Rosa Rubicondior: Refuting Creationism - The Transexual Bearded Dragons Of Australia

Friday, 22 August 2025

Refuting Creationism - The Transexual Bearded Dragons Of Australia

Central bearded dragon, Pogona vitticeps

By Photograph: Frank C. Müller, Baden-Baden - Own work,
CC BY-SA 2.5, Link

Being largely ignorant of any wildlife beyond what could be reached within a day or two’s walk of their pastures — and entirely ignorant of anything invisible to the naked eye — the Bible’s authors consistently imply that all living animals exist only as male or female, and that sexual reproduction is the sole reproductive strategy:

And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth. So God created man in his own image, in the image of God created he him; male and female created he them.

Genesis 1:26–27

And of every living thing of all flesh, two of every sort shalt thou bring into the ark, to keep them alive with thee; they shall be male and female.

Genesis 6:19–20

Of every clean beast thou shalt take to thee by sevens, the male and his female: and of beasts that are not clean by two, the male and his female. Of fowls also of the air by sevens, the male and the female; to keep seed alive upon the face of all the earth.

Genesis 7:2–3

With their parochial worldview, the Bible’s authors had no knowledge of distant continents such as Australia—indeed, they show no awareness of Northern Europe or of Asia beyond their own region, let alone of a spherical Earth divided into two hemispheres. This limitation could not be levelled against an all-knowing creator god, of course—which is precisely how we know no such god was involved in its writing. Had one been, we might reasonably expect the text to reflect a broader knowledge of the world and its history, and a more accurate understanding of living things, their origins, and their reproductive strategies—including those invisible to the unaided eye. Instead, we encounter a world that conforms only to the narrow perceptions and superstitions of its authors.

The Australian central bearded dragon Pogona vitticeps. The Australian central bearded dragon (Pogona vitticeps) is one of the best-studied reptiles, both in ecology and genetics, because it is hardy, widespread, and unusually flexible in its sex determination. Here’s a structured overview:

Taxonomy & Distribution

Scientific name: Pogona vitticeps (Ahl, 1926)
Family: Agamidae (dragon lizards)
Common name: Central bearded dragon
Range: Arid and semi-arid regions of central Australia, mainly New South Wales, Northern Territory, South Australia, and Queensland.
Habitat: Desert, scrubland, dry forests, and savannahs. They prefer open woodlands with scattered bushes, often basking on branches, rocks, or fence posts.

Morphology & Behaviour

Size: Adults typically 40–60 cm (including tail); males tend to be larger than females.
Distinctive feature: The “beard”—a throat pouch lined with spiny scales that can darken (turn black) and flare out in displays of aggression, courtship, or stress.
Colouration: Usually grey, tan, or reddish-brown, with banded patterns that aid camouflage.
Behaviour:

Diurnal (active by day).
Ectothermic, basking to thermoregulate.
Can change body colour slightly for temperature control.
Known for their arm-waving display, thought to be a submissive or social signal.

Diet: Omnivorous. Eats insects, small vertebrates, and vegetation (flowers, leaves, fruit).

Reproduction & Sex Determination

Reproduction: Oviparous; females lay clutches of 11–30 eggs, often burying them in sand.
Sex determination:

Pogona vitticeps has ZZ/ZW sex chromosomes (ZZ = male, ZW = female), similar to birds.
However, high incubation temperatures can override chromosomal sex determination, producing phenotypic females from ZZ embryos.
Remarkably, these sex-reversed females are fertile and can breed successfully.
This makes the species a model for studying the interaction between genetic and environmental sex determination.

Ecological & Evolutionary Significance

P. vitticeps is one of the clearest examples of temperature-dependent sex reversal in reptiles, showing how climate change could disrupt population dynamics.
Sex-reversed ZZ females often have higher fertility than ZW females, raising evolutionary questions about the persistence of sex chromosomes in the species.
Provides a natural system for studying transitions between sex-determining mechanisms in vertebrates.

Research Importance

The genome of P. vitticeps has been sequenced and annotated:

George et al. (2015): First high-coverage genome assembly (GigaScience).
Patel et al. (2023): Near telomere-to-telomere phased assembly, greatly improving resolution of its sex chromosomes.

Used widely in laboratories and classrooms as a model organism for genetics, endocrinology, ecology, and climate change biology.

Human Interaction

Very popular in the pet trade due to docile temperament, ease of handling, and tolerance of captivity.
Lifespan: ~8–12 years in captivity, shorter in the wild.
Threats in the wild: habitat modification and predation, but not considered endangered.

