Molecular systematics of the western rattlesnake, Crotalus viridis (Viperidae), with comments on the utility of the D-loop in phylogenetic studies of snakes

Complement inactivating proteins and intraspecies venom variation in Crotalus oreganus helleri

Complement inactivating properties were detected in venom from the southern California distribution of Crotalus oreganus helleri (Southern Pacific Rattlesnake). This activity showed strong geographic bias to the San Bernardino Mountain range, and venom from this area reacted strongly with Fraction 5 antiserum (AF5). However, venoms from the San Jacinto Mountain range, which have been previously shown to contain Mojave toxin, did not inhibit complement and did not react with AF5. AF5 has been previously shown to recognize a protease in C. scutulatus venom that inactivates complement, but the identity of this protein has remained unknown. Using a functional venomic approach, utilizing two-dimensional gel electrophoresis coupled with liquid chromatography and tandem mass spectrometry (LC/MS/MS), we have identified catrocollastatin and hemorrhagic toxin II (HT-2) as the primary proteins recognized by AF5. The information we present within this manuscript further illustrates the now well-known reality of intraspecies venom variation and the challenges faced in providing comprehensive polyvalent antivenoms.

Molecular evolution of PIII-SVMP and RGD disintegrin genes from the genus Crotalus

Several types of disintegrins have been isolated from Crotalus spp rattlesnakes, including RGD disintegrins, and PIII-SVMPs. We isolated six cDNAs from snake venom glands using RT-PCR. Three RGD disintegrins (atroxatin, mojastin, and viridistatin) and three PIII-SVMPs (catroriarin, scutiarin, and viristiarin) cDNAs were isolated from the rattlesnakes Crotalus atrox, Crotalus scutulatus scutulatus, and Crotalus viridis viridis, respectively. Atroxatin and Viridistatin shared 90% amino acid identity to each other, and 87% identity to Mojastin. Scutiarin and Viristiarin were identical. All PIII-SVMPs isolated in this study shared the highest amino acid identity with Catrocollastatin. cDNA and protein sequences for RGD disintegrins, one MVD disintegrin, and PIII-SVMPs of the genus Crotalus (present in the NCBI database), were used in phylogenetic analysis. Neighbor-joining analysis of PIII-SVMP and RGD/MVD disintegrin-coding DNA sequences showed that these groups of genes separate into separate clades. A Phi(ST) pairwise comparison and Analysis of Molecular Variance (AMOVA) between PIII-SVMPs and RGD/MVD disintegrins showed significant genetic differences. Mutations observed in ten of the cDNAs analyzed did not affect Cys-coding sequences. Our K(A)/K(S) data suggest that rapid evolution occurred between the genes coding for PIII-SVMPs resulting, in the production of RGD disintegrin-coding genes. However, once these genes diverged, mutations in the PIII-SVMP-coding genes were accumulated less frequently.

Phylogeography and Pleistocene refugia of the adder (Vipera berus) as inferred from mitochondrial DNA sequence data

In order to contribute to the debate about southern glacial refugia used by temperate species and more northern refugia used by boreal or cold-temperate species, we examined the phylogeography of a widespread snake species (Vipera berus) inhabiting Europe up to the Arctic Circle. The analysis of the mitochondrial DNA (mtDNA) sequence variation in 1043 bp of the cytochrome b gene and in 918 bp of the noncoding control region was performed with phylogenetic approaches. Our results suggest that both the duplicated control region and cytochrome b evolve at a similar rate in this species. Phylogenetic analysis showed that V. berus is divided into three major mitochondrial lineages, probably resulting from an Italian, a Balkan and a Northern (from France to Russia) refugial area in Eastern Europe, near the Carpathian Mountains. In addition, the Northern clade presents an important substructure, suggesting two sequential colonization events in Europe. First, the continent was colonized from the three main refugial areas mentioned above during the Lower-Mid Pleistocene. Second, recolonization of most of Europe most likely originated from several refugia located outside of the Mediterranean peninsulas (Carpathian region, east of the Carpathians, France and possibly Hungary) during the Mid-Late Pleistocene, while populations within the Italian and Balkan Peninsulas fluctuated only slightly in distribution range, with larger lowland populations during glacial times and with refugial mountain populations during interglacials, as in the present time. The phylogeographical structure revealed in our study suggests complex recolonization dynamics of the European continent by V. berus, characterized by latitudinal as well as altitudinal range shifts, driven by both climatic changes and competition with related species.

