Population structure, genomic diversity and demographic history of Komodo dragons inferred from whole-genome sequencing.

Population and conservation genetics studies have greatly benefited from the development of new techniques and bioinformatic tools associated with next-generation sequencing. Analysis of extensive data sets from whole-genome sequencing of even a few individuals allows the detection of patterns of fine-scale population structure and detailed reconstruction of demographic dynamics through time. In this study, we investigated the population structure, genomic diversity and demographic history of the Komodo dragon (Varanus komodoensis), the world's largest lizard, by sequencing the whole genomes of 24 individuals from the five main Indonesian islands comprising the entire range of the species. Three main genomic groups were observed. The populations of the Island of Komodo and the northern coast of Flores, in particular, were identified as two distinct conservation units. Degrees of genomic divergence among island populations were interpreted as a result of changes in sea level affecting connectivity across islands. Demographic inference suggested that Komodo dragons probably experienced a relatively steep population decline over the last million years, reaching a relatively stable Ne during the Saalian glacial cycle (400-150 thousand years ago) followed by a rapid Ne decrease. Genomic diversity of Komodo dragons was similar to that found in endangered or already extinct reptile species. Overall, this study provides an example of how whole-genome analysis of a few individuals per population can help define population structure and intraspecific demographic dynamics. This is particularly important when applying population genomics data to conservation of rare or elusive endangered species.

The axial anatomy of monitor lizards (Varanidae).

Because the musculoskeletal anatomy of the trunk is the framework for the behaviors of locomotion, ventilation, and body support in lepidosaurs, comparative study of trunk anatomy in this group is critical for unraveling the selective pressures leading to extant diversity in axial form and function among vertebrates. This work uses gross dissection and computed tomography to describe the muscular and skeletal anatomy of the trunk of varanid lizards (Varanidae, Anguimorpha). Gross muscle dissections were conducted to investigate the axial muscular anatomy of Varanus exanthematicus, Varanus giganteus, Varanus rosenbergi, and Varanus panoptes. Computed tomography scans of these and additional varanid lizards from the Varanus and Odatria subgenera were conducted to investigate rib and vertebral number and gross morphology. The number of vertebrae differs between species, with 27-35 presacral and 47-137 postsacral vertebrae. Although the number of floating and abdominal ribs in varanids is variable, most species examined have three to four cervical ribs and three true ribs. Attachment and insertion points of the epaxial and hypaxial musculature are detailed. The body wall has four main hypaxial layers, from superficial to deep: oliquus externus, intercostalis externi, intercostalis internii, and transversus. Varanids differ from other investigated lepidosaurs in having supracostalis dorsus brevis (epaxial) and levator costae (hypaxial), which independently connect each rib to the vertebral column. Although more basic muscle descriptions of the body wall in reptiles are needed, comparisons with the condition in the green iguana (Iguana iguana) can be made.

Lizard tricks: overcoming conflicting requirements of speed versus climbing ability by altering biomechanics of the lizard stride.

Adaptations promoting greater performance in one habitat are thought to reduce performance in others. However, there are many examples of animals in which, despite habitat differences, such predicted differences in performance do not occur. One such example is the relationship between locomotory performance to habitat for varanid lizards. To explain the lack of difference in locomotor performance we examined detailed observations of the kinematics of each lizard's stride. Differences in kinematics were greatest between climbing and non-climbing species. For terrestrial lizards, the kinematics indicated that increased femur adduction, femur rotation and ankle angle all contributed positively to changes in stride length, but they were constrained for climbing species, probably because of biomechanical restrictions on the centre of mass height (to increase stability on vertical surfaces). Despite climbing species having restricted stride length, no differences have been previously reported in sprint speed between climbing and non-climbing varanids. This is best explained by climbing varanids using an alternative speed modulation strategy of varying stride frequency to avoid the potential trade-off of speed versus stability on vertical surfaces. Thus, by measuring the relevant biomechanics for lizard strides, we have shown how kinematic differences among species can mask performance differences typically associated with habitat variation.