What happens what a ZZ female mates with a normal (ZZ) male?

First, let’s recall the genetics:

In P. vitticeps, ZZ = male, ZW = female (like birds).
A sex-reversed female is genetically ZZ, but develops as a female because high incubation temperatures override the chromosomal system.

Now, what happens if a ZZ sex-reversed female mates with a normal ZZ male?

The offspring will inherit one Z from each parent.
Therefore, all offspring will be ZZ.
Genetically, that means all would be male under normal incubation temperatures.

However:

If the eggs are incubated at high temperatures, some of those ZZ embryos will again develop as phenotypic females (sex-reversed).
So the sex ratio of the clutch depends not on the chromosomes (which are all ZZ) but on the environmental conditions during incubation.

In short: the cross between a ZZ female and a ZZ male yields 100% ZZ offspring. Their actual gender (male or female) depends on incubation temperature, not genetics alone.

Modern biology, by contrast, reveals a far richer diversity. Many species are hermaphroditic or parthenogenetic, bypassing the binary of male and female. In plants, hermaphroditism and dioecy are both common: some flowers are self-fertile, while others produce male and female flowers on the same plant. In the animal kingdom too, there are remarkable exceptions to the biblical binary.

One such case is the central bearded dragon (Pogona vitticeps), a reptile capable of sex reversal under certain environmental conditions—much like some fish and a handful of amphibians. That alone challenges the biblical notion of “male and female created he them”: these lizards were “created” with the genetic capacity to change sex after birth.

How this process works has now been elucidated by two teams of researchers—one from BGI, the Chinese Academy of Sciences, and Zhejiang University, and another from the University of Canberra.

Their findings are summarised in a news article in GigaScience (translated from Chinese), and are presented in two detailed publications: George, A., et al. High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps and Patel, H.R., et al. A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps.

Double Dragon Genomes Helping Explain Sex Determination of Reptiles
Two almost complete and gapless genomes of the sex-changing central bearded dragon (Pogona vitticeps) are published back-to-back to help tackle the mystery of reptile sex determination. Alongside a new gapless rice genome showcasing new CycloneSeq nanopore sequencing technologies ability to complete animal and plant genomes.
Two Genomes are Better Than One for Studying Reptile Sex

Today marks the publication of two different groups papers presenting the near-complete reference genomes of the central bearded dragon (Pogona vitticeps), a widely distributed species of dragon lizard common in central eastern Australia and popular as pets in Europe, Asia, and North America. This species has an unusual trait for an animal species: whether this lizard grows up to be a male or a female depends not only on genetics but also on the temperature of its nest. This has long made it a useful model to study the biological basis of sex determination, and the advent of huge technological improvements in genomics has finally found a region of the genome and a potential master sex determination gene likely central to male sexual differentiation. The independent verification of this by two different groups using two different approaches making this a much stronger finding.

Bearded dragons have an unusual sex determination system which is influenced by both genetics and environmental factors, specifically temperature. Unlike most animals where sex is solely determined by chromosomes, bearded dragons can have their sex reversed from male to female by high incubation temperatures. Meaning a lizard with male chromosomes can develop into a reproductively functional female if the egg is incubated at a warm enough temperature.

Like birds and many reptiles, this species has a ZZ/ZW sex chromosome system where females have a pair of dissimilar ZW chromosomes, and males have two similar ZZ chromosomes. Sex determination in this species is complicated further, as ZZ genotypic males can change to phenotypic females at high incubation temperatures without the help of W chromosome or W-linked genes. New ultra-long nanopore sequencing technology now allows us to generate telomere-to-telomere (T2T) assemblies of the sex chromosomes and identify the non-recombining regions to help narrow the field of candidate sex determining genes in species with chromosomal sex determination. The ability of this technology to better separate out the maternal and paternal halves of the genome now allows much easier comparisons of the Z and W sequences to gauge potential loss or difference in function of key sex gene candidates.

