Tuatara Research Articles

Seasonal and spatial dynamics of ectoparasite infestation of a threatened reptile, the tuatara (Sphenodon punctatus)

The conservation of threatened vertebrate species and their threatened parasites requires an understanding of the factors influencing their distribution and dynamics. This is particularly important for species maintained in conservation reserves at high densities, where increased contact among hosts could lead to increased rates of parasitism. The tuatara (Sphenodon punctatus) (Reptilia: Sphenodontia) is a threatened reptile that persists at high densities in forests (approximately 2700 tuatara/ha) and lower densities in pastures and shrubland (< 200 tuatara/ha) on Stephens Island, New Zealand. We investigated the lifecycles and seasonal dynamics of infestation of two ectoparasites (the tuatara tick, Amblyomma sphenodonti, and trombiculid mites, Neotrombicula sp.) in a mark-recapture study in three forest study plots from November 2004 to March 2007, and compared infestation levels among habitat types in March 2006. Tick loads were lowest over summer and peaked from late autumn (May) until early spring (September). Mating and engorgement of female ticks was highest over spring, and larval tick loads subsequently increased in early autumn (March). Nymphal tick loads increased in September, and adult tick loads increased in May. Our findings suggest the tuatara tick has a 2- or 3-year lifecycle. Mite loads were highest over summer and autumn, and peaked in March. Prevalences (proportion of hosts infected) and densities (estimated number of parasites per hectare) of ticks were similar among habitats, but tick loads (parasites per host) were higher in pastures than in forests and shrub. The prevalence and density of mites was higher in forests than in pasture or shrub, but mite loads were similar among habitats. We suggest that a higher density of tuatara in forests may reduce the ectoparasite loads of individuals through a dilution effect. Understanding host-parasite dynamics will help in the conservation management of both the host and its parasites.

Fine‐scale genetic structure of a long‐lived reptile reflects recent habitat modification

Anthropogenic habitat fragmentation--ubiquitous in modern ecosystems--has strong impacts on gene flow and genetic population structure. Reptiles may be particularly susceptible to the effects of fragmentation because of their extreme sensitivity to environmental conditions and limited dispersal. We investigate fine-scale spatial genetic structure, individual relatedness, and sex-biased dispersal in a large population of a long-lived reptile (tuatara, Sphenodon punctatus) on a recently fragmented island. We genotyped individuals from remnant forest, regenerating forest, and grassland pasture sites at seven microsatellite loci and found significant genetic structuring (R(ST)=0.012) across small distances (<500 m). Isolation by distance was not evident, but rather, genetic distance was weakly correlated with habitat similarity. Only individuals in forest fragments were correctly assignable to their site of origin, and individual pairwise relatedness in one fragment was significantly higher than expected. We did not detect sex-biased dispersal, but natural dispersal patterns may be confounded by fragmentation. Assignment tests showed that reforestation appears to have provided refuges for tuatara from disturbed areas. Our results suggest that fine-scale genetic structuring is driven by recent habitat modification and compounded by the sedentary lifestyle of these long-lived reptiles. Extreme longevity, large population size, simple social structure and random dispersal are not strong enough to counteract the genetic structure caused by a sedentary lifestyle. We suspect that fine-scale spatial genetic structuring could occur in any sedentary species with limited dispersal, making them more susceptible to the effects of fragmentation.

Predicting the fate of a living fossil: how will global warming affect sex determination and hatching phenology in tuatara?

How will climate change affect species' reproduction and subsequent survival? In many egg-laying reptiles, the sex of offspring is determined by the temperature experienced during a critical period of embryonic development (temperature-dependent sex determination, TSD). Increasing air temperatures are likely to skew offspring sex ratios in the absence of evolutionary or plastic adaptation, hence we urgently require means for predicting the future distributions of species with TSD. Here we develop a mechanistic model that demonstrates how climate, soil and topography interact with physiology and nesting behaviour to determine sex ratios of tuatara, cold-climate reptiles from New Zealand with an unusual developmental biology. Under extreme regional climate change, all-male clutches would hatch at 100% of current nest sites of the rarest species, Sphenodon guntheri, by the mid-2080s. We show that tuatara could behaviourally compensate for the male-biasing effects of warmer air temperatures by nesting later in the season or selecting shaded nest sites. Later nesting is, however, an unlikely response to global warming, as many oviparous species are nesting earlier as the climate warms. Our approach allows the assessment of the thermal suitability of current reserves and future translocation sites for tuatara, and can be readily modified to predict climatic impacts on any species with TSD.

