Refuting Creationism - The Transexual Bearded Dragons Of Australia

Central bearded dragon, Pogona vitticeps

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:

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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.

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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).

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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.

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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.

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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.

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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.

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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

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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.

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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.

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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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Refuting Creationism - The Difference Between The Bible And Reality - ESA's Picture Of The Week

NGC 2835

Noteworthy nearby spiral | ESA/Hubble

Everywhere science looks, it exposes the widening gulf between the way the Bronze Age authors of the Bible imagined their tiny fragment of the cosmos and the reality we now know. Astronomy, no less than biology, geology, or palaeontology, makes clear just how limited and naïve that worldview was.

Today’s reminder of that contrast comes from the European Space Agency’s “Picture of the Week”: the so-called “nearby” spiral galaxy NGC 2835, lying a mere 35 million light-years away in the constellation Hydra, the Water Snake. In other words, the light now reaching our eyes began its journey 35 million years before the Bible’s writers imagined the universe springing into existence at the command of a magic incantation — יְהִי אוֹר (yehi or! — “Let there be light”), curiously spoken in a language there was no-one else alive to understand.

And God said, Let there be a firmament in the midst of the waters, and let it divide the waters from the waters. And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: and it was so. And God called the firmament Heaven. And the evening and the morning were the second day. And God said, Let the waters under the heaven be gathered together unto one place, and let the dry land appear: and it was so. And God called the dry land Earth; and the gathering together of the waters called he Seas: and God saw that it was good. (Genesis 1.6-10)

And God made two great lights; the greater light to rule the day, and the lesser light to rule the night: he made the stars also. And God set them in the firmament of the heaven to give light upon the earth, And to rule over the day and over the night, and to divide the light from the darkness: and God saw that it was good.(Genesis 1.16-18)

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Today’s NASA/ESA Hubble Space Telescope Picture of the Week offers a closeup of a nearby spiral galaxy. The subject is NGC 2835, which lies 35 million light-years away in the constellation Hydra (The Water Snake).

A previous Hubble image of this galaxy was released in 2020, and the NASA/ESA/CSA James Webb Space Telescope turned its gaze toward NGC 2835 in recent years as well. Do you see anything different between today’s image of NGC 2835 and the previously released versions? Overall, NGC 2835 looks quite similar in all of these images, with spiral arms dotted with young blue stars sweeping around an oval-shaped centre, where older stars reside.

This image differs from previously released images because it incorporates new data from Hubble that captures a specific wavelength of red light called H-alpha. The regions that are bright in H-alpha emission can be seen along NGC 2835’s spiral arms, where dozens of bright pink nebulae appear like flowers in bloom. Astronomers are interested in H-alpha light because it signals the presence of several different types of nebulae that arise during different stages of a star’s life. Newborn massive stars create nebulae called H II regions that are particularly brilliant sources of H-alpha light, while dying stars can leave behind supernova remnants or planetary nebulae that can also be identified by their H-alpha emission.

By using Hubble’s sensitive instruments to survey 19 nearby galaxies, researchers aim to identify more than 50 000 nebulae. These observations will help to explain how stars affect their birth neighbourhoods through intense starlight and winds.

[Image Description: A spiral galaxy seen face-on. Its centre is a bright glowing yellow. The galaxy’s spiral arms contain sparkling blue stars, pink spots of star formation, and dark threads of dust that follow the arms.]

Credit: ESA/Hubble & NASA, R. Chandar, J. Lee and the PHANGS-HST team

NGC 2835.

DSS Finder Chart (30′ × 30′ field) — Highlights NGC 2835 with its approximate size and orientation.

Hydra Constellation Sky Chart — Shows the broader layout of Hydra, aiding visual positioning in the night sky.

Star‑chart zoomed‑in view — A close-up star chart marking the galaxy amid surrounding field stars.

Constellation Grid Overlay — Provides context with grid lines and star positions across Hydra.

Basic Facts

• Type: Barred spiral galaxy (classification: SAB(rs)c).
• Constellation: Hydra (the Water Snake).
• Distance: Approximately 35 million light-years from Earth.
• Size: Roughly 65,000 light-years in diameter (about two-thirds the size of the Milky Way).
• Apparent magnitude: About 10.3 – faint, but visible in medium-sized amateur telescopes.
• Discovery: Found by William Herschel in 1785.

