Nautilus sex determination is unique among cephalopods.

Mechanisms for sex determination are highly diverse among animals and can evolve rapidly across taxonomic groups. This fundamental process dictates an animal's sexual fate and ultimately its development. Recent research has suggested that cephalopods follow a ZZ/Z0 sex determination (where males are homozygous and females are hemizygous) that originated at least 480 million years ago, making it one of the oldest conserved sex determination systems known for animals.¹ By combining phenotypic sex data with three genomic datasets from the highly divergent cephalopod clade Nautiloidea (including the raw data from 2 published genomes, 28 low-coverage whole genomes, and 63 restriction-site associated DNA sequencing (RAD-seq) datasets from 6 species across 9 populations), we suggest that nautiloids follow an XX/XY sex determination system, where females are homogametic and males are heterogametic. We also identified chromosome #4 as the X chromosome rather than the Z chromosome, as previously suggested.¹ Lastly, we identified five scaffolds representing a putative Y chromosome, based on combined evidence from Bayesian analyses, differences in genome coverage across sexes, and extremely low levels of heterozygosity. Our study identified 36 genes on the putative Y scaffolds, 30 of which are known to be linked to male reproductive functions and include sexual markers conserved across bilaterians. Our findings thus add to previous assumptions about sex determination in cephalopods and their common ancestor and illuminate the diversity of sexual systems and their remarkable turnover in animals.