Climate warming and environmental sex determination in tuatara: the Last of the Sphenodontians?

Climate warming and environmental sex determination in tuatara: the Last of the Sphenodontians?

New resources inform study of genome size, content, and organization in nonavian reptiles

Genomic resources for studies of nonavian reptiles have recently improved and will reach a new level of access once the genomes of the painted turtle (Chrysemys picta) and the green anole (Anolis carolinensis) have been published. Eleven speakers gathered for a symposium on reptilian genomics and evolutionary genetics at the 2008 meeting of the Society for Integrative and Comparative Biology in San Antonio, Texas. Presentations described results of reptilian genetic studies concerning molecular evolution, chromosomal evolution, genomic architecture, population dynamics, endocrinology and endocrine disruption, and the evolution of developmental mechanisms. The presented studies took advantage of the recent generation of genetic and genomic tools and resources. Novel findings demonstrated the positive impact made by the improved availability of resources like genome annotations and bacterial artificial chromosomes (BACs). The symposium was timely and important because it provided a vehicle for the dissemination of novel findings that advance the field. Moreover, this meeting fostered the synergistic interaction of the participants as a group, which is anticipated to encourage the funding and creation of further resources such as additional BAC libraries and genomic projects. Novel data have already been collected and studies like those presented in this symposium promise to shape and improve our understanding of overall amniote evolution. Additional reptilian taxa such as the American alligator (Alligator mississippiensis), tuatara (Sphenodon punctatus), and garter snake (Thamnophis sirtalis) should be the foci of future genomic projects. We hope that the following articles in this volume will help promote these efforts by describing the conclusions and the potential that the improvement of genomic resources for nonavian reptiles can continue having in this important area of integrative and comparative biology.

Three tiers of genome evolution in reptiles

Characterization of reptilian genomes is essential for understanding the overall diversity and evolution of amniote genomes, because reptiles, which include birds, constitute a major fraction of the amniote evolutionary tree. To better understand the evolution and diversity of genomic characteristics in Reptilia, we conducted comparative analyses of online sequence data from Alligator mississippiensis (alligator) and Sphenodon punctatus (tuatara) as well as genome size and karyological data from a wide range of reptilian species. At the whole-genome and chromosomal tiers of organization, we find that reptilian genome size distribution is consistent with a model of continuous gradual evolution while genomic compartmentalization, as manifested in the number of microchromosomes and macrochromosomes, appears to have undergone early rapid change. At the sequence level, the third genomic tier, we find that exon size in Alligator is distributed in a pattern matching that of exons in Gallus (chicken), especially in the 101-200 bp size class. A small spike in the fraction of exons in the 301 bp-1 kb size class is also observed for Alligator, but more so for Sphenodon. For introns, we find that members of Reptilia have a larger fraction of introns within the 101 bp-2 kb size class and a lower fraction of introns within the 5-30 kb size class than do mammals. These findings suggest that the mode of reptilian genome evolution varies across three hierarchical levels of the genome, a pattern consistent with a mosaic model of genomic evolution.