Characterisation and comparative genomics of three new Varanus-associated Borrelia spp. from Indonesia and Australia.

BACKGROUND: Borrelia are important disease-causing tick- and louse-borne spirochaetes than can infect a wide variety of vertebrates, including humans and reptiles. Reptile-associated (REP) Borrelia, once considered a peculiarity, are now recognised as a distinct and important evolutionary lineage, and are increasingly being discovered worldwide in association with novel hosts. Numerous novel Borrelia spp. associated with monitor lizards (Varanus spp.) have been recently identified throughout the Indo-Pacific region; however, there is a lack of genomic data on these Borrelia. METHODS: We used metagenomic techniques to sequence almost complete genomes of novel Borrelia spp. from Varanus varius and Varanus giganteus from Australia, and used long- and short-read technologies to sequence the complete genomes of two strains of a novel Borrelia sp. previously isolated from ticks infesting Varanus salvator from Indonesia. We investigated intra- and interspecies genomic diversity, including plasmid diversity and relatedness, among Varanus-associated Borrelia and other available REP Borrelia and, based on 712 whole genome orthologues, produced the most complete phylogenetic analysis, to the best of our knowledge, of REP Borrelia to date. RESULTS: The genomic architecture of Varanus-associated Borrelia spp. is similar to that of Borrelia spp. that cause relapsing fever (RF), and includes a highly conserved megaplasmid and numerous smaller linear and circular plasmids that lack structural consistency between species. Analysis of PF32 and PF57/62 plasmid partitioning genes indicated that REP Borrelia plasmids fall into at least six distinct plasmid families, some of which are related to previously defined Borrelia plasmid families, whereas the others appear to be unique. REP Borrelia contain immunogenic variable major proteins that are homologous to those found in Borrelia spp. that cause RF, although they are limited in copy number and variability and have low sequence identities to RF variable major proteins. Phylogenetic analyses based on single marker genes and 712 single copy orthologs also definitively demonstrated the monophyly of REP Borrelia as a unique lineage. CONCLUSIONS: In this work we present four new genomes from three novel Borrelia, and thus double the number of REP Borrelia genomes publicly available. The genomic characterisation of these Borrelia clearly demonstrates their distinctiveness as species, and we propose the names Borrelia salvatorii, 'Candidatus Borrelia undatumii', and 'Candidatus Borrelia rubricentralis' for them.

A new stem-varanid lizard (Reptilia, Squamata) from the early Eocene of China.

Monitor lizards (genus Varanus) are today distributed across Asia, Africa and Australasia and represent one of the most recognizable and successful lizard lineages. They include charismatic living species like the Komodo dragon of Indonesia and the even larger extinct Varanus prisca (Megalania) of Australia. The fossil record suggests that living varanids had their origins in a diverse assemblage of stem (varaniform) species known from the Late Cretaceous of China and Mongolia. However, determining the biogeographic origins of crown-varanids has proved problematic, with Asia, Africa and Australia each being proposed. The problem is complicated by the fragmentary nature of many attributed specimens, and the fact that the most widely accepted, and most complete, fossil of a stem-varanid, that of Saniwa ensidens, is from North America. In this paper, we describe a well-preserved skull and skeleton of a new genus of stem-varanid from the Eocene of China. Phylogenetic analysis places the new genus as the sister taxon of Varanus, suggesting that the transition from Cretaceous varaniform lizards to Varanus occurred in East Asia before the origin and dispersal of Varanus to other regions. The discovery of the new specimen thus fills an important gap in the fossil record of monitor lizards. The similar lengths of the fore- and hindlimbs in this new taxon are unusual among the total group Varanidae and suggest it may have had a different lifestyle, at least from the contemporaneous North American S. ensidens. This article is part of the theme issue 'The impact of Chinese palaeontology on evolutionary research'.

Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards.

How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.

