Biology subjects

Whiteley, S. L.

Publications and source records attributed to Whiteley, S. L..

8 recordsLinked to original sources

bioRxiv2026

Impact of heat and sex on embryonic brain growth in dragons with temperature induced sex-reversal (Pogona vitticeps, Lacertilia: Agamidae)

Climate warming can influence sex determination and embryonic growth in oviparous reptiles that rely on external temperatures during development. Warmer incubation temperatures can stimulate growth in ectotherms until oxygen supply can no longer keep pace with growth rate; at which point metabolically expensive organs like the brain suffer. We aimed to understand the impact of heat and sex on brain development in central bearded dragons, Pogona vitticeps (Agamidae), a uniquely thermosensitive species that exhibits sex-reversal at warm incubation temperatures. Three sexual phenotypes are possible in P. vitticeps: genetically driven ZW females and ZZ males, with the latter phenotype thermally overridden at incubation temperatures >32C to induce ZZ sex-reversed females. To visualise changes in brain anatomy, we used buffered Lugols iodine to perform contrast-enhanced micro computed tomography (microCT) and synchrotron propagation-based phase-contrast CT scanning. A total of 57 embryos were sampled across developmental stages and incubated at two temperature treatments: cool (28C, n = 26) and warm (36C, n = 21). Using high-resolution models of neuroanatomy, we found that the telencephalic region of the forebrain is significantly larger in individuals with ZZ genotypes (males and sex-reversed females) compared to concordant ZW females. Although incubation temperature significantly influenced growth rate and body size during development, overall brain size was not significantly different across temperature treatments. Our results indicate that the effects of genotypic sex on brain development are more important than thermal influences, and thus the brain may be somewhat buffered to the effects of warm incubation temperatures in this arid-adapted dragon.

neuroscience↗

bioRxiv2026

Optimising neural contrast and minimising tissue shrinkage in dragon lizard brains: buffered Lugol's iodine versus phosphotungstic acid for contrast-enhanced μCT

Contrast-enhanced micro-computed tomography (CT) has become a valuable tool for addressing neuroanatomical questions that previously required destructive histology. As a relatively new technique, it remains subject to ongoing technical refinement, and taxon- and tissue-specific protocol optimisation. We evaluated the performance of two common contrast-enhancing agents, buffered Lugol's iodine and phosphotungstic acid (PTA) in aqueous solution, for CT visualisation of the nervous system in the Jacky dragon lizard, Amphibolurus muricatus by comparing staining time, contrast specificity and brain tissue shrinkage evaluated at three concentrations (1.25%, 2.5% and 5%). Buffered Lugol's iodine outperformed aqueous PTA by requiring shorter staining times (as short as four days) and providing better white matter-grey matter differentiation, whereas PTA required longer incubation periods of approximately three weeks and produced poorer white-grey matter differentiation. Importantly, buffered Lugol's iodine produced higher brain-to-endocast occupancy estimates than aqueous PTA, suggesting substantially reduced tissue shrinkage. PTA-treated specimens exhibited an estimated 13.3% reduction in occupancy and approximately 20% greater brain tissue shrinkage than buffered Lugol's-treated specimens. Together, these findings demonstrate that buffered Lugol's iodine staining provides the high level of internal tissue contrast required to resolve fine-scale neuroanatomical organisation in three dimensions, preserves the spatial relationships among anatomical structures, and reduces artefacts, all of which result in a closer correspondence between the brain and endocranial cavity. From a practical perspective, the study provides guidance for contrast agent selection in future CT studies and reveals that buffered Lugol's iodine is better suited to fine-scale neuroanatomical, volumetric and geometric morphometric analyses, whereas PTA is advantageous for applications prioritising general soft-tissue or musculoskeletal visualisation.

neuroscience↗

bioRxiv2026

DNA methylation regulates a key sex differentiation gene in Pogona vitticeps, a dragon lizard with sex reversal

During embryonic development bipotential gonads differentiate into either testes or ovaries under the direction of mutually exclusive gene networks. DNA methylation has been shown to regulate gene expression and to play a role in many developmental processes. This includes sex differentiation in which DNA methylation is linked to control of key sex genes. Whether DNA methylation regulates sexual differentiation in species where environmental influences such as temperature are involved is less clear. We conducted a genome-wide study in embryonic gonads of the central bearded dragon (Pogona vitticeps), a lizard with temperature induced sex reversal, and compared DNA methylation patterns to gene expression profiles at a stage of early sex differentiation. Overall, sex reversed ZZf females were found to have lower global methylation than both canonical sexes, ZZm males and ZWf females. We found that the expression of a key gene in sex differentiation, Amh, is regulated via DNA methylation. Amh is a driver of testis differentiation and is repressed in genetically determined females, as well as in temperature sex-reversed females, by hypermethylation around its transcription start site. Although the trigger of ovary determination is different in both groups of females, one by genetic complement and one by a temperature signal, downstream regulation of gene expression converges and seems to follow similar mechanisms.