Skull shape and feeding strategy in Sphenodon and other Rhynchocephalia (Diapsida: Lepidosauria)

The Rhynchocephalia are a group of small diapsid reptiles that were globally distributed during the early Mesozoic. By contrast, the only extant representatives, Sphenodon punctatus and S. guntheri (Tuatara), are restricted to New Zealand off-shore islands. The Rhynchocephalia are widely considered to be morphologically uniform but research over the past 30 years has revealed unexpected phenotypic and taxonomic diversity. Phylogenetically "basal taxa" generally possess relatively simple conical or columnar teeth whereas more derived taxa possessed stouter flanged teeth and sophisticated shearing mechanisms: orthal in some (e.g., Clevosaurus hudsoni) and propalinal in others (e.g., S. punctatus). This variation in feeding apparatus suggests a wide range of feeding niches were exploited by rhynchocephalians. The relationship of skull shape to skull length, phylogenetic grouping, habit, and characters relating to the feeding apparatus are explored here with geometric morphometric analysis on two-dimensional landmarks. Principle components analysis demonstrates that there are significant differences between phylogenetic groups. In particular, Sphenodon differs significantly from all well known fossil taxa including the most phylogenetically basal forms. Therefore, it is not justifiable to use Sphenodon as a solitary outgroup when studying skull shape and feeding strategy in squamates; rhynchocephalian fossil taxa also need to be considered. There are also significant differences between the skull shapes of aquatic taxa and those of terrestrial taxa. Of the observed variation in skull shape, most variation is subsumed by variation in dentary tooth base shape, the type of jaw movement employed (e.g., orthal vs. propalinal) and the number of palatal tooth rows. By comparison, the presence or absence of flanges, dentary tooth number and palatal tooth row orientation subsume much less. Skull length was also found to be a poor descriptor of overall skull shape. Compared to basal rhynchocephalians members of more derived terrestrial radiations possess an enlarged postorbital area, a high parietal, and a jaw joint positioned ventral to the tooth row. Modification of these features is closely associated with increased biting performance and thus access to novel food items. Some of these same trends are apparent during Sphenodon ontogeny where skull growth is allometric and there is evidence for ontogenetic variation in diet.

Reduced MHC variation in a threatened tuatara species

AbstractThe relationship between neutral and adaptive genetic diversity is important to understand in assessing the implications of a population bottleneck. Fitness‐related genes, such as those of the major histocompatibility complex (MHC), may be influenced by selection, and so retain diversity even when it is lost at neutral markers. We measured MHC class I variation in an archaic reptile species Sphenodon guntheri [North Brother Island (NBI) tuatara], which naturally occurs on one 4 ha island in Cook Strait, New Zealand, and has low levels of microsatellite diversity. MHC variation in S. guntheri was compared with microsatellite DNA variation, and with MHC variation in a large population of Sphenodon punctatus (Cook Strait tuatara) on Stephens Island. The NBI population shows significantly decreased levels of genetic diversity compared with the Stephens Island population. Only three different MHC sequences and three genotypes were found on NBI, compared with 15 sequences and 21 genotypes in a similar sample size from Stephens Island. Two sequences appear to be unique to the NBI population. The assortment of sequence variants into genotypes suggests strong gametic disequilibrium between two MHC class I loci in S. guntheri, and only two haplotypes that were present in Hardy–Weinberg proportions were identified. MHC diversity in NBI tuatara appears to be largely influenced by genetic drift, consistent with a recent population bottleneck. This may compromise the ability of this population to respond to novel disease threats.

Morphological, functional and evolutionary aspects of tail autotomy and regeneration in the ‘living fossil’Sphenodon (Reptilia: Rhynchocephalia)

Tail autotomy and regeneration are less known in Sphenodon (‘Reptilia’: Rhynchocephalia) than in Squamata. We examined museum specimens, Sphenodon guntheri (N = 8) and Sphenodon punctatus (N = 172), wild Sphenodon punctatus (N = 19) and Sphenodon sp. skeletons (N = 8). In S. punctatus, unlike in typical Squamata, sexes had similar relative (intact) tail lengths, and regeneration frequencies; tail and body growth was isometric. Tail breakage was usually intravertebral, usually followed by ablation of a variably sized terminal vertebral piece, partly deviating from lizards. Hypothetically, imperfect autotomy results from sphenodon's primitiveness. As in squamates, tail-losers were morphologically more left-side dominant than tail-retainers. Individual directional asymmetries in digit morphology and in digit injury were correlated (in lizards observed only at population level); tail-losers had more fluctuating asymmetry but their exclusion did not facilitate morphological taxonomic distinctions (no ‘Seligmann effect’). In S. punctatus, extents and directions of sexual dimorphism paralleled differences between tail-retainers and tail-losers, females resembling tail-losers, also accounting for character interdependence (developmental constraints; employing a method similar to phylogenetic contrasts). The variation in the location of tail injury was correlated with the continuum of variation between injured and intact (pholidotic) morphotypes. These last two phenomena remain to be explored in Squamates. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 721–743.