Here Be Dragons

The first paper from researchers from BGI, Chinese Academy of Sciences and Zhejiang University, uses DNBSEQ short-reads combined with long-reads from the new CycloneSEQ nanopore sequencer, this being the first animal genome published using this technology. Generation of the second genome was led by researchers from the University of Canberra with funding from Bioplatforms Australia, the Australian Research Council and PacBio Singapore, and with contributions to analyses from researchers of the Australian National University, Garvan Institute for Medical Research, University of New South Wales and CSIRO alongside Universitat Autònoma de Barcelona (UAB) in Spain. This assembly uses PacBio HiFi, ONT ultralong reads and Hi-C sequencing. Having reference genomes published using these two different technologies allows a like-for-like comparison between the ONT and CycloneSEQ technologies for the first time. Both technologies also complement each other by investigating the sex determination question using different approaches. The first genome sequenced a ZZ male central bearded dragon to characterize the whole Z sex chromosome for the first time while the second assembled the genome of a female ZW individual. The new nanopore sequencer also enabled therecovery of around 124 million base pairs of previously undescribed and missing sequences (nearly 7% of the genome), which included numerous genes and regulatory elements to better elucidate the complicated sex determination system.

Both projects assembled 1.75 Gbp genome assemblies of exceptionally high quality to assemble all but one of the telomeres, and only a few gaps remained mostly located in the microchromosomes. Using this data showed the Z and W specific sex chromosomes were assembled into single scaffolds, and a “pseudo-autosomal region” (PAR) where the sex chromosomes pair and recombine was also detected on chromosome 16. The sequencing of the male dragon by the BGI team looked for genes specific to Z but not the W chromosomes, and Amh and Amhr2 (the Anti-Müllerian hormone gene and its receptor) plus Bmpr1a were determined as strong candidates for the sex determining genes in this species. The sequencing of the female dragon by the Australian-led team pinpointed to the same candidate Sex Determination Region (SDR) of their dragon genome, and also highlighted Amh and Amhr2 as the likely candidate genes. Studying the expression in different developmental stages found Amh had significant male-biased expression patterns making it the most likely candidate as the master sex-determining gene. The differential expression of another sex-related gene Nr5a1 in the PAR suggests that the story may be more complicated, as Nr5a1 encodes a transcription factor with binding sites on the Amh promoter region. Unlike many fish that enlist Amh-like genes in sex determination, the autosomal copies of Amh and its receptor gene Amhr2 remain intact and functional. It could be that sex is determined by some form of caucus among genes on the sex chromosomes of the bearded dragon moderated by their residual autosomal copies.

The main highlight of these assemblies is therefore the discovery of genetic elements central to male sexual differentiation in vertebrates, on the sex chromosomes. The genes Amh and that coding its receptor AMHR2 have been copied to the Z chromosome in the non-recombining region, and so are obvious candidates for the master sex determining gene working via a dosage-based mechanism in this species, a discovery that has eluded discovery for so many years. No master sex determining gene akin to Sry in mammals or Dmrt1 in birds has to date been discovered in any reptile species. This new work provides a clear candidate in Amh, which is present in double dose in the ZZ male and single dose in the ZW female.

Arthur Georges from University of Canberra and senior author on the second paper says on the utility of this work:

We anticipate accelerated research in other areas arising from these newly available assemblies, such as cranial development, brain development, behavioural studies, gene-gene and gene-environment interactions in comparative studies of vertebrate sex determination and in many other areas looking for a well-supported squamate model against which to compare with their model species be it mouse, human or bird. I never cease to be amazed by the rapidity of progress of Chinese science. In relatively few years, BGI and its companion enterprises have developed sequencing technologies that deliver outcomes as good, and throughput and cost effectiveness that is better, than competing technologies on the market. These genome assemblies are testimony to that level of achievement.

Arthur Georges, lead author of the 2015 paper.
Institute for Applied Ecology
University of Canberra, Canberra, ACT, Australia.

CycloneSeq Storms the Year of the Dragon
Qiye Li from BGI Research and senior author on the first paper of the Chinese project explains their rationale for using this approach:

We decided to start working on the bearded dragon genome last year as the first animal genome for this new sequencer because it was the Year of the Dragon in China. Benefiting from the unbiased long-reads provided by the CycloneSEQ sequencer, we readily obtained a highly contiguous genome assembly and resolved highly repetitive and high-GC regions that were traditionally challenging for assembly. The two reference genomes, derived from opposite sex and generated by different technologies, are indeed complementary to each other. I am excited that both genomes pinpoint the key role of AMH signaling in sex determination in this species. But how did the sex chromosomes arise? We anticipate that additional high‑quality genomes from related species will further elucidate the evolutionary origin of the ZW system and complete the story

Qiye Li, senior author of the 2015 paper
China National GeneBank
BGI-Shenzhen, Shenzhen, China.

