Rosa Rubicondior: Unintelligent Design - Sex Determination in Octopuses

Californian two-spot octopus, Octopus bimaculoides

Octopuses have some of the oldest known sex chromosomes | OregonNews

Although few of them will know enough to understand why, the genetic basis for sex determination in different organisms is a problem for intelligent design advocates because it illustrates a few embarrassing things which can't be explained as the design of an intelligent designer.

Firstly, there are several ways in which gender is determines, rather than the single method a single intelligent designer of all living things would have settled for (see the AI information panel). Secondly, the actual basis is consistent within major clades such as mammals, birds and orders of insects such as Hymenoptera (Bees, wasps and ants), and thirdly, because the methods are unstable over evolutionary time, since the sex chromosomes are unpaired in the heterozygous gender, so the unpaired chromosome tends to acquire mutations, which are not corrected by cross over during meiosis, and the non-sex-determining genes tend to be conserved on the chromosome which is paired in the homozygous gender.

In mammals, this means that the Y-chromosome tends to degenerate; in some species of rodents, which have a short generation time and large litters, so evolution can progress faster than in most other mammals, the Y-chromosome has disappeared, to be replaced by an alternative sex-determining system. No intelligent designer worthy of the name would design a process that degenerates and need to be replaced every few million years.

Please explain the genetic basis of sex determination in animals and why these tend to be short-lived in evolutionary time. Genetic Basis of Sex Determination in Animals

Sex determination in animals is governed by a variety of genetic and environmental mechanisms. The most well-known systems include:

Chromosomal Sex Determination

XX/XY System (e.g., mammals, some insects)

Males are heterogametic (XY), females are homogametic (XX).
The Y chromosome carries a dominant sex-determining gene (SRY in mammals).

ZZ/ZW System (e.g., birds, some reptiles, some fish)

Males are homogametic (ZZ), females are heterogametic (ZW).
The W chromosome determines femaleness, but mechanisms vary.

Haplodiploidy (e.g., bees, ants, wasps)

Females are diploid (fertilized eggs), males are haploid (unfertilized eggs).
A single gene locus (CSD in honeybees) determines whether an individual develops as a female.

Environmental Sex Determination

Temperature-Dependent Sex Determination (TSD) (e.g., crocodiles, some turtles)

Incubation temperature during embryonic development influences sex.

Social Sex Determination (e.g., some fish, like clownfish)

Individuals can change sex depending on social hierarchy or environmental cues.

Why Sex Determination Systems Are Short-Lived in Evolutionary Time

Despite their diversity, sex determination systems tend to be evolutionarily unstable. Several factors contribute to their frequent replacement or modification:

Degradation of Sex Chromosomes

The Y or W chromosome often accumulates mutations, loses genes, and degrades over time.
In some species (e.g., certain rodents), the Y chromosome has disappeared entirely, leading to new mechanisms of male determination.

Turnover and Evolutionary Transitions

Novel sex-determining genes can arise on autosomes, leading to shifts in sex determination mechanisms.
For example, in some fish and amphibians, sex determination has changed multiple times in a relatively short evolutionary period.

Selection Pressures and Sexual Conflict

Sexually antagonistic selection (where genes beneficial for one sex are harmful to the other) can drive changes in sex-determining loci.
This can lead to the evolution of new sex-determining factors on different chromosomes.

Hybridization and Polyploidy

In plants and some animals, hybridization between species or polyploidy events can disrupt existing sex-determination mechanisms, leading to rapid shifts.

Environmental Influence

Climate change can disrupt temperature-dependent sex determination, leading to selection for genetic sex-determination mechanisms.
In some reptiles, populations with TSD are evolving towards genetic sex determination to avoid skewed sex ratios due to rising temperatures.

Conclusion

Sex determination is a rapidly evolving trait because it is controlled by relatively few genes that are under strong selection pressures. The instability of sex chromosomes, environmental effects, and genetic conflicts all contribute to frequent evolutionary transitions in how sex is determined across different animal lineages.

A recent study shows that the California two-spot octopus uses Z0/ZZ with females being Z0, a system that appears to have been stable for some 480 million years. What are some reasons for this stability?