Circadian emergence and movement of captive juvenile tuatara (Sphenodon spp.)

Knowledge of the circadian behaviour of young tuatara (Sphenodon spp.) is relatively scarce because tuatara are difficult to observe in the wild. We document diurnal, nocturnal and crepuscular emergence and movements (half‐body movement, walking and running) of three groups of captive juvenile tuatara (2‐ and 3‐year‐old Sphenodon guntheri, and 5‐year‐old S. punctatus). Juvenile tuatara emerge predominantly at night, but move around above ground, mainly during the day and around sunset. Differences in emergence andmove‐ment scores between the three study groups were evident, probably linked with age, species or housing conditions, which were inevitably coupled in our study. We found that 2‐year‐old tuatara in captive conditions emerged less frequently than, but once above ground, moved more than 3‐ and 5‐year‐olds in semi‐captive conditions. Activities in semi‐captive conditions were not correlated with temperature, light or humidity. We conclude that young tuatara may be primarily adapted to nocturnal activity, but thermal restrictions and possible hardwired adaptations to avoid predators and conspecifics may make day‐time movements safer.

Two Patterns of Variation among MHC Class I Loci in Tuatara (Sphenodon punctatus)

The genes of the major histocompatibility complex (MHC) are a central component of the immune system in vertebrates and have become important markers of functional, fitness-related genetic variation. We have investigated the evolutionary processes that generate diversity at MHC class I genes in a large population of an archaic reptile species, the tuatara (Sphenodon punctatus), found on Stephens Island, Cook Strait, New Zealand. We identified at least 2 highly polymorphic (UA type) loci and one locus (UZ) exhibiting low polymorphism. The UZ locus is characterized by low nucleotide diversity and weak balancing selection and may be either a nonclassical class I gene or a pseudogene. In contrast, the UA-type alleles have high nucleotide diversity and show evidence of balancing selection at putative peptide-binding sites. Twenty-one different UA-type genotypes were identified among 26 individuals, suggesting that the Stephens Island population has high levels of MHC class I variation. UA-type allelic diversity is generated by a mixture of point mutation and gene conversion. As has been found in birds and fish, gene conversion obscures the genealogical relationships among alleles and prevents the assignment of alleles to loci. Our results suggest that the molecular mechanisms that underpin MHC evolution in nonmammals make locus-specific amplification impossible in some species.

Responses of Tuatara (Sphenodon punctatus) to Removal of Introduced Pacific Rats from Islands

Invasive mammalian predators such as rats are now widespread on islands, but hypotheses about their effects have rarely been tested. Circumstantial evidence from New Zealand indicates that, when introduced to islands, Pacific rats (Rattus exulans) have negative effects on endemic plants, invertebrates, birds, and reptiles, including the tuatara (Sphenodon punctatus). We tested the effects of Pacific rats on tuatara by comparing the demographic structure and body condition of tuatara populations on three islands before and after removal of rats and on a fourth island where rats remained. In the presence of rats, juvenile tuatara constituted on average 0-5% of the sample tuatara populations. When Pacific rats were removed after at least 200 years' occupancy, the proportion of juvenile tuatara increased 3.5- to 17-fold and body condition of adult males and females also improved (sometimes dramatically). We predict that, unless Pacific rats are removed from Taranga Island, the tuatara population will collapse because of low population density and the lack of juvenile recruitment. Our results demonstrate that when invasive species exert subtle effects on recruitment and body condition, the effects on populations of long-lived endemic species may only become apparent long after the invasion.