It is nice to have Qiye publish with us again, as on top of the first generation bearded genome he published the Eastern banjo frog genome in the launch papers of GigaByte, and also recorded a video abstract in GigaTV. Having two separate projects finding the same key candidate master genes independently of each other greatly increases the confidence in these findings. And openly sharing all of the data allows others to build upon this work, especially as the exact role of some of the other contributing transcription factors linked to sex determination are not yet fully resolved. The generation of these two new high quality genome assemblies however, is a massive step forward towards understanding the complete story of sex determination in this species.

Also published today by the same group at BGI is the Telome-to-Telomere assembly of the is perennial wild rice Oryza longistaminata. This follows our recent microbial genome benchmarking paper in GigaByte, taking this a step further by showing the same CycloneSEQ genome technology coupled with PacBio HiFi and Hi-C data can handle plant genomes. And is also the first time a T2T assembly has been published using this new technology, making it suitable for the strict criteria of our T2T series and demonstrating the successful validation of CycloneSEQ across diverse branches of the tree of life. A Cassyni webinar with the two lead authors is organized for 26th August at 00:00 UTC and provides an opportunity to ask them questions on this work. Sign up here to watch and post questions https://cassyni.com/events/SWHReTL1j8YPEvxnLsyKYq

References:

Guo Q, Pan Y, Dai W et al., A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes. GigaScience 2025. https://doi.org/10.1093/gigascience/giaf079

Patel HR, Alreja K, Reis AML, et al., A near telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps. GigaScience 2025. https://doi.org/10.1093/gigascience/giaf085

Georges A, Li Q, Lian J, et al., High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. GigaScience. 2015 Sep 28;4:45. https://doi.org/10.1186/s13742-015-0085-2

Guang X, Yang J, Zhang, S, et al., Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation. GigaScience 2025. https://doi.org/10.1093/gigascience/giaf074

Liang H, Zou Y, Wang M, et al., Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies. GigaByte. 2025 Apr 25;2025:gigabyte154. https://doi.org/10.46471/gigabyte.154

Li Q, Guo Q, Zhou Y, et al., A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae). GigaByte. 2020 Jul 1;2020:gigabyte2. https://doi.org/10.46471/gigabyte.2

Abstract

Background
Vertebrate sex is typically determined either by genetic factors, such as sex chromosomes, or by environmental cues like temperature. Therefore, the agamid dragon lizard Pogona vitticeps is remarkable in this regard, as it exhibits both ZZ/ZW genetic and temperature-dependent sex determination. However, complete sequence and full gene content of P. vitticeps sex chromosomes remain unclear, hindering the investigation of sex-determining cascade in this model lizard.

Results
Using CycloneSEQ and DNBSEQ sequencing technologies, we generated a near-complete chromosome-scale genome assembly for a ZZ male P. vitticeps. Compared with previous reference genome (GCF_900067755.1/Pvi1.1), this ∼1.8-Gb new assembly displayed >5,700-fold improvement in contiguity (contig N50: 202.5 Mb vs. 35.5 kb) and achieved complete chromosome anchoring (16 vs. 13,749 scaffolds). We found that over 80% of the P. vitticeps Z chromosome remains as a pseudo-autosomal region, where recombination is not suppressed. The sexually differentiated region (SDR) is small and occupied mostly by transposons, yet it aggregates genes involved in male development, such as AMH, AMHR2, and BMPR1A. Finally, by tracking the evolutionary origin and developmental expression of SDR genes, we proposed a model for the origin of P. vitticeps sex chromosomes that considered the Z-linked AMH as the master sex-determining gene.

Conclusions
In this study, we fully characterized the Z sex chromosome of P. vitticeps, identified AMH as the candidate sex-determining gene, and proposed a new model for the origin of P. vitticeps sex chromosomes. The near-complete P. vitticeps reference genome will also benefit future study of reptile evolution.

Introduction
Sex determination is a fundamental process in sexual organisms, influencing reproductive strategies, population dynamics, and genetic diversity [1]. Among vertebrates, the mechanisms of sex determination are diverse, ranging from genetic sex determination (GSD) to those determined by environmental factors such as temperature-dependent sex determination (TSD) [2–5]. The central bearded dragon Pogona vitticeps (NCBI:txid103695) represents a fantastic model in studying the molecular cascades of sex determination, as this species possesses a unique ZZ/ZW GSD system that is influenced by temperature. Normally, ZW embryos of P. vitticeps develop as females and ZZ embryos as males. However, high incubation temperatures can induce functional male-to-female sex reversal in genetically male (ZZ) individuals [6]. The capacity of a ZZ embryo to develop as a normal female without the help of the W chromosome suggests that sexual fate is most likely determined by a dosage-sensitive gene on the Z chromosome [7], making the complete Z chromosome sequence particularly crucial for deciphering the sex-determining cascade in this species.