Taxonomy, population status and ecology of Indian desert monitor lizard Varanus griseus koniecznyi Mertens 1954 in the Thar desert of Rajasthan.

Among monitor lizards of the family Varanidae, Indian desert monitor lizard Varanus griseus koniecznyi Mertens 1954 is one of the lesser-known species globally and due to lack of data on this species it is so far not evaluated by IUCN and excluded from the latest assessment of monitor lizards of Southeast Asia and Indo-Australian Archipelago. The present study was undertaken from January 2013 to June 2017 to fill this gap during which taxonomic evaluation along with an assessment of population and ecology of this species was carried out in the Thar desert of Rajasthan (TDR). The study brought into knowledge many morphological variations along with intraspecific variations of scale microstructure of this lizard. The population density was found to be highest in the Jaisalmer (0.102/ha) district of western Rajasthan, followed by Bikaner (0.08/ha) and Sikar (0.077/ha) districts. The overall population was quite low (0.068/ha) in the area. The study further revealed the species is habitat specialist and lives in a narrow range of habitats and microhabitats, and hence, the species may not adapt to the rapidly changing environment in the TDR. Their activity was found to be highest between 9ndash;12 hrs followed by 12-15 hrs and foraging was found to be their predominant activity followed by resting and feeding. In the absence of any detailed study on this species, the study points towards immediate conservation efforts for the species in its current distribution. Baseline data generated through this study will no doubt help to safeguard the species in the TDR and further research on this species in the future.

Anthropogenically modified habitats favor bigger and bolder lizards.

Anthropogenic activities often create distinctive but discontinuously distributed habitat patches with abundant food but high risk of predation. Such sites can be most effectively utilized by individuals with specific behaviors and morphologies. Thus, a widespread species that contains a diversity of sizes and behavioral types may be pre-adapted to exploiting such hotspots. In eastern Australia, the giant (to >2 m) lizard Varanus varius (lace monitor) utilizes both disturbed (campground) and undisturbed (bushland) habitats. Our surveys of 27 sites show that lizards found in campgrounds tended to be larger and bolder than those in adjacent bushland. This divergence became even more marked after the arrival of a toxic invasive species (the cane toad, Rhinella marina) caused high mortality in larger and bolder lizards. Some of the behavioral divergences between campground and bushland lizards may be secondary consequences of differences in body size, but other habitat-associated divergences in behavior are due to habituation and/or nonrandom mortality.

Computational Fluid Dynamics Reveals a Unique Net Unidirectional Pattern of Pulmonary Airflow in the Savannah Monitor Lizard (Varanus exanthematicus).

This report models pulmonary airflow in the savannah monitor (Varanus exanthematicus) using computational fluid dynamics simulations, which are based on computed tomography data. Simulations were validated by visualizing the flow of aerosolized lipids in excised lungs with good but not perfect agreement. The lung of this lizard has numerous successive bronchi branching off a long intrapulmonary bronchus, which are interconnected by intercameral perforations. Unidirectional flow has been documented in the lateral secondary bronchi of the savannah monitor, but patterns of airflow in the rest of the lung remain unknown, hindering our understanding of the evolution of pulmonary patterns of airflow in tetrapods. These results indicate that the lung contains a unique net unidirectional flow, where the overall flow scheme is similar during expiration and late inspiration, but dissimilar during early inspiration. Air is transported net caudally through the intrapulmonary bronchus and net craniad through secondary bronchi, much like the pattern of flow in birds. The simulations show that many chambers feature flow in multiple directions during parts of the respiratory cycle, but some regions also show robust unidirectional airflow. Air moves craniad through secondary bronchi and between adjacent secondary bronchi through intercameral perforations. The first secondary bronchus, the hilar-cranial bronchus, contains tidal flow that may improve ventilation of the central and dorsal lung parenchyma. These results expand our understanding of flow patterns in varanid lungs and suggest lungs with net unidirectional flow as an evolutionary pathway between tidal flow and complete unidirectional flow in multicameral lungs. Anat Rec, 2020. © 2019 American Association for Anatomy Anat Rec, 303:1768-1791, 2020. © 2019 American Association for Anatomy.