Are crocodiles really monophyletic?—Evidence for subdivisions from sequence and morphological data

Recently, the phylogenetic placement of the African slender snouted crocodile, Crocodylus cataphractus, has come under scrutiny and herein we address this issue using molecular and morphological techniques. Although it is often recognized as being a "basal" form, morphological studies have traditionally placed C. cataphractus within the genus Crocodylus, while molecular studies have suggested that C. cataphractus is very distinct from other Crocodylus. To address the relationship of this species to its congeners we have sequenced portions of two nuclear genes (C-mos 302bp and ODC 294bp), and two mitochondrial genes (ND6-tRNA(glu)-cytB 347bp and control region 457bp). Analyses of these molecular datasets, both as individual gene sequences and as concatenated sequences, support the hypothesis that C. cataphractus is not a member of Crocodylus or Osteolaemus. Examination of 165 morphological characters supports and strengthens our resurrection of an historic genus, Mecistops (Gray 1844) for cataphractus.

California Ground Squirrel (Spermophilus beecheyi) Defenses Against Rattlesnake Venom Digestive and Hemostatic Toxins

Previous studies have shown that some mammals are able to neutralize venom from snake predators. California ground squirrels (Spermophilus beecheyi) show variation among populations in their ability to bind venom and minimize damage from northern Pacific rattlesnakes (Crotalus oreganus), but the venom toxins targeted by resistance have not been investigated. Four California ground squirrel populations, selected for differences in local density or type of rattlesnake predators, were assayed for their ability to neutralize digestive and hemostatic effects of venom from three rattlesnake species. In Douglas ground squirrels (S. b. douglasii), we found that animals from a location where snakes are common showed greater inhibition of venom metalloprotease and hemolytic activity than animals from a location where snakes are rare. Effects on general proteolysis were not different. Douglas ground squirrels also reduced the metalloprotease activity of venom from sympatric northern Pacific rattlesnakes (C. o. oreganus) more than the activity of venom from allopatric western diamondback rattlesnakes (C. atrox), but enhanced the fibrinolysis of sympatric venom almost 1.8 times above baseline levels. Two Beechey ground squirrel (S. b. beecheyi) populations had similar inhibition of venoms from northern and southern Pacific rattlesnakes (C. o. helleri), despite differences between the populations in the locally prevalent predator. However, the venom toxins inhibited by Beechey squirrels varied among venom from Pacific rattlesnake subspecies, and between these venoms and venom from allopatric western diamondback rattlesnakes. Blood plasma from Beechey squirrels showed highest inhibition of metalloprotease activity of northern Pacific rattlesnake venom, general proteolytic activity and hemolysis of southern Pacific rattlesnake venom, and hemolysis by allopatric western diamondback venom. These results reveal previously cryptic variation in venom activity against resistant prey that suggests reciprocal adaptation at the molecular level.

Mitochondrial DNA sequences from dried snake venom: a DNA barcoding approach to the identification of venom samples

Outdated nomenclature and incorrect taxonomic characterisation of snake venoms in the current toxinological literature have serious implications for the replicability of results from snake venom toxin research. The situation has not improved, despite attempts to supply toxinologists with regular updates on snake systematics. Here, we demonstrate the successful extraction of DNA, and subsequent sequencing of the mitochondrial 12S gene, from dried snake venoms. This approach offers a new and potentially straightforward method for accurate species identification. Mitochondrial DNA (mtDNA) sequences isolated from snake venom can be used to clarify or validate snake species identification through comparison against existing sequences in the GenBank database, and through phylogenetic analyses with other sequences. Pooled venoms can also be screened a priori for the presence of multiple species, and the species names on the labels of commercial venoms verified. Moreover, if the species from which the venom sample has been taken is known, and the specimen is available as a voucher, the mtDNA sequence of the haplotype isolated from that species venom sample could serve as a sequence standard (or 'DNA barcode') for that species. Our new method of DNA barcoding venoms ensures the identification of venoms even after future taxonomic changes.