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Structure & Appearance

• Spiral arms: Loosely wound, full of star-forming regions and young blue stars.
• Bar: Weakly barred, meaning it has a small central bar feature that helps channel gas inward.
• Core: Contains a supermassive black hole, though smaller than the one in the Milky Way. Estimates put it at around 3–10 million solar masses.
• Dust lanes: Dark filaments of interstellar dust wind through the spiral arms, silhouetted against the starlight.
• Star formation: Active in the outer arms, with pinkish H II regions where new stars are being born.

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Observations

• Amateur astronomy: At magnitude 10.3, it’s not visible to the naked eye, but can be seen with a small-to-medium telescope under dark skies. It appears as a faint oval haze with a brighter core.
• Professional imaging: The Hubble Space Telescope has taken a detailed image of NGC 2835, showing the spiral arms rich in blue stars and reddish star-forming regions.

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Scientific Interest

• NGC 2835 is often studied as a nearby example of a typical spiral galaxy.
• Its moderate distance and orientation (almost face-on) make it ideal for examining:
  • Stellar population gradients (how star ages vary from core to arms).
  • Gas and dust distribution in spirals.
  • Black hole scaling relations (comparing the mass of central black holes to properties of host galaxies).

Imagine being so ignorant and/or brain-washed as to believe that description in the Bible was the best available description of the universe, far surpassing for accuracy and reliability anything that science can reveal. And yet, there are adults alive today, with access to free information on a scale of which our forebears could only dream, whose understanding of the universe and how it works is no better than that of a Bronze Age pastoralist from the ignorant and fearful infancy of our species.

This wilful ignorance can only be the result of a pathological mind virus.

Refuting Creationism - Earliest Known Hominins In Europe - 1.4 Million Years Before Creation Week

A researcher holds a stone tool in Korolevo.

CAS Prague Institute of Archaeology

This article is best read on a laptop, desktop, or tablet

Press release | The First Humans Came to Europe 1.4 Million Years Ago - ARUP

A map showing the migration of hominins through Europe.

CAS Prague Institute of Archaeology

This news release slipped beneath my radar back in March 2024, but as it’s now being discussed on social media, I thought I’d take a look and track down the original press release and the publication in Nature.

The news came from the Czech Institute of Archaeology: research by an international team led by Roman Garba, from the Institute of Nuclear Physics and the Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, has uncovered the earliest evidence of hominins in Europe at a site in Ukraine.

This is, like most discoveries in biology, archaeology, and geology, compelling evidence that the Bible’s account of creation is not only wrong, but so far removed from reality that it can’t even be rescued as metaphor or allegory. Increasingly large portions of the Bible now have to be explained away in this manner as mainstream Christianity retreats from the doctrine of Biblical inerrancy and the idea of a creator god. What’s left is a dwindling rump of die-hard creationists, clinging desperately to the wreckage of their beliefs as the tsunami of evidence sweeps them further into irrelevance.

The discovery was made at Korolevo, Ukraine, and consisted of stone tools—sadly, no bones were found. If confirmed, this pushes back the timeline of hominin migration into Eurasia by 200,000 to 300,000 years from the previous earliest known date at Sima de los Huesos, Atapuerca, Spain. The scale of denialism required to dismiss this discovery can be measured in the response of one such creationist on Facebook:

since the earth is less then [sic] 6,000 years old where was this skeliton [sic – it’s actually a stone tool] for the remiander [sic] of that time seeing there was no universe?

How Science Works - The Mystery In Great White Shark DNA

Photo by Greg Skomal.

There’s something fishy going on with great white sharks that scientists can’t explain – Research News

Here is something that should bring both delight and disappointment to creationists. It concerns a mystery in the genetics of the great white shark, Carcharodon carcharias — a finding that runs counter to what the theory of evolution would predict. In fact, it is precisely a failed evolutionary prediction that is the subject of a paper recently published in Proceedings of the National Academy of Sciences (PNAS).

The disappointment for creationists comes from the simple fact of its publication. It directly refutes the oft-repeated claim that the scientific community refuses to publish anything that does not fully align with the theory of evolution. As with so many creationist accusations, this is a projection of their own malpractice. Major creationist organisations — such as Ken Ham’s Answers in Genesis — require contributors to sign statements of faith that commit them never to publish anything inconsistent with their predetermined beliefs. In other words, only creationist organisations demand strict adherence to conclusions before research is even carried out.