The geographical diversification in varanid lizards: the role of mainland versus island in driving species evolution.

Monitor lizards (Varanidae) inhabit both the mainland and islands of all geological types and have diversified into an exceptionally wide range of body sizes, thus providing an ideal model for examining the role of mainland versus island in driving species evolution. Here we use phylogenetic comparative methods to examine whether a link exists between body size-driven diversification and body size-frequency distributions in varanid lizards and to test the hypothesis that island lizards differ from mainland species in evolutionary processes, body size, and life-history traits (offspring number and size). We predict that: 1) since body size drives rapid diversification in groups, a link exists between body size-driven diversification and body size-frequency distributions; 2) because of various environments on island, island species will have higher speciation, extinction, and dispersal rates, compared with mainland species; 3) as a response to stronger intraspecific competition, island species will maximize individual ability associated with body size to outcompete closely-related species, and island species will produce smaller clutches of larger eggs to increase offspring quality. Our results confirm that the joint effect of differential macroevolutionary rates shapes the species richness pattern of varanid lizards. There is a link between body size-driven diversification and body size-frequency distributions, and the speciation rate is maximized at medium body sizes. Island species will have higher speciation, equal extinction, and higher dispersal rates compared with mainland species. Smaller clutch size and larger hatchling in the island than in mainland species indicate that offspring quality is more valuable than offspring quantity for island varanids.

The Cephalic Osteoderms of Varanus komodoensis as Revealed by High-Resolution X-Ray Computed Tomography.

Osteoderms constitute a morphological system that plays an important role in squamate systematics. However, their study and visualization have always been difficult due to their isolated occurrence in the skin, among the first organs to be removed during the skeletonization process. High-resolution X-ray computed tomography (HRXCT) offers a nondestructive means of visualizing osteoderms both in their natural relationship to each other and to the underlying cranial bones. Although it is often stated that Varanus komodoensis has a "chain mail" of osteoderms, this morphological system was never described in this taxon. Further, given its size, it might be expected that V. komodoensis would present the extreme of osteoderm development in extant varanids, a group that tends to have weakly developed osteoderms or none at all. Indeed, our HRXCT scan of a 19-year-old captive individual reveals an elaborate mesh of cephalic osteoderms that are incredibly numerous and morphologically diverse. We describe this skeletal system and compare it to the cephalic osteoderms in other varanoids. Anat Rec, 302:1675-1680, 2019. © 2019 American Association for Anatomy.

Claw morphometrics in monitor lizards: Variable substrate and habitat use correlate to shape diversity within a predator guild.

Numerous studies investigate morphology in the context of habitat, and lizards have received particular attention. Substrate usage is often reflected in the morphology of characters associated with locomotion, and, as a result, claws have become well-studied ecomorphological traits linking the two. The Kimberley predator guild of Western Australia consists of 10 sympatric varanid species. The purpose of this study was to quantify claw size and shape in the guild using geometric morphometrics, and determine whether these features correlated with substrate use and habitat. Each species was assigned a Habitat/substrate group based on the substrate their claws interact with in their respective habitat. Claw morphometrics were derived for both wild caught and preserved specimens from museum collections, using a 2D semilandmark analysis. Claw shape significantly separated based on Habitat/substrate group. Varanus gouldii and Varanus panoptes claws were associated with sprinting and extensive digging. Varanus mertensi claws were for shallow excavation. The remaining species' claws reflected specialization for some form of climbing, and differed based on substrate compliance. Varanus glauerti was best adapted for climbing rough sandstone, whereas Varanus scalaris and Varanus tristis had claws ideal for puncturing wood. Phylogenetic signal also significantly influenced claw shape, with Habitat/substrate group limited to certain clades. Positive size allometry allowed for claws to cope with mass increases, and shape allometry reflected a potential size limit on climbing. Claw morphology may facilitate niche separation within this trophic guild, especially when considered with body size. As these varanids are generalist predators, morphological traits associated with locomotion may be more reliable candidates for detecting niche partitioning than those associated directly with diet.

