2016-12-23T18:52:10

Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new r package, dartr, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. dartr provides user-friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy-Weinberg equilibrium, gametic-phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F-statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., newhybrids, faststructure and phylogeny applications) outside of the r environment. The package serves two main purposes: first, a user-friendly approach to lower the hurdle to analyse such data-therefore, the package comes with a detailed tutorial targeted to the r beginner to allow data analysis without requiring deep knowledge of r. Second, we use a single, well-established format-genlight from the adegenet package-as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. The dartr package is available via the r CRAN network and GitHub.

Sex determination in animals is amazingly plastic. Vertebrates display contrasting strategies ranging from complete genetic control of sex (genotypic sex determination) to environmentally determined sex (for example, temperature-dependent sex determination). Phylogenetic analyses suggest frequent evolutionary transitions between genotypic and temperature-dependent sex determination in environmentally sensitive lineages, including reptiles. These transitions are thought to involve a genotypic system becoming sensitive to temperature, with sex determined by gene-environment interactions. Most mechanistic models of transitions invoke a role for sex reversal. Sex reversal has not yet been demonstrated in nature for any amniote, although it occurs in fish and rarely in amphibians. Here we make the first report of reptile sex reversal in the wild, in the Australian bearded dragon (Pogona vitticeps), and use sex-reversed animals to experimentally induce a rapid transition from genotypic to temperature-dependent sex determination. Controlled mating of normal males to sex-reversed females produces viable and fertile offspring whose phenotypic sex is determined solely by temperature (temperature-dependent sex determination). The W sex chromosome is eliminated from this lineage in the first generation. The instantaneous creation of a lineage of ZZ temperature-sensitive animals reveals a novel, climate-induced pathway for the rapid transition between genetic and temperature-dependent sex determination, and adds to concern about adaptation to rapid global climate change.

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.

Sex in reptiles is determined by genes on sex chromosomes or by incubation temperature. Previously these two modes were thought to be distinct, yet we show that high incubation temperatures reverse genotypic males (ZZ) to phenotypic females in a lizard with ZZ and ZW sex chromosomes. Thus, the W chromosome is not necessary for female differentiation. Sex determination is probably via a dosage-sensitive male-determining gene on the Z chromosome that is inactivated by extreme temperatures. Our data invite a novel hypothesis for the evolution of temperature-dependent sex determination (TSD) and suggest that sex chromosomes may exist in many TSD reptiles.

Mean daily temperature in natural nests of freshwater turtles with temperature dependent sex determination is a poor predictor of hatchling sex ratios when nest temperatures fluctuate. To account for this, a mathematical model has been developed on the assumption that hatchling sex depends on the daily proportion of embryonic development that occurs above the threshold temperature for sex determination rather than the proportion of time spent above the threshold. The model predictions are borne out by experiments using the marine turtle Caretta caretta. Average developmental rates, both overall and during the period that sexual differentiation is sensitive to temperature, are unaffected by diel fluctuations about the mean incubation temperature. Sex ratios, on the other hand, were affected by diel fluctuations and ranged from ca. 100% males under regimes 26 2 0°C and 26 2 3°C to 100% females for regimes 26 7°C and 26 c 8°C. These and intermediate sex ratios were in close agreement with model predictions. Demonstration of a n impact of temperature on sex, while holding overall developmental rate constant, gives support to hypotheses invoking a direct role for temperature rather than alternative hypotheses invoking overall developmental rate as a more proximal influence on sex. The model explains why mean temperature is a poor predictor of hatchling sex ratios. It urges caution in using "hours above the threshold for predicting sex ratios, because 1 h r at 1°C above the threshold will not be equivalent to 1 hr at 4°C above the threshold. It provides a general framework for integrating experiments a t constant temperatures with those in the field or laboratory using fluctuating regimes. I t provides greater scope for exploring how reptiles with temperature dependent sex determination might respond to climatic change or other disturbances to the incubation environment. And it provides a n explanation of why secondary factors such a hydric conditions and oxygen potentials might influence hatchling sex, even if temperature acts directly t o influence sex ratios rather than through its influence on overall developmental rate.

Two prevailing paradigms explain the diversity of sex‐determining modes in reptiles. Many researchers, particularly those who study reptiles, consider genetic and environmental sex‐determining mechanisms to be fundamentally different, and that one can be demonstrated experimentally to the exclusion of the other. Other researchers, principally those who take a broader taxonomic perspective, argue that no clear boundaries exist between them. Indeed, we argue that genetic and environmental sex determination in reptiles should be seen as a continuum of states represented by species whose sex is determined primarily by genotype, species where genetic and environmental mechanisms coexist and interact in lesser or greater measure to bring about sex phenotypes, and species where sex is determined primarily by environment. To do otherwise limits the scope of investigations into the transition between the two and reduces opportunities to use studies of reptiles to advance understanding of vertebrate sex determination generally. BioEssays 26:639–645, 2004. © 2004 Wiley Periodicals, Inc.

Theoretical models suggest that in changing environments natural selection on two traits, maternal nesting behaviour and pivotal temperatures (those that divide the sexes) is important for maintaining viable offspring sex ratios in species with environmental sex determination (ESD). Empirical evidence, however, is lacking. In this paper, we provide such evidence from a study of clinal variation in four sex-determining traits (maternal nesting behaviour, pivotal temperatures, nesting phenology, and nest depth) in Physignathus lesueurii, a wide-ranging ESD lizard inhabiting eastern Australia. Despite marked differences in air and soil temperatures across our five study sites spanning 19°latitude and 1200 m in elevation, nest temperatures did not differ significantly among sites. Lizards compensated for climatic differences chiefly by selecting more open nest sites with higher incident radiation at cooler sites. Clinal variation in the onset of nesting also compensated for climatic differences, but to a lesser extent. There was no evidence of compensation through pivotal temperatures or nest depth. More broadly, our results extend to the egg stage the life history prediction that behaviour is the chief compensatory mechanism for climatic differences experienced by species spanning environmental extremes. Furthermore, our study was unique in revealing that nest site choice influenced mainly the daily range in nest temperatures, rather than mean temperatures, in a shallow-nesting reptile. Finally, indirect evidence suggests that the cue used by nesting lizards was radiation or temperature (through basking or assessing substrate temperatures), not visual detection of canopy openness. We conclude that maternal nesting behaviour and nesting phenology are traits subject to sex ratio selection in P. lesueurii, and thus, must be considered among the repertoire of ESD species for responding to climate change.