Molecular evidence and marine snake origins

A molecular phylogeny was used to refute the marine scenario for snake origins. Nuclear gene sequences suggested that snakes are not closely related to living varanid lizards, thus also apparently contradicting proposed relationships between snakes and marine mosasaurs (usually considered to be varanoids). However, mosasaurs share derived similarities with both snakes and living varanids. A reanalysis of the morphological data suggests that, if the relationships between living taxa are constrained to the proposed molecular tree, with fossil forms allowed to insert in their optimal positions within this framework, mosasaurs cluster with snakes rather than with varanids. Combined morphological and molecular analyses also still unite marine lizards with snakes. Thus, the molecular data do not refute the phylogenetic evidence for a marine origin of snakes.     

ISOLATION BREEDS NAIVETY: ISLAND LIVING ROBS AUSTRALIAN VARANID LIZARDS OF TOAD‐TOXIN IMMUNITY VIA FOUR‐BASE‐PAIR MUTATION

Since their introduction to the toad‐free Australian continent cane toads (Bufo marinus) have caused a dramatic increase in naïve varanid mortality when these large lizards attempt to feed on this toxic amphibian. In contrast Asian–African varanids, which have coevolved with toads, are resistant to toad toxin. Toad toxins, such as Bufalin target the H1‐H2 domain of the α₁ subunit of the sodium‐potassium‐ATPase enzyme. Sequencing of this domain revealed identical nucleotide sequences in four Asian as well as in three African varanids, and identical sequences in all 11 Australian varanids. However, compared to the Asian–African varanids, the Australian varanids showed four‐base‐pair substitutions, resulting in the alteration in three of the 12 amino acids representing the H1‐H2 domain. The phenotypic effect of the substitutions was investigated in human embryonic kidney (HEK) 293 cells stably transfected with the Australian and the Asian–African H1‐H2 domains. The transfections resulted in an approximate 3000‐fold reduction in resistance to Bufalin in the Australian HEK293 cells compared to the Asian–African HEK293 cells, demonstrating the critical role of this minor mutation in providing Bufalin resistance. Our study hence presents a clear link between genotype and phenotype, a critical step in understanding the evolution of phenotypic diversity.     

Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes

Most previous phylogenetic analyses of squamates (‘lizards’ and snakes) employing large character sets have focused on osteology. Soft anatomical traits bearing on this problem have usually been considered in small subsets. Here, a comprehensive phylogenetic analysis of squamate soft anatomy is attempted. 126 informative characters are assessed for 23 squamate lineages, representing snakes, amphisbaenians, dibamids, and all the traditionally recognized ‘families’ of lizards. The traditionally recognized groupings Iguania, Scleroglossa, Gekkota, Scincomorpha, Anguimorpha and Varanoidea are corroborated in this analysis. More controversial taxa are resolved as follows. Xantusiids, amphisbaenians and dibamids cluster with gekkotans, and snakes are strongly allied with anguimorphs in general, and varanids in particular. Nearly all these clades are congruent with those found in a recent comprehensive osteological analysis; the strong support for snake‐varanid relationships found in both studies is particularly notable. This congruence is surprising given that previous studies of soft anatomy tended to give differing and often heterodox results. These previous results can be attributed to overrepresentation of misleading characters in small isolated data sets. Such misleading signals are minimized when data sets are combined. For instance, the snake‐varanid clade is contradicted by many characters, and analyses of particular organ systems therefore give differing results. However, characters that are incongruent with the snake‐varanid clade also disagree with each other (diffuse homoplasy), rather than forming coherent support for some particular alternative clade (concerted homoplasy). In a combined analysis these incongruent but diffuse characters cancel each other out to leave a very strong (and orthodox) phylogenetic signal. These results underscore the view that the raw amount of homoplasy — as revealed by consistency and retention indices — is not the only determinant of phylogenetic signal; the distribution of that homoplasy is also important. Thus, questioning a phylogenetic hypothesis (e.g. the snake‐varanid clade) by identifying numerous conflicting characters is insufficient — the structure of the conflicting characters should be assessed in a rigorous phylogenetic analysis.     

