Gut microbiome of the sole surviving member of reptile order Rhynchocephalia reveals biogeographic variation, influence of host body condition and a substantial core microbiota in tuatara across New Zealand

Abstract Tuatara are the sole extant species in the reptile order Rhynchocephalia. They are ecologically and evolutionarily unique, having been isolated geographically for ~84 million years and evolutionarily from their closest living relatives for ~250 million years. Here we report the tuatara gut bacterial community for the first time. We sampled the gut microbiota of translocated tuatara at five sanctuaries spanning a latitudinal range of ~1000 km within Aotearoa New Zealand, as well as individuals from the source population on Takapourewa (Stephens Island). This represents a first look at the bacterial community of the order Rhynchocephalia and provides the opportunity to address several key hypotheses, namely that the tuatara gut microbiota: (1) differs from those of other reptile orders; (2) varies among geographic locations but is more similar at sites with more similar temperatures and (3) is shaped by tuatara body condition, parasitism and ambient temperature. We found significant drivers of the microbiota in sampling site, tuatara body condition, parasitism and ambient temperature, suggesting the importance of these factors when considering tuatara conservation. We also derived a ‘core’ community of shared bacteria across tuatara at many sites, despite their geographic range and isolation. Remarkably, >70% of amplicon sequence variants could not be assigned to known genera, suggesting a largely undescribed gut bacterial community for this ancient host species

Sex Ratio Bias and Extinction Risk in an Isolated Population of Tuatara (<i>Sphenodon punctatus</i>)

<div><p>Understanding the mechanisms underlying population declines is critical for preventing the extinction of endangered populations. Positive feedbacks can hasten the process of collapse and create an ‘extinction vortex,’ particularly in small, isolated populations. We provide a case study of a male-biased sex ratio creating the conditions for extinction in a natural population of tuatara (<i>Sphenodon punctatus</i>) on North Brother Island in the Cook Strait of New Zealand. We combine data from long term mark-recapture surveys, updated model estimates of hatchling sex ratio, and population viability modeling to measure the impacts of sex ratio skew. Results from the mark-recapture surveys show an increasing decline in the percentage of females in the adult tuatara population. Our monitoring reveals compounding impacts on female fitness through reductions in female body condition, fecundity, and survival as the male-bias in the population has increased. Additionally, we find that current nest temperatures are likely to result in more male than female hatchlings, owing to the pattern of temperature-dependent sex determination in tuatara where males hatch at warmer temperatures. Anthropogenic climate change worsens the situation for this isolated population, as projected temperature increases for New Zealand are expected to further skew the hatchling sex ratio towards males. Population viability models predict that without management intervention or an evolutionary response, the population will ultimately become entirely comprised of males and functionally extinct. Our study demonstrates that sex ratio bias can be an underappreciated threat to population viability, particularly in populations of long-lived organisms that appear numerically stable.</p></div

Proportions of tuatara nest types and the aggregate hatchling sex ratio predicted at current nesting locations under current and future climates.

<p>Oviposition occurs in early November or early December. These predictions update those previously reported, due to new information on the timing of the thermosensitive period for sex determination in tuatara, which was previously thought to fall at 50% of development, but is now known to occur at 35% of embryonic development.</p

Top model results from a candidate model set using tuatara survey data from 1998 – 2011 analyzed using an open mark-recapture population model.

<p>Survival was modeled testing all combinations of sex- and time-dependent effects, including either an interaction (sex*time) or additive effects (sex+time). Temporal variation in survival was also modeled as a linear trend (<i>T</i>). Capture probability was modeled to include the effects of sex, time, sex+time, or constant. The top models gaining the majority of support are shown in bold. The rankings of the full model set can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094214#pone.0094214.s001" target="_blank">File S1</a>.</p

Temporal trends in tuatara population sex ratio on North Brother Island.

<p>We find an increasing male-biased trend in the adult sex ratio both using the count ratio directly from the number of individuals captured in each survey (1988–2012; black circles) and using an abundance ratio corrected for detection probability from the mark-recapture results (1988–2011; open triangles). The dashed line indicates the linear trend in the abundance ratio. Error bars on the abundance ratio data are ±1 SE calculated using the delta method.</p

North Brother Island in the Cook Strait of Zealand.

<p>A rocky, 4 hectare wildlife sanctuary and lighthouse station that rises to 66</p

Annual survival estimates for male and female tuatara.

<p>Estimates were model averaged across the complete candidate model set based on the amount of support for each model. Estimates are shown ±1 SE.</p