The new findings show that the great white shark passed through an extreme population bottleneck in the Indo-Pacific at the end of the last Ice Age, around 10,000 years ago. From this single population, they began diversifying about 7,000 years ago. Today, there are roughly 20,000 individuals across three distinct populations: one in the southern hemisphere (around Australia and South Africa), one in the North Atlantic, and another in the North Pacific. Genetic analysis reveals this divergence in their mitochondrial DNA (mtDNA), which is inherited solely through the female line. Curiously, however, their nuclear DNA (nDNA) — inherited equally from both parents — shows almost no diversity at all. All populations are remarkably similar in nDNA, far more so than evolutionary theory would predict.

This raises the mystery: why does the mtDNA show clear evidence of diversification and population isolation, while the nDNA does not?

One early idea was that males roam widely while females remain tied to their birthplace, or else return there to breed — a theory known as philopatry. A research team led by Gavin J.P. Naylor of the Florida Museum of Natural History tested this hypothesis by running simulations using DNA from about 150 sharks. The results showed that philopatry could not account for the observed mtDNA variation.

Another possibility was a skewed sex ratio, similar to species such as meerkats, cichlid fish, and some social insects, where only dominant females reproduce. But again, simulations and evidence ruled this out — there is no indication of such a hierarchy in female great whites.

That leaves natural selection. Yet here lies the problem. While natural selection can explain variation in nDNA — because these genes govern traits that affect survival and reproduction — it cannot explain variation in mtDNA. Moreover, natural selection tends to be strongest in large populations, whereas genetic drift dominates in small ones. But the great whites show the reverse pattern: a small founder population produced much mtDNA variation but almost no nDNA variation, and today’s larger population still shows little nDNA diversity.

So the puzzle remains. Why do mtDNA and nDNA tell such different evolutionary stories in the great white shark?

What creationists cannot claim, however, is that this anomaly somehow lends support to creationism. The scientists have not abandoned evolution in favour of untestable claims about supernatural beings working magic. Instead, they have drawn the only truly scientific conclusion available: more research is needed, because the mystery is one that can be solved through reason and the scientific method.

The Evolution of the Great White Shark.

• Origins: The great white shark belongs to the family Lamnidae, which includes makos and porbeagles. Its evolutionary story stretches back over 60 million years.
• Megalodon confusion: For years, great whites were thought to be direct descendants of the gigantic Megalodon (Otodus megalodon), but fossil evidence has shown this is incorrect. Megalodon is now placed in the Otodontidae, a separate family.
• Closer relatives: The great white’s closest fossil relatives are the broad-toothed mako sharks (Carcharodon hastalis and related species), which lived from about 11–3 million years ago. Their teeth show transitional forms between makos and modern great whites.
• Appearance of Carcharodon carcharias: Fossils of the modern species appear in the early Pliocene (~4–5 million years ago). By this time, they had developed the serrated triangular teeth characteristic of today’s great white.
• Key adaptations:
  • Large, serrated teeth specialised for tackling marine mammals.
  • Gigantothermy (a form of regional endothermy) allowing activity in cooler waters.
  • A wide distribution, paralleling the global spread of pinnipeds (seals and sea lions), one of their major prey groups.
• Evolutionary significance: The great white represents a case of convergent evolution with Megalodon in terms of size and ecological role, but it evolved independently within the lamnid lineage.

The Florida Museum has also provided a plain-language summary of the findings in this news release by Jerald Pinson.

There’s something fishy going on with great white sharks that scientists can’t explain

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Key points:

• White sharks exhibit stark differences between the DNA in their nuclei and the DNA in their mitochondria. Until now, scientists have pointed to the migration patterns of great whites to explain the discrepancy.
• Scientists tested this theory in a new study by analyzing genetic differences between global white shark populations. In doing so, they discovered that great whites were restricted to a single population in the Indo-Pacific Ocean at the end of the last ice age 10,000 years ago and have since expanded to their current global distribution.
• The results also invalidate the migration theory, but an alternative explanation remains elusive.

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White sharks (Carcharodon carcharias) almost went bottom-up during the last ice age, when sea levels were much lower than they are today and sharks had to get by with less space. The most recent cold snap ended about 10,000 years ago, and the planet has been gradually warming ever since. As temperatures increased, glaciers melted, and sea levels rose, which was good news for great whites.

Results of a study published in the journal Proceedings of the National Academy of Sciences show that white sharks had been reduced to a single, well-mixed population somewhere in the southern Indo-Pacific Ocean. White sharks began genetically diverging about 7,000 years ago, suggesting that they had broken up into two or more isolated populations by this time.