California ground squirrel (Spermophilus beecheyi) defenses against rattlesnake venom digestive and hemostatic toxins

Previous studies have shown that some mammals are able to neutralize venom from snake predators. California ground squirrels (Spermophilus beecheyi) show variation among populations in their ability to bind venom and minimize damage from northern Pacific rattlesnakes (Crotalus oreganus), but the venom toxins targeted by resistance have not been investigated. Four California ground squirrel populations, selected for differences in local density or type of rattlesnake predators, were assayed for their ability to neutralize digestive and hemostatic effects of venom from three rattlesnake species. In Douglas ground squirrels (S. b. douglasii), we found that animals from a location where snakes are common showed greater inhibition of venom metalloprotease and hemolytic activity than animals from a location where snakes are rare. Effects on general proteolysis were not different. Douglas ground squirrels also reduced the metalloprotease activity of venom from sympatric northern Pacific rattlesnakes (Crotalus oreganus oreganus) more than the activity of venom from allopatric western diamondback rattlesnakes (C. atrox), but enhanced fibrinolysis of sympatric venom almost 1.8 times above baseline levels. Two Beechey ground squirrel (S. b. beecheyi) populations had similar inhibition of venoms from northern and southern Pacific rattlesnakes (C. o. helleri), despite differences between the populations in the locally prevalent predator. However, the venom toxins inhibited by Beechey squirrels did vary among venom from Pacific rattlesnake subspecies, and between these venoms and venom from allopatric western diamondback rattlesnakes. Blood plasma from Beechey squirrels showed highest inhibition of metalloprotease activity of northern Pacific rattlesnake venom, general proteolytic activity and hemolysis of southern Pacific rattlesnake venom, and hemolysis by allopatric western diamondback venom. These results reveal previously cryptic variation in venom activity against resistant prey that suggests reciprocal adaptation at the molecular level.

Presence of peptide inhibitors in rattlesnake venoms and their effects on endogenous metalloproteases

Long-term storage of proteins with retention of biological activity is a concern for many actual and potential protein drugs. A model for stabilization of proteins for long periods could exist in natural systems, particularly among viperid snakes whose venoms are rich in lytic enzymes, because when secreted into the lumen, they are stored in an inactive and competent state for many months. One mechanism inhibiting autolysis is the production of (relatively) low affinity peptide enzyme inhibitors. We investigated the distribution of two of these peptides (pEQW and pENW) in venoms from nine species of rattlesnakes and evaluated the role of these peptides in inhibiting and stabilizing isolated major venom metalloproteases (Cvo Pr V and cromipyrrhin) from Crotalus oreganus oreganus and C. mitchelli pyrrhus venom. We show that two endogenous peptides, pEQW and pENW, are present in venoms from ten taxa of Crotalus and Sistrurus and that pEQW inhibits Cvo PrV and cromipyrrhin. The peptide inhibitor pEQW also stabilizes cromipyrrhin against autoproteolysis under extreme conditions (heat). Using these peptides as models, it may be possible to design similar low affinity peptide inhibitors of protein drugs which will increase their stability and/or allow for storage under less stringently controlled conditions.

Tracing an invasion: landbridges, refugia, and the phylogeography of the Neotropical rattlesnake (Serpentes: Viperidae: Crotalus durissus)

Abstract Pleistocene fragmentation of the Amazonian rainforest has been hypothesized to be a major cause of Neotropical speciation and diversity. However, the role and even the reality of Pleistocene forest refugia have attracted much scepticism. In Amazonia, previous phylogeographical studies have focused mostly on organisms found in the forests themselves, and generally found speciation events to have predated the Pleistocene. However, molecular studies of open-formation taxa found both north and south of the Amazonian forests, probably because of vicariance resulting from expansion of the rainforests, may provide novel insights into the age of continuous forest cover across the Amazon basin. Here, we analyse three mitochondrial genes to infer the phylogeography of one such trans-Amazonian vicariant, the Neotropical rattlesnake (Crotalus durissus), which occupies primarily seasonal formations from Mexico to Argentina, but avoids the rainforests of Central and tropical South America. The phylogeographical pattern is consistent with gradual dispersal along the Central American Isthmus, followed by more rapid dispersal into and across South America after the uplift of the Isthmus of Panama. Low sequence divergence between populations from north and south of the Amazon rainforest is consistent with mid-Pleistocene divergence, approximately 1.1 million years ago (Ma). This suggests that the Amazonian rainforests must have become fragmented or at least shrunk considerably during that period, lending support to the Pleistocene refugia theory as an important cause of distribution patterns, if not necessarily speciation, in Amazonian forest organisms. These results highlight the potential of nonforest species to contribute to an understanding of the history of the Amazonian rainforests themselves.