The California two-spot octopus (Octopus bimaculoides) has been found to use a Z0/ZZ sex determination system, where females are Z0 (lacking a second sex chromosome) and males are ZZ. The remarkable stability of this system—persisting for an estimated 480 million years-is unusual given that many sex-determining systems tend to change over shorter evolutionary timescales. Several factors may explain this exceptional stability:

Lack of Sex Chromosome Degradation
One of the main drivers of sex chromosome turnover in other taxa is the progressive degradation of the sex-limited chromosome (e.g., the Y chromosome in mammals). However, in the Z0 system, females simply lack a second sex chromosome rather than possessing a highly degraded W or Y equivalent. This eliminates the problem of accumulating deleterious mutations on a non-recombining sex chromosome, thereby reducing the pressure to evolve an alternative system.
Robust and Conserved Genetic Regulation
The genes responsible for sex determination in octopuses may be highly conserved and functionally robust, reducing the likelihood of a transition to a new system. If the key genes that trigger male and female differentiation are located on autosomes rather than on the Z chromosome itself, sex determination remains stable even if minor chromosomal rearrangements occur.
Low Recombination and Structural Stability
If the Z chromosome in octopuses has low recombination in males, it could maintain structural integrity over long periods without significant genetic loss. Additionally, chromosomal rearrangements that often drive sex chromosome turnover in other groups may be less common in cephalopods, preserving the existing system.
Absence of Strong Sexual Conflict Over Sex Determination
Sexually antagonistic selection (where genes beneficial for one sex are harmful for the other) often drives the evolution of new sex-determining loci in other animals. In octopuses, however, sex-specific traits may be determined primarily by hormonal or epigenetic factors, reducing the need for alternative sex chromosome configurations.
Evolutionary Constraints on Cephalopods
Cephalopods, including octopuses, have highly derived developmental and neurological systems, making them distinct from many other molluscs and animals. It is possible that fundamental constraints on their genetic and developmental networks make sex chromosome transitions less likely, as any major disruption to the existing system could have detrimental effects on development or reproductive success.
Environmental and Ecological Stability
In species with environmentally influenced sex determination, climate shifts can drive changes in sex determination mechanisms. However, octopuses rely strictly on genetic sex determination, shielding them from environmental pressures that might otherwise cause rapid shifts in sex chromosome systems.
Conclusion

The Z0/ZZ sex determination system in the California two-spot octopus has likely remained stable due to a combination of chromosomal integrity, lack of degrading sex chromosomes, conserved genetic regulation, and minimal sexual conflict over sex determination. These factors have protected the system from the common evolutionary pressures that drive sex chromosome turnover in many other animal lineages.

But there is one method which appears to be stable, at least it has been in a species of octopus, the Californian two-spot octopus, Octopus bimaculoides, for some 480 million years, ever since the octopuses and nautilus diverged shortly after the Cambrian.

The additional problem for creationists, other than the obvious one that if there is a stable method of sex-determination, why their designer didn't make it the universal method, is that it has been stable since almost 480 million years before creationists believe there was an Earth to have evolving life on.

This discovery, made by a team from the University of Oregon, is the subject of an open access paper in Current Biology and is explained in a news item from the University of Oregon:

Octopuses have some of the oldest known sex chromosomes
The octopus just revealed another one of its secrets: what determines its sex.

University of Oregon researchers have identified a sex chromosome in the California two-spot octopus. This chromosome has likely been around for 480 million years, since before octopuses split apart from the nautilus on the evolutionary tree. That makes it one of the oldest known animal sex chromosomes.
The finding also is evidence that octopuses and other cephalopods, a class of sea animals that includes squid and nautiluses, do use chromosomes to determine their sex, answering a longstanding mystery among biologists.

Cephalopods are already such interesting creatures, and there are so many things we’re still learning about them, especially in neuroscience. This is just showing one more interesting thing about them: They have really ancient sex chromosomes.

Gabrielle C. Coffing, lead author
Institute of Ecology and Evolution
University of Oregon, Eugene, OR, USA.

Coffing, Kern and their team described the findings Feb. 3 in the journal Current Biology.

In humans and most mammals, sex is determined largely by chromosomes. But “there’s a tremendous amount of diversity” in how animals determine their sex, Kern said. So scientists couldn’t assume the same was true for octopuses.

In turtles, for instance, sex is determined by the temperature at which the eggs are incubated. Some fish have a gene that determines sex, but not a whole chromosome. Even in humans, the X/Y sex chromosome system isn’t as clear-cut as it might look on paper; gene mutations or inheriting extra sex chromosomes can lead to development that doesn’t neatly fit in a male/female binary.

Plus, because cephalopods aren’t standard lab animals, like mice or fruit flies, they haven’t been subject to nearly as much genetic exploration. Scientists have sequenced the genomes of a handful of octopus species, but they can’t link genes to specific traits the way they can in mice or even humans.