This is new information but not particularly surprising. There are never many white sharks around even at the best of times, as befits their status at the top of the tapered food chain, where a lack of elbow room limits their numbers. Today, there are three genetically distinct white shark populations: one in the southern hemisphere around Australia and South Africa, one in the northern Atlantic and another in the northern Pacific. Though widespread, the number of white sharks still remains low.

There are probably about 20,000 individuals globally. There are more fruit flies in any given city than there are great white sharks in the entire world.

Gavin Naylor, co-author
Director of the Florida Program for Shark Research
Florida Museum of Natural History.

Organisms with small populations can be pushed dangerously close to the edge of extinction when times are tough. Mile-high glaciers extended from the poles and locked away so much water that by 25,000 years ago, sea levels had plunged by about 40 meters (131 feet), eliminating habitat and restricting great whites to an oceanic corral.

But something happened to great whites during their big comeback that remains as much of a mystery now as it was when it was first discovered more than 20 years ago. The primary motivation for this study was to lay out a definitive explanation, but despite using one of the largest genetic datasets on white sharks ever compiled, things did not go quite according to plan.

The honest scientific answer is we have no idea

Gavin Naylor.

Female great white sharks wander off for years to feed but come back home to breed

Scientists first got a whiff of something strange in 2001, when a research team published a paper that opened with the line, “… information about … great white sharks has been difficult to acquire, not least because of the rarity and huge size of this fish.”

The authors of that study compared genetic samples taken from dozens of sharks in Australia, New Zealand and South Africa. They found that though the DNA produced and stored in the nuclei of their cells were mostly the same between individuals, the mitochondrial DNA of sharks from South Africa were distinctly different from those in Australia and New Zealand.

The seemingly obvious explanation was that great whites tend to stick together and rarely make forays into neighboring groups. Over time, unique genetic mutations would have accumulated in each group, which, if it went on long enough, would result in the formation of new species.

This would explain the observed differences in their mitochondrial DNA but not why the nuclear DNA was virtually identical among all three populations. To account for that, the authors suggested that male sharks traveled vast distances throughout the year, but females either never traveled far, or if they did, they most often came back to the same place during the breeding season, a type of migration pattern called philopatry.

This idea was based on the fact that nuclear and mitochondrial DNA are not inherited in equal proportion in plants and animals. The DNA inside nuclei is passed down by both parents to their offspring, but only one — most often the female — contributes mitochondria to the next generation. This is a holdover from the days when mitochondria were free-living bacteria, before they were unceremoniously engulfed and repurposed by the ancestor of eukaryotes.

This was a good guess and had the added benefit of later turning out to be mostly accurate. Male and female great whites do travel large distances in search of food throughout the year, and females consistently make the return journey before it’s time to mate.

Thus, the nuclear DNA of great whites should have less variation, because itinerant males go around mixing things up, while the mitochondrial DNA in different populations should be distinct because philopatric females ensure all the unique differences stay in one place. This has remained the favored explanation for the last two decades, one that seemed to fit like a well-worn glove. Except, no one ever got around to actually putting it on to test its size. This is primarily because the data needed to do so was hard to get for the same reasons mentioned in the touchstone study: There aren’t many great white sharks, and when researchers do manage to find one, taking a DNA sample without losing any appendages in the process can be tricky business.

Shark migration cannot explain nuclear and mitochondrial discordance, so what can?

Naylor and his colleagues began collecting the necessary data back in 2012.

I wanted to get a white shark nuclear genome established to explore its molecular properties. White sharks have some very peculiar attributes, and we had about 40 or 50 samples that I thought we could use to design probes to look at their population structure.

Gavin Naylor.

Over the next few years, they also sequenced DNA from about 150 white shark mitochondrial genomes, which are smaller and less expensive to assemble than their nuclear counterparts. The samples came from all over the world, including the Atlantic, Pacific and Indian oceans.

When they compared the two types of DNA, they found the same pattern as the one discovered in 2001. At the population level, white sharks in the North Atlantic rarely mixed with those from the South Atlantic. The same was true of sharks in the Pacific and Indian oceans. At a molecular level, the nuclear DNA among all white sharks remained fairly consistent, while the mitochondrial DNA showed a surprising amount of variation.

The researchers were aware of the philopatric theory and ran a few tests to see if it held up, first by looking specifically at the nuclear DNA. If the act of returning to the same place to mate really were the cause of the strange mitochondrial patterns, some small signal of that should also show up in the nuclear DNA, of which females contribute half to their offspring.

