Transition from Environmental to Partial Genetic Sex Determination inDaphniathrough the Evolution of a Female-Determining Incipient W Chromosome

Abstract

Sex chromosomes can evolve during the evolution of genetic sex determination (GSD) from environmental sex determination (ESD). Despite theoretical attention, early mechanisms involved in the transition from ESD to GSD have yet to be studied in nature. No mixed ESD-GSD animal species have been reported, except for some species of Daphnia, small freshwater crustaceans in which sex is usually determined solely by the environment, but in which a dominant female sex-determining locus is present in some populations. This locus follows Mendelian single-locus inheritance, but has otherwise not been characterized genetically. We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations of D. magna, and spans 3.6 Mb. Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium among the 36 associated SNPs. The region carries numerous genes involved in sex differentiation in other taxa, including transformer2 and sox9. Taken together, the region determining the genetic females shows characteristics of a sex-related supergene, suggesting that LG3 is potentially an incipient W chromosome despite the lack of significant additional restriction of recombination between Z and W. The occurrence of the female-determining locus in a pre-existing low recombining region illustrates one possible form of recombination suppression in sex chromosomes. D. magna is a promising model for studying the evolutionary transitions from ESD to GSD and early sex chromosome evolution.

Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages

“…inopinata , which are good, though very closely related biological species with reproductive isolation strongly supported by differences in male morphology [ 33 ]. Second, no concordant subdivision was observed in nuclear genes ( S1 Text , though this may be due to a lack of sufficient variability of these genes), and, third, and most importantly, individuals from the two super-clades readily interbreed, at least in the laboratory [ 100 ]. Therefore, to date there is no evidence of the existence of cryptic species within D .…”

Sex-Biased Gene Expression and Dosage Compensation on theArtemia franciscanaZ-Chromosome

“…For instance, there are over 20 crustacean genomes listed on NCBI (https://www.ncbi.nlm.nih.gov/genome/?term=txid6657[Organism:exp]; last accessed March 26, 2019), but these do not for the most part contain linkage information, and, aside from a few exceptions (Cui et al. 2015; Reisser et al. 2017; Baldwin-Brown et al.…”

Transgenerational response to early spring warming in Daphnia

“… GeneID ScaffoldID Start End S Pi θ Gene function Ref Tajima’s D Fu&Li’s D Fu&Li’s F Dapma7bEVm001004t1 scaffold00027 2877 6078 23 0.36 0.21 Serine arginine-rich splicing factor 7 Reisser et al . 40 2.13* 1.76** 2.25** Dapma7bEVm005301t1 scaffold00848 96321 97283 5 0.29 0.21 Aldo-keto reductase family 1, member C4 Reisser et al . 40 0.8 1.08 1.16 Dapma7bEVm002245t1 scaffold02003 35289 35935 2 0.3 0.21 Poly-U-binding splicing factor Half Pint Reisser et al .…”

“…The genome of the 30 genotypes used in this study has been sequenced and will be published elsewhere. Here, we use the sequenced genome to identify SNP polymorphisms at 15 candidate genes previously associated with environmentally driven local adaptation, including male formation and the induction of sexual reproduction 40 , 41 by mapping the sequences of the candidate genes against the reference genome of D. magna 2.4 (NBCI: LRGB00000000.1). The panel of SNPs at the 15 candidate genes is shown in Table S2 .…”

“…We quantified WGP and TGP as changes in trait values of fitness-linked life history traits between environments and across generations. We quantified genetic responses to photoperiod as mean trait differences among populations and as genetic divergence at 15 candidate genes, previously linked to environmentally driven local adaptation 40 , 41 . We also performed a gene-traits association analysis between the life history traits measured in the parental generation and the 15 candidate genes in an effort to identify the genetic basis of fitness-linked life history traits responding to photoperiod and temperature cues.…”