CHEMICAL DISCRIMINATION OF FOOD, CONSPECIFICS AND PREDATORS BY APPARENTLY VISUALLY-ORIENTED DIURNAL GECKOS, NAULTINUS MANUKANUS

Animal life history strategies evolve in response to a range of selective pressures, and often are tightly linked to sensory cues. Squamate reptiles possess well-developed chemosensory systems, which evolved early in their history and remain highly conserved. However, chemosensory abilities are secondarily reduced in primarily visual agamid and chameleonid lizards, which casts doubt on the ubiquity of reliance on chemosensory cues among squamates. Diurnal geckos from New Zealand avoid predators using visual crypsis and are primarily ambush foragers; reliance on visual cues may be a product of strong avian predation pressure and minimal influence from mammals and snakes for the past 80 my. We used New Zealand's diurnal geckos to test the role of local adaptation versus evolutionary conservatism in defining chemosensory systems. Specifically, we tested whether Marlborough green geckos, Naultinus manukanus, use chemoreception to detect and behaviorally respond to (1) food, (2) opposite-sex conspecifics, and (3) native reptilian predators (tuatara, Sphenodon punctatus). Chemosensory cues mediated gecko interactions with all three stimuli tested: (1) the scent of fruit induced greater exploratory behavior, (2) male geckos responded to scent of female conspecifics by increasing lingual sampling and activity, and (3) tuatara fecal cues (but not skin secretions) elicited characteristic antipredator freeze behavior in geckos. Neither the primarily visual life history strategies nor the reduced range of predators of New Zealand's diurnal geckos appears to have reduced their chemosensory abilities relative to other noniguanid squamate reptiles. Instead, our findings support the notion that chemosensory traits remain highly conserved.

Failure to detect Salmonella species in a population of wild tuatara (Sphenodon punctatus)

AIM: To assess the prevalence of faecal excretion of Salmonella serovars by wild tuatara (Sphenodon punctatus) on Stephens Island, New Zealand. METHODS: One hundred cloacal swabs obtained as part of health-screening for the translocation of adult tuatara from Stephens Island were subjected to general aerobic culture and enrichment, and cultured specifically for Salmonella spp. RESULTS: No Salmonella spp were cultured from any of the cloacal samples, which suggests that, at the 95% confidence interval, the maximum prevalence of tuatara in the island population that were shedding Salmonella spp not detected by our sample size was 1.5%. Mixed bacteria were grown from the 70 cloacal swabs cultured aerobically. A predominant organism was evident in 30 cultures, and these were identified as Hafnia alvei type 1 (n=16) and type 2 (n=7), Corynebacterium spp (n=4), Klebsiella oxytoca (n=2), and Moraxella spp (n=1). CONCLUSIONS: The absence of intestinal carriage of Salmonella spp by the tuatara sampled in this study may indicate either lack of exposure, or an innate resistance to intestinal colonization in tuatara. The significance of the other bacteria cultured as potential pathogens to the tuatara and as zoonotic risks is also uncertain. Wildlife managers should screen translocated reptiles for Salmonella spp, and thereby avoid exposing wild and managed populations to infection.

Epidermal differentiation in embryos of the tuatara Sphenodon punctatus (Reptilia, Sphenodontidae) in comparison with the epidermis of other reptiles