genomics↗

bioRxiv2026

Co-Circulation of Multiple Kolmioviridae Lineages Through Vertebrate Evolution

Although once only characterized by human hepatitis deltavirus (HDV), membership of the family Kolmioviridae has dramatically expanded in recent years. Despite this transformation in our understanding of the host range of kolmioviruses, the evolutionary history of this enigmatic group of RNA viruses is unclear. Kolmioviruses are characterized as small ([~]1.7kb) satellite viruses that encode a single [~]200 amino acid delta antigen (DAg) and require unrelated helper viruses for replication. Here, we describe eight novel kolmioviruses from metatranscriptomic studies of the American alligator (Alligator missippiensis), red kangaroo (Osphranter rufus), and central bearded dragon (Pogona vitticeps), as well as avian kolmioviruses mined from the Sequence Read Archive (SRA). Although the novel kolmioviruses were often found in samples co-infected by other viruses, there was no evidence for the presence of hepatitis B virus as seen in HDV. By employing a range of sequence data sets, alignment methods, alignment trimming methods, and substitution models, we provide an evolutionary history of the Kolmioviridae that maximizes the extent of virus-host co-divergence and refines estimates of their evolutionary timescale. Although DAg amino acid sequences are more conserved than nucleotide sequences and hence might be expected to result in more accurate phylogenetic trees, we show that full genome nucleotide sequences likely provide the best representation of kolmiovirus evolution. More broadly, our results reveal that irrespective of the data set used, multiple distinct kolmiovirus lineages have co-circulated throughout vertebrate evolution over timescales spanning hundreds of millions of years, with the association between HDV and HBV appearing only recently. Significance StatementKolmioviruses are satellite RNA viruses, with hepatitis deltavirus (HDV) associated with human disease following co-infection with hepatitis B virus (HBV) the best characterized. Although a growing number of animal kolmioviruses have been identified in metagenomic studies and associated with a range of helper viruses, the evolutionary origins and history of this important and unique group of viruses is unknown. By identifying novel kolmioviruses in a range vertebrate hosts, including American alligators, we show that highly diverse lineages of kolmioviruses have co-circulated for the duration of vertebrate evolution with clear evidence of virus-host co-divergence, and are associated with a variety of potential helper viruses. Despite this antiquity, we present evidence that the HDV-HBV association only recently evolved in human populations.

microbiology↗

bioRxiv2025

A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps

BackgroundThe central bearded dragon (Pogona vitticeps) is widely distributed in central eastern Australia and adapts readily to captivity. Among other attributes, it is distinctive because it undergoes sex reversal from ZZ genotypic males to phenotypic females at high incubation temperatures. Here, we report an annotated telomere to telomere phased assembly of the genome of a female ZW central bearded dragon. ResultsGenome assembly length is 1.75 Gbp with a scaffold N50 of 266.2 Mbp, N90 of 28.1 Mbp, 26 gaps and 42.2% GC content. Most (99.6%) of the reference assembly is scaffolded into 6 macrochromosomes and 10 microchromosomes, including the Z and W microchromosomes, corresponding to the karyotype. The genome assembly exceeds standard recommended by the Earth Biogenome Project (6CQ40): 0.003% collapsed sequence, 0.03% false expansions, 99.8% k-mer completeness, 97.9% complete single copy BUSCO genes and an average of 93.5% of transcriptome data mappable back to the genome assembly. The mitochondrial genome (16,731 bp) and the model rDNA repeat unit (length 9.5 Kbp) were assembled. Male vertebrate sex genes Amh and Amhr2 were discovered as copies in the small non-recombining region of the Z chromosome, absent from the W chromosome. This, coupled with the prior discovery of differential Z and W transcriptional isoform composition arising from pseudoautosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies and their resultant transcription factors and intermediaries, determines sex in the bearded dragon. ConclusionThis high-quality assembly will serve as a resource to enable and accelerate research into the unusual reproductive attributes of this species and for comparative studies across the Agamidae and reptiles more generally. Species TaxonomyEukaryota; Animalia; Chordata; Reptilia; Squamata; Iguania; Agamidae; Amphibolurinae; Pogona; Pogona vitticeps (Ahl, 1926) (NCBI:txid103695). Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/651798v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1a9d5fforg.highwire.dtl.DTLVardef@1206061org.highwire.dtl.DTLVardef@97acf7org.highwire.dtl.DTLVardef@1dc939d_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2021