The Only Known Jawed Vertebrate with Four Eyes and the Bauplan of the Pineal Complex.

The pineal and parapineal organs are dorsal outpocketings of the vertebrate diencephalon that play key roles in orientation and in circadian and annual cycles. Lampreys are four eyed in that both the pineal and parapineal form eyelike photosensory structures, but the pineal is the dominant or sole median photosensory structure in most lower vertebrate clades. The pineal complex has been thought to evolve in a single direction by losing photosensory and augmenting secretory function in the transitions from three-eyed lower vertebrates to two-eyed mammals and archosaurs [1-3]. Yet the widely accepted elaboration of the parapineal instead of the pineal as the primary median photosensory organ [4] in Lepidosauria (lizards, snakes, and tuataras) hints at a more complex evolutionary history. Here we present evidence that a fourth eye re-evolved from the pineal organ at least once within vertebrates, specifically in an extinct monitor lizard, Saniwa ensidens, in which pineal and parapineal eyes were present simultaneously. The tandem midline location of these structures confirms in a striking fashion the proposed homology of the parietal eye with the parapineal organ and refutes the classical model of pineal bilaterality. It furthermore raises questions about the evolution and functional interpretation of the median photosensory organ in other tetrapod clades.

Who are the important predators of sea turtle nests at Wreck Rock beach?

Excessive sea turtle nest predation is a problem for conservation management of sea turtle populations. This study assessed predation on nests of the endangered loggerhead sea turtle (Caretta caretta) at Wreck Rock beach adjacent to Deepwater National Park in Southeast Queensland, Australia after a control program for feral foxes was instigated. The presence of predators on the nesting dune was evaluated by tracking plots (2 × 1 m) every 100 m along the dune front. There were 21 (2014-2015) and 41 (2015-2016) plots established along the dune, and these were monitored for predator tracks daily over three consecutive months in both nesting seasons. Predator activities at nests were also recorded by the presence of tracks on top of nests until hatchlings emerged. In addition, camera traps were set to record the predator activity around selected nests. The tracks of the fox (Vulpes vulpes) and goanna (Varanus spp) were found on tracking plots. Tracking plots, nest tracks and camera traps indicated goanna abundance varied strongly between years. Goannas were widely distributed along the beach and had a Passive Activity Index (PAI) (0.31 in 2014-2015 and 0.16 in 2015-2016) approximately seven times higher than that of foxes (PAI 0.04 in 2014-2015 and 0.02 in 2015-2016). Five hundred and twenty goanna nest visitation events were recorded by tracks but no fox tracks were found at turtle nests. Camera trap data indicated that yellow-spotted goannas (Varanus panoptes) appeared at loggerhead turtle nests more frequently than lace monitors (V. varius) did, and further that lace monitors only predated nests previously opened by yellow-spotted goannas. No foxes were recorded at nests with camera traps. This study suggests that large male yellow-spotted goannas are the major predator of sea turtle nests at the Wreck Rock beach nesting aggregation and that goanna activity varies between years.

A new blue-tailed Monitor lizard (Reptilia, Squamata, Varanus) of the Varanus indicus group from Mussau Island, Papua New Guinea.

We describe a new species of Varanus from Mussau Island, north-east of New Guinea. The new species is a member of the Varanus indicus species group and is distinguished from all other members by both morphological and molecular genetic characters. It is the third species of Varanus reported from the Bismarck Archipelago and the first record of a yellow tongued member of the Varanus indicus species group from a remote oceanic island. The herpetofauna of Mussau Island has not been well studied but the discovery of this new species is in accordance with recent findings indicating that the island may harbor several unknown endemic vertebrates. The distribution of the closely related Varanus finschi is also discussed in the light of recent fieldwork and a review of old records.