Limited evidence of a genetic basis for sex determination in the common creek chub, Semotilus atromaculatus

Abstract

Sexual reproduction is almost universal in vertebrates; therefore, each animal species which uses it must have a mechanism for designating sex as male or female. Fish, especially, have a wide range of sex determining systems. In the present study, we aimed to identify a genetic basis for sex determination in the common creek chub (Semotilus atromaculatus) using genotyping‐by‐sequencing data. No sex‐associated markers were found by RADSex or a GWAS using GEMMA; however, Weir and Cockerham locus‐specific FST analysis and discriminant analysis of principal components revealed genetic differentiation between the sexes at several loci. While no explicit sex determination mechanism has been yet discovered in creek chub, these loci are potential candidates for future studies. Incompatible systems are thought to increase reproductive isolation but interspecific hybridization is common among groups such as cyprinid minnows; thus, studies such as ours can provide insight into hybridization and evolutionary diversification of this clade. We also highlight technical challenges involved in studying sex determination in evolutionary groups with extremely variable mechanisms and without heteromorphic sex chromosomes.

A high-quality reference genome for the common creek chub,Semotilus atromaculatus

“…The contiguity and completeness of this assembly makes it a valuable resource for genomic studies of non-model leuciscid fish. The high contiguity of sequence enabled by PacBio will allow recovery of genetic architecture of traits where linkage of multiple loci might be extremely relevant (for example, examining the genetic basis of sex determination; Meuser et al 2022).…”

“…Creek chub are not known to have a large sex determining region (Meuser et al 2022) or heteromorphic sex chromosomes (Gold et al 1979), which could be part of the reason why there are no other large regions lacking synteny between the two genomes.…”

“…In consequence, previous genomic studies of creek chub have relied on artificial reference genomes or reference genomes from distantly related taxa (e.g. Meuser et al 2022).…”

Identification of sex-determining loci in hybridizing Catostomus fish species

“…We also identified candidate sex-associated loci using DAPC (discriminant analysis of principal components, Jombart 2008), implemented through the adegenet package in R (Jombart et al 2010) and following analyses from Junker et al 2020 andMeuser et al 2022. This approach uses a principal components analysis to identify major axes of genetic variation, then uses discriminant analysis with sex as the grouping variable to identify sexassociated loci.…”

Sex chromosome evolution: The remarkable diversity in the evolutionary rates and mechanisms

“…In a small minnow, the common creek chub, Meuser et al (2022) find almost zero sex-linked markers with a RAD-seq approach, providing insights into the limitations of this technique for species with poorly differentiated sex chromosomes. Applying a similar RAD-seq pipeline, Keating et al (2022) successfully identify male-specific markers in a banded gecko, suggesting the presence of a XX/XY sex chromosome system.…”