Studying the epidermis in primitive reptiles can provide clues regarding evolution of the epidermis during land adaptation in vertebrates. With this aim, the development of the skin of the relatively primitive reptile Sphenodon punctatus in representative embryonic stages was studied by light and electron microscopy and compared with that of other reptiles previously studied. The dermis organizes into a superficial and deep portion when the epidermis starts to form the first layers. At embryonic stages comparable with those of lizards, only one layer of the inner periderm is formed beneath the outer periderm. This also occurs in lizards and snakes so far studied. The outer and inner periderm form the embryonic epidermis and accumulate thick, coarse filaments (25-30 nm thick) and sparse alpha-keratin filaments as in other reptiles. Beneath the embryonic epidermis an oberhautchen and beta-cells form small horny tips that represent overlapping borders along the margin of beta-cells that overlap other beta-cells (in a tile-like arrangement). The tips resemble those of agamine lizards but at a small scale, forming a lamellate-spinulated pattern as previously described in adult epidermis. The embryonic epidermis matures by the dispersion of coarse filaments among keratin at the end of embryonic development and is shed around hatching. The presence of these matrix organelles in the embryonic epidermis of this primitive reptile further indicates that amniote epidermis acquired interkeratin matrix proteins early for land adaptation. Unlike the condition in lizards and snakes, a shedding complex is not formed in the epidermis of embryonic S. punctatus that is like that of the adult. Therefore, as in chelonians and crocodilians, the epidermis of S. punctatus also represents an initial stage that preceded the evolution of the shedding complex for moulting.

Phylogenomic Investigation of CR1 LINE Diversity in Reptiles

It is unlikely that taxonomically diverse phylogenetic studies will be completed rapidly in the near future for nonmodel organisms on a whole-genome basis. However, one approach to advancing the field of "phylogenomics" is to estimate the structure of poorly known genomes by mining libraries of clones from suites of taxa, rather than from single species. The present analysis adopts this approach by taking advantage of megabase-scale end-sequence scanning of reptilian genomic clones to characterize diversity of CR1-like LINEs, the dominant family of transposable elements (TEs) in the sister group of mammals. As such, it helps close an important gap in the literature on the molecular systematics and evolution of retroelements in nonavian reptiles. Results from aligning more than 14 Mb of sequence from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta), Bahamian green anole (Anolis smaragdinus), Tuatara (Sphenodon punctatus), Emu (Dromaius novaehollandiae), and Zebra Finch (Taeniopygia guttata) against a comprehensive library approximately 3000 TE-encoding peptides reflect an increasing abundance of LINE and non-long-terminal-repeat (non-LTR) retrotransposon repeat types with the age of common ancestry among exemplar reptilian clades. The hypothesis that repeat diversity is correlated with basal metabolic rate was tested using comparative methods and a significant nonlinear relationship was indicated. This analysis suggests that the age of divergence between an exemplary clade and its sister group as well as metabolic correlates should be considered in addition to genome size in explaining patterns of retroelement diversity. The first phylogenetic analysis of the largely unexplored chicken repeat 1 (CR1) 3' reverse transcriptase (RT) conserved domains 8 and 9 in nonavian reptiles reveals a pattern of multiple lineages with variable branch lengths, suggesting presence of both old and young elements and the existence of several distinct well-supported clades not apparent from previous characterization of CR1 subfamily structure in birds and the turtle. This mode of CR1 evolution contrasts with historical patterns of LINE 1 diversification in mammals and hints toward the existence of a rich but still largely unexplored diversity of nonavian retroelements of importance to advancing both comparative vertebrate genomics and amniote systematics.

Health screening for a translocation of captive-reared tuatara (Sphenodon punctatus) to an island refuge

AIMS: To screen tuatara undergoing translocation from a captive crèche to an island refuge for evidence of health and known diseases, and apply basic epidemiological techniques to assess the significance of disease test results. METHODS: Tuatara (n=353) were physically examined and samples were taken from a random selection (n=30) for estimated white cell counts, screening for haemoparasites, and culture for Salmonella, Yersinia, Aeromonas and Campylobacter spp. Direct faecal smears were carried out on-site, and faecal floats were later performed to assess levels of endoparasitism with helminths and protozoa (n=69). Modified Ziehl-Neelsen staining was used to screen faecal smears, and positive specimens were further screened using an immunofluorescence antibody (IFA) test for Cryptosporidium oocysts. RESULTS: There was no evidence of external parasites on any of the animals examined and only one animal had a gross abnormality. All estimated white cell counts were in the range 2.8– 17.5 × 109/L. No haemoparasites were observed. There were no enteric pathogens cultured, indicating the intestinal carriage of these bacteria in the tuatara was 9.4%. Of the 69 individual faecal samples examined, 12 (17%) had unidentified coccidial oocysts, 21 (30%) had nematode ova of various kinds, and 12 (17%) had intestinal carriage of motile protozoa consistent with Trichomonas spp and another unidentified organism. Nineteen (28%) tuatara had acid-fast oocysts present; however, IFA staining failed to detect any Cryptosporidium oocysts. CONCLUSIONS: Our understanding of the diversity of gastrointestinal endoparasites affecting tuatara is inadequate as many of the parasite ova seen could not be identified. This is the first record of tuatara as a host for Trichomonas spp of protozoa in the gastrointestinal tract.