Metabolic rate and endurance capacity in Australian varanid lizards (Squamata: Varanidae: Varanus)

In ecomorphological and ecophysiological studies, locomotor performance is often considered to be an intermediate step between the form of an organism and its environment. We examined this premise by measuring morphology, physiology and circular track endurance in the closely related group of Australian varanid lizards. Body size, body mass and relative body proportions were poor indicators of endurance. Body mass was not correlated with endurance and size-free lower forelimb length had only a weak relationship with endurance. Instead, maximal metabolic rate was positively correlated with endurance capacity in varanids. A comparison of varanids with other groups of lizards supported this result as varanids showed both elevated maximal metabolic rate and elevated endurance scores when compared with similar sized non-varanid lizards. There was support for a strong association between endurance with foraging mode and climate. Varanid species with higher endurance tended to be widely foraging and from xeric climates, while sit-and-wait and mesic species showed reduced endurance.   © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 664–676.     

Dragon's Paradise Lost: Palaeobiogeography,Evolution and Extinction of the Largest-Ever Terrestrial Lizards (Varanidae)

Background

The largest living lizard species, Varanus komodoensis Ouwens 1912, is vulnerable to extinction, being restricted to a few isolated islands in eastern Indonesia, between Java and Australia, where it is the dominant terrestrial carnivore. Understanding how large-bodied varanids responded to past environmental change underpins long-term management of V. komodoensis populations.

Methodology/Principal Findings

We reconstruct the palaeobiogeography of Neogene giant varanids and identify a new (unnamed) species from the island of Timor. Our data reject the long-held perception that V. komodoensis became a giant because of insular evolution or as a specialist hunter of pygmy Stegodon. Phyletic giantism, coupled with a westward dispersal from mainland Australia, provides the most parsimonious explanation for the palaeodistribution of V. komodoensis and the newly identified species of giant varanid from Timor. Pliocene giant varanid fossils from Australia are morphologically referable to V. komodoensis suggesting an ultimate origin for V. komodoensis on mainland Australia (>3.8 million years ago). Varanus komodoensis body size has remained stable over the last 900,000 years (ka) on Flores, a time marked by major faunal turnovers, extinction of the island''s megafauna, the arrival of early hominids by 880 ka, co-existence with Homo floresiensis, and the arrival of modern humans by 10 ka. Within the last 2000 years their populations have contracted severely.

Conclusions/Significance

Giant varanids were once a ubiquitous part of Subcontinental Eurasian and Australasian faunas during the Neogene. Extinction played a pivotal role in the reduction of their ranges and diversity throughout the late Quaternary, leaving only V. komodoensis as an isolated long-term survivor. The events over the last two millennia now threaten its future survival.     

Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae)

Accumulating evidence for alternative gene orders demonstrates that vertebrate mitochondrial genomes are more evolutionarily dynamic than previously thought. Several lineages of parthenogenetic lizards contain large, tandem duplications that include rRNA, tRNA, and protein-coding genes, as well as the control region. Such duplications are hypothesized as intermediate stages in gene rearrangement, but the early stages of their evolution have not been previously studied. To better understand the evolutionary dynamics of duplicated segments of mitochondrial DNA, we sequenced 10 mitochondrial genomes from recently formed ( approximately 300,000 years ago) hybrid parthenogenetic geckos of the Heteronotia binoei complex and 1 from a sexual form. These genomes included some with an arrangement typical of vertebrates and others with tandem duplications varying in size from 5.7 to 9.4 kb, each with different gene contents and duplication endpoints. These results, together with phylogenetic analyses, indicate independent and frequent origins of the duplications. Small, direct repeats at the duplication endpoints imply slipped-strand error as a mechanism generating the duplications as opposed to a false initiation/termination of DNA replication mechanism that has been invoked to explain duplications in other lizard mitochondrial systems. Despite their recent origin, there is evidence for nonfunctionalization of genes due primarily to deletions, and the observed pattern of gene disruption supports the duplication-deletion model for rearrangement of mtDNA gene order. Conversely, the accumulation of mutations between these recent duplicates provides no evidence for gene conversion, as has been reported in some other systems. These results demonstrate that, despite their long-term stasis in gene content and arrangement in some lineages, vertebrate mitochondrial genomes can be evolutionary dynamic even at short timescales.     