When UO researchers recently sequenced the DNA of a female California two-spot octopus, they found something unexpected: a chromosome with only half the amount of genetic material. It looked different from all the others, and it hadn’t been found in male octopuses whose DNA was previously sequenced.

This particular chromosome had half the amount of sequencing data, which indicated there was only one copy. Then as we explored that more, we reached the conclusion that we must have stumbled upon a sex chromosome.

Gabrielle C. Coffing.

To confirm, the researchers sorted through other octopus genomic data previously collected by other researchers. Not all that data was clearly labeled as being from male or female octopuses.

But they found another example of the half-sized chromosome in another species of octopus. They also found it in squid, which diverged evolutionarily from octopuses somewhere between 248 and 455 million years ago. And after more digging, they also found evidence for the chromosome in the nautilus, a mollusk that split apart from the octopus approximately 480 million years ago.

The fact that these species share this unique chromosome suggests that it’s been around in some form for a very long time.

This indicates that their common ancestor had this similar sex determination system.

Gabrielle C. Coffing.

That’s somewhat unusual for sex chromosomes, Kern said. Because they directly impact reproductive capabilities, they’re subject to a lot of selective pressure and so tend to undergo rapid evolutionary change. But cephalopods seem to have found what works and have stuck with it.

Other ancient sex chromosomes have been discovered in plant groups like mosses and liverworts, which were some of the first plants to evolve. And insect sex chromosomes might be 450 million years old, but they’ve also changed a lot over time.

Kern and his colleagues initially thought octopuses might have a sex determination system similar to birds and butterflies, where males are ZZ and females are ZW. (Biologists have given sex determination systems where males have two copies of the same sex chromosome different letters, to avoid confusion with the XX/XY system where females have two copies of the same chromosome.)

But the team hasn’t yet found a W chromosome in an octopus. Alternatively, octopuses could use a sex determination system that only involves the Z chromosome — males have a pair, and females just have one. That’s still to be determined, Coffing said. For now, the octopus keeps some of its secrets.

Highlights

A new genome assembly reveals a hemizygous Z sex chromosome in female octopus
High density of LINE repeat elements is a signature of the Z chromosome
Syntenic relationships of genes on the Z chromosome are conserved across cephalopods
The cephalopod Z chromosome system has a single, ancient origin, including Nautilus

Graphical abstract

Summary
Octopuses, squids, and cuttlefishes—the coleoid cephalopods—are a remarkable branch in the tree of life whose members exhibit a repertoire of sophisticated behaviors.¹ As a clade, coleoids harbor an incredible variety of novel traits, including the most complex nervous system among invertebrates, derived camera-type eyes, and rapid adaptive camouflage abilities.^2,3 The burst of evolutionary novelty that distinguishes cephalopods is even more striking in a phylogenetic context; cephalopods are a deeply diverged lineage that last shared a common ancestor with other extant molluscs in the Cambrian period, roughly 550 million years ago.^4,5 With recent advances in genome sequencing technologies, we have the capability to explore the genomic foundations of cephalopod novelties. Here, using PacBio long-read sequencing of genomic DNA and Iso-Seq full-length mRNA sequencing, we provide a novel chromosome-scale reference genome and annotation for a female California two-spot octopus (O. bimaculoides). Our assembly reveals that the female octopus has just one sex chromosome, consistent with a ZO karyotype, whereas the male has two (ZZ), providing the first evidence of genetic sex determination in cephalopods. We use our assembly and annotation in combination with existing genomic information from other cephalopods to create the first whole-genome alignments from this group and demonstrate that the sex chromosome is of an ancient origin, before the radiation of extant cephalopods approximately 480 million years ago,⁴ and has been conserved to the present day in all cephalopod genomes available.

Overall, there is a lot for creationists to ignore, lie about or shout abuse at to make it go away. Firstly there is the fact that this arrangement appears to have been remarkably stable compared to other sex-determining systems, yet it arose early in the history of multicellular organisms, so there appears to be no reason why an intelligent designer didn't use the same system for all multicellular life, but instead used lots of different systems, all of which degenerate over time in ways that an omniscient, intelligent designer should have foreseen.

Then, of course there is the trivial problem of the divergence between the octopuses (and squids) and nautilus happened so long before creationists mythology says there was even a universe, let alone a planet with evolving and diversifying multicellular life on it.

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