But that wasn’t reflected in the nuclear data at all.

Gavin Naylor.

Next, they concocted a sophisticated test for the mitochondrial genomes. To do this, they first had to reconstruct the recent evolutionary history of white sharks, which is how they discovered the single southern population they’d been reduced to during the last ice age.

Seals are a dietary staple of white sharks.

Photo by Greg Skomal.

They were really few and far between when sea levels were lowest. Then the population increased and moved northward as the ice melted. We suspect they remained in those northern waters because they found a reliable food source

Gavin Naylor.

Specifically, they encountered seals, which are a dietary staple among white sharks and one of the main reasons why they have such a strong fidelity to specific locations.

These white sharks come along, get a nice blubbery sausage. They fatten up, they breed, and then they move off around the ocean.

Gavin Naylor.

Knowing when the sharks split up was key, as each group would have begun genetically diverging from each other at this time. All the researchers had to do was determine whether the 10,000 years between now and the last ice age would have been enough time for the mitochondrial DNA to have accumulated the number of differences observed in the data if philopatry was the primary culprit.

They ran a simulation to find the answer, which came back negative. Philopatry is undoubtedly a behavioral pattern among great whites, but it was not responsible for the large mitochondrial schism.

So Naylor and his colleagues went back to the drawing board to figure out what sort of evolutionary force could account for the differences.

“I came up with the idea that sex ratios might be different — that just a few females were contributing to the populations from one generation to the next,” Naylor said. This type of reproductive skew can be observed in a variety of organisms, including meerkats, cichlid fish and many types of social insects.

But yet another test showed that reproductive skew did not apply to white sharks.

It’s currently unclear why white sharks, which often venture out into the depths of the ocean, nevertheless seem to remain in discrete populations, with very little mixing in-between.

Photo by Greg Skomal.

There is a third, albeit less likely, option the team members said they can’t rule out at this stage, namely that natural selection is responsible for the differences. The reason why this is far-fetched has to do with the relative strength of evolutionary forces. Natural selection — the idea that the organisms best suited to leave behind offspring will, in fact, generally be the ones that have the most offspring — is always active, but it has the strongest effect in large populations. Smaller populations, in contrast, are more susceptible to something called genetic drift, in which random traits — even harmful ones — have a much higher chance of being passed down to the next generation.

Florida panthers, for example, are highly endangered, with only a few hundred individuals left in the wild. Most of them have a kink at the end of their tail, likely inherited from a single ancestor. In a large population, subject primarily to natural selection, this trait would have either remained uncommon or disappeared entirely over time. But in a small population, a single cat with a kinked tail can change the world purely by chance through the auspices of genetic drift.

By way of comparison, gravity exerts a force at all scales of matter and energy, but it is by far the weakest of the four fundamental physical forces. At the scale of planets and stars, gravity can hold solar systems and galaxies together, but it has very little influence on the shape or interactions of atoms, which are governed by the three stronger but more localized forces, such as electromagnetism.

According to the study’s results, genetic drift cannot explain the differences between mitochondria in great whites. Because it is a completely random process, it cannot selectively target one type of DNA and spare another. If it were the culprit, similar changes would also be evident in the nuclear DNA.

This leaves natural selection as the only other possibility, which seems unlikely because of the small population sizes among white sharks. If it is the causative agent, Naylor said, the selective force “would have to be brutally lethal.”

If you collect enough mass in a concentrated space, say on the order of a black hole, the otherwise benign force of gravity becomes powerful enough to devour light.

If natural selection is at play in this case, it would manifest itself in a similarly powerful way. Any deviation from the mitochondrial DNA sequence most common in a given population would likely be fatal, thus ensuring it was not passed on to the next generation.

But this is far from certain, and Naylor has his doubts about the validity of such a conclusion. For now, scientists are left with an open-ended question that can only be resolved with further study.

Additional co-authors of the study are: Romuald Laso-Jadart, Elise Gaya, Pierre Lesturgie and Stefano Mona of the Muséum National d’Histoire Naturelle; Shannon L. Corrigan, Lei Yang and Adrian Lee of the Florida Museum of Natural History; Olivier Fedrigo of the The Rockefeller University; Christopher Lowe and Kady Lyons of California State University Long Beach; Greg Skomal of the University of Massachusetts Dartmouth; Geremy Cliff of the University of KwaZulu-Natal; Mauricio Hoyos Padilla of Pelagios-Kakunjá Marine Conservation; Charlie Huveneers of Flinders University; Keiichi Sato of the Okinawa Churaumi Aquarium; and James Glancy of the British Museum of Natural History.