Molecular phylogeny of Vipera Laurenti, 1768 and the related genera Macrovipera (Reuss, 1927) and Daboia (Gray, 1842), with comments about neurotoxic Vipera aspis aspis populations

We used mtDNA sequences (cytochrome b and NADH dehydrogenase subunit 2) to reconstruct molecular phylogenies of Vipera sensu lato, Vipera sensu stricto, and Vipera aspis. Three major clades were identified within the Vipera s.l. group: (1) the European vipers, (2) the oriental vipers, consisting of Montivipera (Vipera 2) plus Macrovipera lebetina, and (3) a group of Asian and North African vipers consisting of Daboia russelii, V. palaestinae, and Macrovipera mauritanica. We also distinguished three clades within the monophyletic European Vipera group: V. ammodytes, V. aspis, and V. latastei, and Pelias with monophyly of Vipera 1 uncertain. Within V. aspis, the specimens collected in France formed the sister group of an Italian clade. The "neurotoxic" French population of V. aspis, which has a specific venom profile, separated from other French V. aspis early in the history of this group.

Genetic structure of desert ground squirrels over a 20-degree-latitude transect from Oregon through the Baja California peninsula

The genetic structure of populations over a wide geographical area should reflect the demographic and evolutionary processes that have shaped a species across its range. We examined the population genetic structure of antelope ground squirrels (Ammospermophilus leucurus) across the complex of North American deserts from the Great Basin of Oregon to the cape region of the Baja California peninsula. We sampled 73 individuals from 13 major localities over this 2500-km transect, from 43 to 22 degrees north. Our molecular phylogeographical analysis of 555 bp of the mitochondrial cytochrome b gene and 510 bp of the control region revealed great genetic uniformity in a single clade that extends from Oregon to central Baja California. A second distinct clade occupies the southern half of the peninsula. The minimal geographical structure of the northern clade, its low haplotype diversity and the distribution of pairwise differences between haplotypes suggest a rapid northward expansion of the population that must have followed a northward desert habitat shift associated with the most recent Quaternary climate warming and glacial retreat. The higher haplotype diversity within the southern clade and distribution of pairwise differences between haplotypes suggest that the southern clade has a longer, more stable history associated with a southern peninsular refugium. This system, as observed, reflects both historical and contemporary ecological and evolutionary responses to physical environmental gradients within genetically homogeneous populations.

Comparing phylogenetic signal in intraspecific and interspecific body size datasets

Phylogenetic comparative methods have become a standard statistical approach for analysing interspecific data, under the assumption that traits of species are more similar than expected by chance (i.e. phylogenetic signal is present). Here I test for phylogenetic signal in intraspecific body size datasets to evaluate whether intraspecific datasets may require phylogenetic analysis. I also compare amounts of phylogenetic signal in intraspecific and interspecific body size datasets. Some intraspecific body size datasets contain significant phylogenetic signal. Detection of significant phylogenetic signal was dependant upon the number of populations (n) and the amount of phylogenetic signal (K) for a given dataset. Amounts of phylogenetic signal do not differ between intraspecific and interspecific datasets. Further, relationships between significance of phylogenetic signal and sample size and amount of phylogenetic signal are similar for intraspecific and interspecific datasets. Thus, intraspecific body size datasets are similar to interspecific body size datasets with respect to phylogenetic signal. Whether these results are general for all characters requires further study.

Phylogeny of the Mexican coastal leopard frogs of the Rana berlandieri group based on mtDNA sequences

Phylogenetic relationships among specimens from 25 different locations for the six Mexican coastal leopard frog species of the Rana berlandieri species group were investigated using 797 bp of the mitochondrial 12S rDNA gene. Relationships among the haplotypes obtained were recovered using maximum parsimony and Bayesian analyses. Most of the clades recovered by both tree building methods are strongly supported, but conflicting clades recovered by each analysis are generally poorly supported. Both analyses reject the previously proposed subgroupings of the R. berlandieri species group. Based on the strongly supported relationships, genetic differentiation, and geographic distribution of the haplotypes examined, nine independent lineages appear to comprise the group of study. However, confirmation of the new proposed lineages will require further analyses based on other genetic markers and additional samples that cover their entire geographic distribution. Concordance was noted between Miocene-Pliocene geological and climatic events in Mexico and the relationships recovered among the lineages proposed and their geographic distribution.