Draft genomes of a male and female Australian jacky dragon (Amphibolurus muricatus)

Australia is remarkable for its lizard diversity, with very high endemicity because of continental-scale diversification and adaptive radiation during prolonged isolation. We here employed stLFR linked-read technology to generate male and female draft genomes of the jacky dragon Amphibolurus muricatus, an Australian dragon lizard (family Agamidae; the agamids). The assemblies are 1.8 Gb in size and have a repeat content (39%) and GC content (42%) similar to other dragon lizards. The longest scaffold was 39.7 Mb (female) and 9.6 Mb (male), with corresponding scaffold N50 values of 6.8 Mb and 1.6 Mb. The BUSCO (Sauropsida database) completeness percentages were 90.2% and 88.8% respectively. Phylogenetic comparisons show that Australian and Asian agamids split from a common ancestor about 80 million years ago, while the Australian genera Amphibolurus, Pogona, and the basal Intellagama split [~]37 million years ago. The draft A. muricatus assemblies will be a valuable resource for understanding lizard sex determination and the evolution and conservation of Australian dragon lizards.

genomics↗

bioRxiv2021

Developmental dynamics of sex reprogramming by high incubation temperatures in a dragon lizard

In some vertebrate species, gene-environment interactions can determine sex, driving bipotential gonads to differentiate into either ovaries or testes. In the central bearded dragon (Pogona vitticeps), the genetic influence of sex chromosomes (ZZ/ZW) can be overridden by high incubation temperatures, causing ZZ male to female sex reversal. Previous research showed ovotestes, a rare gonadal phenotype with traits of both sexes, develop during sex reversal, leading to the hypothesis that sex reversal relies on high temperature feminisation to outcompete the male genetic cue. To test this, we conducted temperature switching experiments at key developmental stages, and analysed the effect on gonadal phenotypes using histology and transcriptomics. We found sexual fate is more strongly influenced by the ZZ genotype than temperature. Any exposure to low temperatures (28{degrees}C) caused testes differentiation, whereas sex reversal required longer exposure to high temperatures. We revealed ovotestes exist along a spectrum of female-ness to male-ness at the transcriptional level. We found inter-individual variation in gene expression changes following temperature switches, suggesting both genetic sensitivity to, and the timing and duration of the temperature cue influences sex reversal. These findings bring new insights to the mechanisms underlying sex reversal, improving our understanding of thermosensitive sex systems in vertebrates.

developmental biology↗

bioRxiv2021

Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination

How temperature determines sex remains unknown. A recent hypothesis proposes that conserved cellular mechanisms (calcium and redox; CaRe status) sense temperature and identify genes and regulatory pathways likely to be involved in driving sexual development. We take advantage of the unique sex determining system of the model organism, Pogona vitticeps, to assess predictions of this hypothesis. P. vitticeps has ZZ male: ZW female sex chromosomes whose influence can be overridden in genetic males by high temperatures, causing male-to-female sex reversal. We compare a developmental transcriptome series of ZWf females and temperature sex reversed ZZf females. We demonstrate that early developmental cascades differ dramatically between genetically driven and thermally driven females, later converging to produce a common outcome (ovaries). We show that genes proposed as regulators of thermosensitive sex determination play a role in temperature sex reversal. Our study greatly advances the search for the mechanisms by which temperature determines sex. Author SummaryIn many reptiles and fish, environment can determine, or influence, the sex of developing embryos. How this happens at a molecular level that has eluded resolution for half a century of intensive research. We studied the bearded dragon, a lizard that has sex chromosomes (ZZ male and ZW female), but in which that temperature can override ZZ sex chromosomes to cause male to female sex reversal. This provides an unparalleled opportunity to disentangle, in the same species, the biochemical pathways required to make a female by these two different routes. We sequenced the transcriptomes of gonads from developing ZZ reversed and normal ZW dragon embryos and discovered that different sets of genes are active in ovary development driven by genotype or temperature. Females whose sex was initiated by temperature showed a transcriptional profile consistent with the recently-proposed Calcium-Redox hypotheses of cellular temperature sensing. These findings are an important for understanding how the environment influences the development of sex, and more generally how the environment can epigenetically modify the action of genes.

genetics↗