Publication:

R. Laso-Jadart,S.L. Corrigan,L. Yang,S. Lee,E.J. Gay,O. Fedrigo,C.G. Lowe,G. Skomal,G. Cliff,M.H. Padilla,C. Huveneers,K. Lyons,K. Sato,J. Glancy,P. Lesturgie,S. Mona, & G.J.P. Naylor
A genomic test of sex-biased dispersal in white sharks
Proc. Natl. Acad. Sci. U.S.A. 122(32) e2507931122, https://doi.org/10.1073/pnas.2507931122 (2025).

Significance
The mitonuclear discordance seen in sharks is widely attributed to female philopatry but has never been explicitly tested. Herein, we explore the issue in white sharks, for which we assembled a high-resolution genome and reconstructed the demographic history using resequencing data. We used backward and forward simulations to examine the genetic consequences of sex-specific migration patterns using parameter values derived from the demographic analyses of autosomal data. The mitochondrial variability observed in natural populations was never reproduced in any of the simulations—even under extreme female philopatry, suggesting that other forces have contributed to the discordance. The same approach would benefit other species of shark where female philopatry has previously been assumed based on genetic data.

Abstract
Mitonuclear discordance has been observed in several shark species. Female philopatry has often been invoked to explain such discordance but has never been explicitly tested. Here, we focus on the white shark, for which female philopatry has been previously proposed, and produced a chromosome-level genome, high-coverage whole-genome autosomal, and uniparental datasets to investigate mitonuclear discordance. We first reconstructed the historical population demography of the species based on autosomal data. We show that this species once comprised a single panmictic population, which experienced a steady decline until recent times when it fragmented into at least three main autosomal genetic groups. Mitochondrial data depict a strikingly different picture, inconsistent with the spatial distribution of autosomal diversity. Using the demographic scenario established from autosomal data, we performed coalescent and forward simulations to test for the occurrence of female philopatry. Coalescent simulations showed that the model can reproduce the autosomal variability, confirming its robustness. A forward simulation framework was further built to explicitly account for a sex-biased reproduction model and track both autosomal and uniparental markers (Y chromosome and mitochondrial DNA). While our model generates data that are consistent with the observed Y chromosome variation, the mitochondrial pattern is never reproduced even under extreme female philopatry (no female migration), strongly suggesting that demography alone cannot explain the mitonuclear discordance. Our framework could, and perhaps should, be extended to other shark species where philopatry has been suggested. It is possible that the proposed widespread occurrence of female philopatry in sharks should be revisited.

R. Laso-Jadart,S.L. Corrigan,L. Yang,S. Lee,E.J. Gay,O. Fedrigo,C.G. Lowe,G. Skomal,G. Cliff,M.H. Padilla,C. Huveneers,K. Lyons,K. Sato,J. Glancy,P. Lesturgie,S. Mona, & G.J.P. Naylor
A genomic test of sex-biased dispersal in white sharks
Proc. Natl. Acad. Sci. U.S.A. 122(32) e2507931122, https://doi.org/10.1073/pnas.2507931122 (2025).

© 2025 The National Academy of Science of the USA.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

Creationists will no doubt seize on this puzzle as supposed evidence that the theory of evolution has failed. In reality, the opposite is true. Evolutionary theory remains the best and only scientific explanation for the diversity of life precisely because it is testable. When unexpected results arise, scientists don’t abandon the framework — they investigate further, refine their models, and expand understanding. Far from being a weakness, this capacity for self-correction is a hallmark of genuine science.

The discrepancy between mitochondrial and nuclear DNA in great white sharks does not undermine evolution; it highlights a fascinating technical challenge in population genetics. The evidence still shows beyond question that great whites passed through a bottleneck, diversified into distinct global populations, and share evolutionary ancestry with earlier lamnid sharks. The unresolved issue is why different parts of their genome tell different stories — an open research problem, not a crisis for evolutionary biology.

By contrast, creationism offers no explanation at all. Invoking a supernatural designer “doing it that way” makes no predictions, cannot be tested, and adds nothing to knowledge. Evolutionary science, on the other hand, continues to uncover the history of these remarkable predators and the mechanisms that shaped them. This new mystery doesn’t weaken evolution — it strengthens it, by showing that the search for answers goes on, and that those answers lie in evidence and reason, not in dogma.