Bergmann's rule in nonavian reptiles: turtles follow it, lizards and snakes reverse it

Bergmann's rule is currently defined as a within-species tendency for increasing body size with increasing latitude or decreasing environmental temperature. This well-known ecogeographic pattern has been considered a general trend for all animals, yet support for Bergmann's rule has only been demonstrated for mammals and birds. Here we evaluate Bergmann's rule in two groups of reptiles: chelonians (turtles) and squamates (lizards and snakes). We perform both nonphylogenetic and phylogenetic analyses and show that chelonians follow Bergmann's rule (19 of 23 species increase in size with latitude: 14 of 15 species decrease in size with temperature), whereas squamates follow the converse to Bergmann's rule (61 of 83 species decrease in size with latitude; 40 of 56 species increase in size with temperature). Size patterns of chelonians are significant using both nonphylogenetic and phylogenetic methods, whereas only the nonphylogenetic analyses are significant for squamates. These trends are consistent among major groups of chelonians and squamates for which data are available. This is the first study to document the converse to Bergmann's rule in any major animal group as well as the first to show Bergmann's rule in a major group of ectotherms. The traditional explanation for Bergmann's rule is that larger endothermic individuals conserve heat better in cooler areas. However, our finding that at least one ectothermic group also follows Bergmann's rule suggests that additional factors may be important. Several alternative processes, such as selection for rapid heat gain in cooler areas, may be responsible for the converse to Bergmann's rule in squamates.

Phylogeographic analysis of the green python, Morelia viridis, reveals cryptic diversity

Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test whether significantly differentiated populations occur within the species range. Phylogenetic analysis of mtDNA sequences revealed hierarchal phylogeographic structure both within New Guinea and between New Guinea and Australia. Strongly supported reciprocally monophyletic mitochondrial lineages, northern and southern, were found either side of the central mountain range that runs nearly the length of New Guinea. Limited allozyme data suggest that population differentiation is reflected in the nuclear as well as the mitochondrial genome. A previous morphological analysis did not find any phenotypic concordance with the pattern of differentiation observed in the molecular data. The southern mitochondrial lineage includes all of the Australian haplotypes, which form a single lineage, nested among the southern New Guinean haplotypes.

Geographic variations, cloning, and functional analyses of the venom acidic phospholipases A2 of Crotalus viridis viridis

Geographic venom samples of Crotalus viridis viridis were obtained from South Dakota, Wyoming, Colorado, Oklahoma, Texas, New Mexico, and Arizona. From these samples, the phospholipases A(2) (PLA(2)s) were purified and their N-terminal sequences, precise masses, and in vitro enzymatic activities were determined. We purified two to four distinct acidic PLA(2)s from each sample; some of them displayed different inhibition specificities toward mammalian platelets. One of the acidic PLA(2)s induced edema, but had no anti-platelet activity. There was also a common basic PLA(2) myotoxin in all the samples. We have cloned five acidic PLA(2)s and several hybrid-like nonexpressing PLA(2)s. Molecular masses and N-terminal sequences of the purified PLA(2)s were matched with those deduced from the cDNA sequences, and the complete amino acid sequences of five novel acidic PLA(2)s were thus solved. They share 78% or greater sequence identity, and a cladogram based on the sequences of many venom acidic PLA(2)s of New World pit vipers revealed at least two subtypes. The results contribute to a better understanding of the ecogenetic adaptation of rattlesnakes and the structure-activity relationships and evolution of the acidic PLA(2)s in pit viper venom.

Body size variation among mainland populations of the western rattlesnake (Crotalus viridis)

In general, squamate reptiles follow the converse to Bergmann's rule, attaining smaller sizes in cooler environments, whereas other vertebrate groups follow Bergmann's rule, attaining larger sizes in cooler areas. Intensive studies of body size evolution for species of squamates are necessary to understand the processes responsible for this trend. Here I present data on body size variation among mainland populations of the western rattlesnake, Crotalus viridis. This species consists of two well-differentiated phylogenetic clades, therefore all analyses were performed for the C. viridis group as a whole and separately for each of the two clades within the C. viridis group. Although both phylogenetic and nonphylogenetic analyses were performed, the data did not show phylogenetic conservatism, and therefore the nonphylogenetic results are preferred. I found no significant relationships between mean adult female snout-vent length and any of the physical and climatic variables that were examined for the C. viridis group using simple linear regression analysis. Examined separately, I found that individuals of the western clade, C. oreganus, were smaller in cooler and more seasonal environments, whereas individuals of the eastern clade. C. viridis sensu stricto, were larger in cooler and more seasonal areas. Thus, the observed size trends were in opposite directions for the two clades. Multiple regression analysis revealed that seasonality was a stronger predictor of body size variation than was temperature for both clades. The differences in body size trends between these clades may be due to differences in mortality rates among populations.