Physiological ecology of the mangrove-dwelling varanid Varanus indicus

Some species of terrestrial lizards in wet-dry tropical climates reduce their body temperatures (T(b)'s) and activity and lower their metabolic rates during the dry season when food and water resources are scarce. However, semiaquatic lizards have access to water and presumably food throughout the year, so it is possible that they will not have the seasonal response seen in terrestrial species. We studied the thermal biology, energetics, and water flux of Varanus indicus, a semiaquatic, mangrove-dwelling varanid in tropical northern Australia. Although V. indicus remained active all year, they reduced their activity in the dry season, but not to the extent of terrestrial varanids. Varanus indicus field metabolic rates decreased by 38% in the dry season mostly as a result of the reduction in activity. Although food and water depletion are the driving forces behind decreases in dry season T(b) selection and energetics for many varanids, V. indicus appears not to be subject to these pressures to the same extent. Thermoregulatory indices indicate that V. indicus actively thermoregulate in the wet and dry seasons, but they do not fully exploit the available thermal resources. These lizards are unusual among varanid lizards in that their midday T(b)'s are relatively low (about 31 degrees C) despite the availability of thermal resources that would allow them to attain substantially higher T(b)'s.     

Reproduction of varanid lizards (Reptilia: Squamata: Varanidae) at the Bronx Zoo

Captivity provides many opportunities for studying the reproductive biology of varanid lizards (Family: Varanidae; genus: Varanus). This article presents reproductive data for 12 varanid species maintained in captivity at the Bronx Zoo between 1977 and 2010. Five species, V. prasinus, V. beccarii, V. melinus, V. mertensi, and V. ornatus have successfully reproduced at the zoo, for which clutch, incubation, and hatchling data are presented, and compared with previously published values. Clutch, incubation, and hatchling measurements typically fell within the known ranges for each species, or represent minor range extensions. V. mertensi was the only species that reproduced seasonally (χ(2) = 9.061, P = 0.029). Five species multiclutched; individual V. mertensi and V. prasinus females produced as many as four clutches per year. The shortest intervals between successive clutches observed for V. kordensis (61 days), V. melinus (77 days), V. mertensi (51 days), and V. prasinus (68 days) represent the shortest known values for each species. Relative clutch mass (RCM) ranged from 0.187 to 0.437. A mean RCM of 0.370 ± 0.092 for V. prasinus is substantially higher than previously published values for the species. These results illustrate that when maintained under favorable conditions in captivity, some varanids are capable of remarkably high fecundities, rapid reproductive turnover rates, and sizeable maternal investments. Periodicals, Inc.     

The respiratory system in varanid lizards: determinants of O(2) transfer

Varanids in general exhibit greater aerobic capacities than other lizards. In a similar approach to the extensive investigations undertaken in mammals, the respiratory system in varanids is examined in terms of oxygen transfer from the air to the blood during rest and sustained locomotory activity. The parameters controlling the transfer of O(2) through the various steps of the respiratory system are appropriate to meet the maximum demands for oxygen with one possible exception, circulatory convection. Ventilatory convection is maintained during maximal aerobic locomotion ensuring adequate pulmonary ventilation and the protection of alveolar P(O(2)). Little evidence exists to indicate a mechanically imposed constraint to breathe and the possibility of a gular pump acting to assist ventilation, as a general feature of varanids remains to be determined. Alterations in the relative contributions of the ventilation-perfusion ratio, pulmonary diffusion, diffusion equilibrium and right-left shunts preserved the alveolar-arterial P(O(2)) difference, ensuring that arterial oxygenation was maintained. In those species where increases in cardiac output were limited, maximum O(2) transfer was achieved through increased extraction of oxygen at the tissues. Overall, the interrelationship of adjacent steps in the respiratory system ensures that one step cannot become limiting. Compensatory changes occur in various parameters to offset those parameters that are 'limited'. The high aerobic activity of varanid lizards would not be achievable without a compensated circulatory convection.     