While many studies involving P. vitticeps in the past decade tightly rely on its genome assembly and annotation, the current reference genome (GCF_900067755.1/Pvi1.1) is still quite fragmented. This reference genome was constructed with a wild-caught ZZ male individual, based on Illumina short-read sequencing data generated from gradient libraries with an insert size ranging from 250 bp to 40 kb [8]. Due to the limitation of short-read sequencing, the contig N50 of this assembly version is merely 35.5 kb in length, lagging far behind the common standard of a reference genome (>1 Mb), as proposed by the Earth BioGenome Project (EBP) [9] and the Vertebrate Genomes Project (VGP) [10] in recent years. Furthermore, telomeres, which are essential for chromosome stability and composed of thousands of telomeric repeat units (TRUs) (TTAGGG)n [11] in vertebrates, are almost absent in Pvi1.1 due to the limitation of short reads in assembling highly repetitive regions. Additionally, P. vitticeps possesses microchromosomes [12], which, like those in birds and some reptiles, present significant assembly challenges due to their high gene density, elevated GC content, and intense interchromosomal interaction signals [13]. These characteristics make the assembly of a complete P. vitticeps genome particularly challenging. Although subsequent scaffolding efforts anchored ∼42% of the genomic sequences to chromosomes [14], the low anchoring percentage still limits its use in chromosome-scale investigation. For example, the sex chromosomes of P. vitticeps are well known to be heteromorphic based on cytogenetic evidence, implying the existence of sequence divergence between Z and W due to recombination suppression [15]. However, the PAR and SDR of both sex chromosomes remain undefined so far, which in turn hamper the search for the master sex-determining gene.

In this study, we generated a chromosome-scale genome assembly for a ZZ male P. vitticeps, via a combination of long- and short-read whole-genome sequencing (WGS), as well as long-range sequencing technologies. With this near-complete genome assembly, we fully characterized the Z sex chromosome of P. vitticeps and demarcated the PAR and SDR on Z, tracked the evolutionary origin and developmental expression of the Z-linked SDR genes, and proposed an alternative model for explaining the origin of sex chromosomes with the Z-linked AMH as the candidate of master sex-determining gene in P. vitticeps.

Qunfei Guo, Youliang Pan, Wei Dai, Fei Guo, Tao Zeng, Wanyi Chen, Yaping Mi, Yanshu Zhang, Shuaizhen Shi, Wei Jiang, Huimin Cai, Beiying Wu, Yang Zhou, Ying Wang, Chentao Yang, Xiao Shi, Xu Yan, Junyi Chen, Chongyang Cai, Jingnan Yang, Xun Xu, Ying Gu, Yuliang Dong, Qiye Li,
A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosome
GigaScience, 14, 2025, giaf079, https://doi.org/10.1093/gigascience/giaf079

Copyright: © 2025 BGI.
Published by Oxford University Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Abstract

Background
The 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 near telomere-to-telomere phased assembly of the genome of a female ZW central bearded dragon.

Results
Genome 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 ribosomal DNA 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 pseudo-autosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies, and their resultant transcription factors and intermediaries determine sex in the bearded dragon.

Conclusion
This 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.

Graphical Abstract Assembly of a ZW female of the Central Bearded Dragon.

Introduction
The family Agamidae, commonly known as dragon lizards, is a diverse group of lizards found in Africa, Asia, Australia, the Western Pacific, and warmer regions of southern Europe. The Agamidae family is well represented in Australia, in part because of their successful radiation in response to the progressive aridification of the Australian continent during the Pleistocene. New species are continually being described, but on recent count, they comprise 81 species in 15 genera [1.1] that occupy a very wide array of habitats ranging from the inland deserts to the mesic habitats of the coast and the Australian Alps below the treeline. The family includes some iconic species, such as the thorny devil Moloch horridus and the frillneck lizard Chlamydosaurus kingii. Less spectacular perhaps is the central bearded dragon Pogona vitticeps, a widely distributed species of Amphibolurine dragon common in central eastern Australia (Fig. 1). The bearded dragon feeds on insects and other invertebrates, but a substantial component of the diet of adults is vegetable matter. It lives in the dry sclerophyll forests and woodlands in the southeast of its range, mallee and arid acacia scrublands further north and west, and the sandy deserts of the interior. Semi-arboreal, the species often perches on fallen timber and tree branches, only to retreat to ground cover when disturbed.