Waiting reveals waning weight: Monitoring over 54 years shows a decline in body condition of a long-lived reptile (tuatara, Sphenodon punctatus)

Knowledge gained from monitoring has been the basis for many critical decisions in threatened and endangered species and ecosystem management. Long-term monitoring has been recognized as a necessity for elucidating population trends and community interactions, particularly for long-lived species or ecosystems with slow rates of change. We examine seasonal and annual cycles of morphological changes in a threatened, long-lived, insular reptile, the tuatara ( Sphenodon punctatus), on Stephens Island, New Zealand. We used body condition indices as a surrogate measure of fitness, and examined seasonal fluctuations, using data from an intensive mark-recapture study, and long-term trends using a dataset that spans 54 years. In spite of seasonal and annual fluctuations, body condition of tuatara has declined significantly between 1949 and 2003; the decline was only evident after >22 years of monitoring. We hypothesize that increasing numbers of tuatara have resulted in a density-dependent population response driven by past habitat modification on Stephens Island. We emphasize the need for long-term monitoring and suggest that potentially costly management decisions, particularly for long-lived species or ecosystems with slow rates of change, should not be based solely on short-term monitoring.

Tuatara (Sphenodon) Genomics: BAC Library Construction, Sequence Survey, and Application to the DMRT Gene Family

The tuatara (Sphenodon punctatus) is of "extraordinary biological interest" as the most distinctive surviving reptilian lineage (Rhyncocephalia) in the world. To provide a genomic resource for an understanding of genome evolution in reptiles, and as part of a larger project to produce genomic resources for various reptiles (evogen.jgi.doe.gov/second_levels/BACs/our_libraries.html), a large-insert bacterial artificial chromosome (BAC) library from a male tuatara was constructed. The library consists of 215 424 individual clones whose average insert size was empirically determined to be 145 kb, yielding a genomic coverage of approximately 6.3x. A BAC-end sequencing analysis of 121 420 bp of sequence revealed a genomic GC content of 46.8%, among the highest observed thus far for vertebrates, and identified several short interspersed repetitive elements (mammalian interspersed repeat-type repeats) and long interspersed repetitive elements, including chicken repeat 1 element. Finally, as a quality control measure the arrayed library was screened with probes corresponding to 2 conserved noncoding regions of the candidate sex-determining gene DMRT1 and the DM domain of the related DMRT2 gene. A deep coverage contig spanning nearly 300 kb was generated, supporting the deep coverage and utility of the library for exploring tuatara genomics.

Natural halting probabilities, partial randomness, and zeta functions

We introduce the zeta number, natural halting probability, and natural complexity of a Turing machine and we relate them to Chaitin's Omega number, halting probability, and program-size complexity. A classification of Turing machines according to their zeta numbers is proposed: divergent, convergent, and tuatara. We prove the existence of universal convergent and tuatara machines. Various results on (algorithmic) randomness and partial randomness are proved. For example, we show that the zeta number of a universal tuatara machine is c.e. and random. A new type of partial randomness, asymptotic randomness, is introduced. Finally we show that in contrast to classical (algorithmic) randomness--which cannot be naturally characterised in terms of plain complexity--asymptotic randomness admits such a characterisation.