Taking the bait: Developing a bait delivery system to target free‐ranging crocodiles and varanid lizards with a novel conservation strategy

In tropical Australia, conditioned taste aversion (CTA) can buffer vulnerable native predators from the invasion of a toxic prey species (cane toads, Rhinella marina). Thus, we need to develop methods to deploy aversion‐inducing baits in the field, in ways that maximize uptake by vulnerable species (but not other taxa). We constructed and field‐tested baiting devices, in situ with wild animals. Apparatus were set next to waterbodies and baited concurrently at multiple locations (over water, water''s edge, and on the bank). Baits were checked and replaced twice daily during the trial; remote cameras recorded visitation by native predators. Bait longevity was compared at sun‐exposed and shaded locations over 12 h. The strength required to remove baits from apparatus was measured in varanids and crocodiles. The device promoted high rates of bait uptake by freshwater crocodiles (47% baits consumed), varanid lizards (19% baits consumed), and non‐target taxa (34% baits consumed). Targeting specific predators can be achieved by manipulating bait location and time of deployment, as well as the force required to dislodge the bait. Crocodiles were best targeted with over‐water baits, whereas varanid lizards preferred baits located at the edges of waterbodies. When testing bait longevity in ambient conditions, during the daytime baits desiccated fully within 12 h, and faster in the sun than in the shade. Based on studies using captive animals, the “pulling force” strength of reptilian predators scaled with body size and was greater in crocodiles than in varanid lizards. We present the first conservation baiting protocol designed specifically for reptiles. Our results demonstrate the feasibility of widespread and taxon‐specific deployment of aversion‐inducing baits to buffer the impacts of invasive cane toads, and our methods are applicable (with modification) to other research and management programs globally.     

Survival estimation in a long-lived monitor lizard: radio-tracking of Varanus mertensi

The population dynamics of varanids (large monitor lizards) is poorly understood. We report on the most detailed study to date of a population of one of Australia’s largest semi-aquatic varanids, Varanus mertensi. Survival of V. mertensi was derived from known-fate modelling of radio-tracked individuals over two and a half years. We demonstrate empirically what intuition suggests; that apparent survival probability in long-lived lizards is high over short sampling periods, with body size and gender influencing these estimates. Survival estimation in long-lived species such as varanids clearly requires long-term studies.     

A reevaluation of rice mitochondrial evolution based on the complete sequence of male-fertile and male-sterile mitochondrial genomes

Plant mitochondrial genomes have features that distinguish them radically from their animal counterparts: a high rate of rearrangement, of uptake and loss of DNA sequences, and an extremely low point mutation rate. Perhaps the most unique structural feature of plant mitochondrial DNAs is the presence of large repeated sequences involved in intramolecular and intermolecular recombination. In addition, rare recombination events can occur across shorter repeats, creating rearrangements that result in aberrant phenotypes, including pollen abortion, which is known as cytoplasmic male sterility (CMS). Using next-generation sequencing, we pyrosequenced two rice (Oryza sativa) mitochondrial genomes that belong to the indica subspecies. One genome is normal, while the other carries the wild abortive-CMS. We find that numerous rearrangements in the rice mitochondrial genome occur even between close cytotypes during rice evolution. Unlike maize (Zea mays), a closely related species also belonging to the grass family, integration of plastid sequences did not play a role in the sequence divergence between rice cytotypes. This study also uncovered an excellent candidate for the wild abortive-CMS-encoding gene; like most of the CMS-associated open reading frames that are known in other species, this candidate was created via a rearrangement, is chimeric in structure, possesses predicted transmembrane domains, and coopted the promoter of a genuine mitochondrial gene. Our data give new insights into rice mitochondrial evolution, correcting previous reports.     