.
Figure 1: The central bearded dragon P. vitticeps and the distribution of the species based on records from Australian museums (via Atlas of Living Australia https://www.ala.org.au/).

Central bearded dragons adapt readily to captivity, lay large clutches of eggs several times per season, and are commonly kept as a pet in Europe, Asia, and North America. These attributes also increase its value as a popular reptile research model in a range of disciplines [2.1–7.1]. Central bearded dragons are a particularly compelling model species for sex determination because they display temperature-induced sex reversal in the laboratory and in the wild [8.1–10.1]. The sex chromosomes of central bearded dragons are poorly differentiated morphologically. They exhibit female heterogamety (ZZ/ZW sex chromosome system, [11.1]) with 6 macrochromosome pairs and 10 microchromosome pairs [12.1] that include the sex microchromosome pair [11.1]. Bacterial artificial chromosome (BAC) sequences have been physically mapped uniquely to each of the chromosomes [13.1, 14.1].

Sex determination in this species is particularly subtle until now, with no substantial difference between the Z and W chromosome gene content or single-copy sequence [15.1]. The developmental program initiated by chromosomal sex determination can be reversed by high incubation temperature, allowing for investigations of environmental influences on fundamental developmental processes. Research in these areas of interest will be greatly facilitated by applying modern sequencing technologies to generate a high-quality draft genome assembly for the central bearded dragon. The ability to generate telomere-to-telomere (T2T) assemblies of the sex chromosomes and identify the non-recombining regions within which lies any master sex determining gene will greatly narrow the field of candidate sex-determining genes in species with chromosomal sex determination. Furthermore, the disaggregation of the Z and W sex chromosome haplotypes (phasing) will allow comparisons of the Z and W sequences to gauge putative loss or difference in function of key sex gene candidates.

In this article, we present a draft annotated near-T2T phased assembly of the genome of the Australian central bearded dragon 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. This is a vastly improved assembly in comparison with an earier assembly based on Illumina short-read technology published in 2015 [16.1].

Hardip R Patel, Kirat Alreja, Andre L M Reis, J King Chang, Zahra A Chew, Hyungtaek Jung, Jillian M Hammond, Ira W Deveson, Aurora Ruiz-Herrera, Laia Marin-Gual, Clare E Holleley, Xiuwen Zhang, Nicholas C Lister, Sarah Whiteley, Lei Xiong, Duminda S B Dissanayake, Paul D Waters, Arthur Georges.
A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps
GigaScience, 14, 2025, giaf085, https://doi.org/10.1093/gigascience/giaf085

Copyright: © 2025 BGI.
Published by Oxford University Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

For people who regard the Bible as an inerrant science textbook, the central bearded dragon (Pogona vitticeps) presents a particular difficulty. Genesis repeatedly stresses that living creatures were created “male and female,” with sexual reproduction portrayed as the only mechanism by which animals continue their kind. This reflects the limited knowledge of Iron Age authors, who assumed that the reproductive patterns they observed in their herds and flocks applied universally.

The central bearded dragon, however, undermines that simplistic binary. Like birds, it has a genetic sex-determination system, with ZZ males and ZW females. But under high incubation temperatures, the genetic signal can be overridden: ZZ embryos that should have developed into males instead become fully functional females. These “sex-reversed” females are not only fertile but in some cases more fecund than ZW females. In other words, here is a species that can literally change sex, with environmental conditions reshaping the reproductive role of an individual regardless of its chromosomes.

Such a finding is entirely at odds with the biblical claim that animals exist strictly as “male and female.” If the text were a genuine revelation from an omniscient creator, we might expect at least some recognition that reproduction is more diverse and flexible than the binary categories known to ancient herdsmen. Instead, we find a narrow view that excludes hermaphroditism, parthenogenesis, and the extraordinary capacity for sex reversal found in reptiles, fish, and amphibians.

The existence of Pogona vitticeps and its temperature-dependent sex reversal is a reminder that the natural world is more complex than the Bible’s authors could have imagined. Far from being “male and female, created he them,” life has evolved a wide spectrum of reproductive strategies, demonstrating once again that scripture is a human product of its time rather than a reliable guide to biology.

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