakes. Inhalation hissing sounds lasted longer in vipers than in viperine snakes. The hissing-sound composition of grass snakes differed significantly from that of both asp vipers and viperine snakes; however, the hissing-sound composition between viperine snakes and asp vipers was not statistically distinguishable. Whilst grass snake hissing sounds were characterized by high frequencies (5000–10 000 Hz), both vipers and viperine snake hissing sounds were dominated by low frequencies (200–400 Hz). A principal component analysis revealed no overlap between grass snakes and vipers, but important overlaps between viperine snakes and vipers, and between viperine snakes and grass snakes. The likelihood that these overlaps respectively reflect natural selection for Batesian mimicry and phylogeny constraints is discussed. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 1107–1114.
M. J. Childress - One of the best experts on this subject based on the ideXlab platform.
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Defensive and infrared reception responses of true vipers, pitvipers, Azemiops and colubrids
Journal of Zoology, 2007Co-Authors: Corey E. Roelke, M. J. ChildressAbstract:It has been suggested that true vipers (Viperidae: Viperinae) possess the ability to detect temperature differences between objects despite the lack of an apparent infrared radiation sensor. We tested the ability to distinguish between heated and unheated targets in three species of pitvipers (Viperidae: Crotalinae), four species of true vipers, two species of colubrids (Colubridae: Natricinae, Colubrinae) and Azemiops feae (Viperidae: Azemiopinae). All species of pitvipers tested could distinguish between the warm and cool targets, while no tested species of true viper, colubrid or Azemiops demonstrated this ability. In addition, pitvipers exhibited behaviors that true vipers or Azemiops did not exhibit. Our results suggest that the tested species of true vipers, Azemiops and colubrids may not posses the ability to sense infrared radiation or do not use it in a defensive context, and suggest that some defensive behaviors are associated with the pit organ in pitvipers.