Mitochondrial genomic rearrangements in songbirds

The organization of the mitochondrial genome is generally very conserved among vertebrates. Because of this, examination of the rare rearrangements which do occur has been suggested as offering a powerful alternative to phylogenetic analyses of mitochondrial DNA sequences. Here, we report on an avian mitochondrial rearrangement in a group of oscine passerines (warblers of the genus Phylloscopus). This rearrangement is identical to the mitochondrial organization recently identified in representatives of four orders of birds, including subsoscine Passeriformes. The rearrangement involves the movement of three genes (tRNA(Pro), NADH6, and tRNA(Glu)) from their normal position in birds between tRNA(Thr) and the control region (CR), to a new location between the CR and a novel, supposedly noncoding (NC), region. Our results suggest that this derived arrangement cannot be used to distinguish between suboscine and oscine passerines, as it has multiple origins both within Passeriformes and within birds as a whole. We found short stretches of DNA with high degrees of similarity between the CR and each NC region, respectively, all of which could be located in the same area of the CR. This suggests that the CR and the NC region are homologous and that the mechanism behind this mitochondrial rearrangement is a tandem duplication followed by multiple deletions. However, the similarities between the control and NC regions of each species were less pronounced than those between the control or NC regions from the different species, supporting the hypothesis of a single basal rearrangement in the Phylloscopus warblers.     

Could controlling mammalian carnivores lead to mesopredator release of carnivorous reptiles?

Emerging evidence increasingly illustrates the importance of a holistic, rather than taxon-specific, approach to the study of ecological communities. Considerable resources are expended to manage both introduced and native mammalian carnivores to improve conservation outcomes; however, management can result in unforeseen and sometimes catastrophic outcomes. Varanid lizards are likely to be apex- or mesopredators, but being reptiles are rarely considered by managers and researchers when investigating the impacts of mammalian carnivore management. Instances of mesopredator release have been described for Varanus gouldii as a result of fox and cat management in Australia, with cascading effects on faunal community structure. A meta-analysis showing extensive dietary niche overlap between varanids, foxes and cats plus a review of experimental and circumstantial evidence suggests mesopredator release of V. gouldii and about five other medium to large species of varanid lizard is likely in other regions. This highlights the need for managers to adopt a whole-of-community approach when attempting to manage predators for sustained fauna conservation, and that additional research is required to elucidate whether mesopredator release of varanids is a widespread consequence of carnivore management, altering the intended faunal responses.     

Mitochondrial genome organization and expression associated with cytoplasmic male sterility in sunflower (Helianthus annuus).

A comparative investigation of the organization and expression of the mitochondrial genome in fertile and cytoplasmic male sterile (CMS) sunflower (Helianthus annuus) has been undertaken. A region of mitochondrial genome variation between the two phenotypes has been located in the 3' flanking region of the gene encoding the alpha subunit of the F1 ATPase (atpA). Physical mapping and sequence analysis have been used to show that a rearrangement involving an inversion and an insertion has occurred immediately downstream of the atpA coding region in the mitochondrial DNA from sterile sunflower. This rearrangement has resulted in the creation of a new open reading frame (ORFc) which is co-transcribed with atpA in sterile sunflower. In organello labelling of mitochondrial translation products from the two types of sunflower shows that a 15 kDa protein is synthesized by the mitochondria from sterile sunflower but not by those from fertile plants. The ORFc sequence could encode this 15 kDa protein which may be causally related to the CMS phenotype.     

Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the bell-ring frog, Buergeria buergeri (family Rhacophoridae)

In this study we determined the complete nucleotide sequence (19,959 bp) of the mitochondrial DNA of the rhacophorid frog Buergeria buergeri. The gene content, nucleotide composition, and codon usage of B. buergeri conformed to those of typical vertebrate patterns. However, due to an accumulation of lengthy repetitive sequences in the D-loop region, this species possesses the largest mitochondrial genome among all the vertebrates examined so far. Comparison of the gene organizations among amphibian species (Rana, Xenopus, salamanders and caecilians) revealed that the positioning of four tRNA genes and the ND5 gene in the mtDNA of B. buergeri diverged from the common vertebrate gene arrangement shared by Xenopus, salamanders and caecilians. The unique positions of the tRNA genes in B. buergeri are shared by ranid frogs, indicating that the rearrangements of the tRNA genes occurred in a common ancestral lineage of ranids and rhacophorids. On the other hand, the novel position of the ND5 gene seems to have arisen in a lineage leading to rhacophorids (and other closely related taxa) after ranid divergence. Phylogenetic analysis based on nucleotide sequence data of all mitochondrial genes also supported the gene rearrangement pathway.     

Hypoxic pulmonary vasoconstriction in reptiles: a comparative study of four species with different lung structures and pulmonary blood pressures

Low O2 levels in the lungs of birds and mammals cause constriction of the pulmonary vasculature that elevates resistance to pulmonary blood flow and increases pulmonary blood pressure. This hypoxic pulmonary vasoconstriction (HPV) diverts pulmonary blood flow from poorly ventilated and hypoxic areas of the lung to more well-ventilated parts and is considered important for the local matching of ventilation to blood perfusion. In the present study, the effects of acute hypoxia on pulmonary and systemic blood flows and pressures were measured in four species of anesthetized reptiles with diverse lung structures and heart morphologies: varanid lizards (Varanus exanthematicus), caimans (Caiman latirostris), rattlesnakes (Crotalus durissus), and tegu lizards (Tupinambis merianae). As previously shown in turtles, hypoxia causes a reversible constriction of the pulmonary vasculature in varanids and caimans, decreasing pulmonary vascular conductance by 37 and 31%, respectively. These three species possess complex multicameral lungs, and it is likely that HPV would aid to secure ventilation-perfusion homogeneity. There was no HPV in rattlesnakes, which have structurally simple lungs where local ventilation-perfusion inhomogeneities are less likely to occur. However, tegu lizards, which also have simple unicameral lungs, did exhibit HPV, decreasing pulmonary vascular conductance by 32%, albeit at a lower threshold than varanids and caimans (6.2 kPa oxygen in inspired air vs. 8.2 and 13.9 kPa, respectively). Although these observations suggest that HPV is more pronounced in species with complex lungs and functionally divided hearts, it is also clear that other components are involved.     

A spectacular new Philippine monitor lizard reveals a hidden biogeographic boundary and a novel flagship species for conservation

As humans continue to explore the last uncharted regions of the planet, discoveries of previously unknown species of large vertebrates have become infrequent. Here, we report on the discovery of a spectacular new species of giant, secretive, frugivorous, forest monitor lizard (Genus: Varanus) from the forests of the northern Philippines. Using data from morphology and mitochondrial and nuclear DNA sequences, we demonstrate the taxonomic distinctiveness of this new 2 m long species and provide insight into its historical biogeography and systematic affinities. Our molecular phylogenetic analyses indicate that the new species is closely related to Varanus olivaceus (from southern Luzon and nearby islands), but it differs from this and other varanids with respect to characteristics of scalation, colour pattern, body size, anatomy of the reproductive organs and genetic divergence. The new species appears to be restricted to forests of the central and northern Sierra Madre mountain range; it is separated from the range of V. olivaceus by a more than 150 km stretch that includes at least three low-elevation river valley barriers to dispersal. This discovery identifies a seldom-perceived biogeographic boundary and emphasizes the need for continued biodiversity research in the megadiverse conservation hotspot of the Philippines. It is anticipated that the new species will serve as an important flagship species for conservation efforts aimed at preserving the remaining forests of northern Luzon.     

Analysis of the complete mitochondrial DNA sequence of the brachiopod terebratulina retusa places Brachiopoda within the protostomes

Brachiopod phylogeny is still a controversial subject. Analyses using nuclear 18SrRNA and mitochondrial 12SrDNA sequences place them within the protostomes but some recent interpretations of morphological data support a relationship with deuterostomes. In order to investigate brachiopod affinities within the metazoa further, we compared the gene arrangement on the brachiopod mitochondrial genome with several metazoan taxa. The complete (15 451 bp) mitochondrial DNA (mtDNA) sequence of the articulate brachiopod Terebratulina retusa was determined from two overlapping long polymerase chain reaction products. All the genes are encoded on the same strand and gene order comparisons showed that.only one major rearrangement is required to interconvert the T. retusa and Katharina tunicata (Mollusca: Polvplacophora) mitochondrial genomes. The partial mtDNA sequence of the prosobranch mollusc Littorina saxatilis shows complete congruence with the T. rehtusa gene arrangement with regard to the ribosomal and protein coding genes. This high similarity in gene arrangement is the first to be reported within the protostomes. Sequence analyses of mitochondrial protein coding genes also support a close relationship of the brachiopod with molluscs and annelids, thus supporting the clade Lophotrochozoa. Though being highly informative, sequence analyses of the mitochondrial protein coding genes failed to resolve the branching order within the lophotrochozoa.