Restriction Site-Associated DNA Sequencing (RAD-seq) Reveals an Extraordinary Number of Transitions among Gecko Sex-Determining Systems

Abstract

Sex chromosomes have evolved many times in animals and studying these replicate evolutionary "experiments" can help broaden our understanding of the general forces driving the origin and evolution of sex chromosomes. However this plan of study has been hindered by the inability to identify the sex chromosome systems in the large number of species with cryptic, homomorphic sex chromosomes. Restriction site-associated DNA sequencing (RAD-seq) is a critical enabling technology that can identify the sex chromosome systems in many species where traditional cytogenetic methods have failed. Using newly generated RAD-seq data from 12 gecko species, along with data from the literature, we reinterpret the evolution of sex-determining systems in lizards and snakes and test the hypothesis that sex chromosomes can routinely act as evolutionary traps. We uncovered between 17 and 25 transitions among gecko sex-determining systems. This is approximately one-half to two-thirds of the total number of transitions observed among all lizards and snakes. We find support for the hypothesis that sex chromosome systems can readily become trap-like and show that adding even a small number of species from understudied clades can greatly enhance hypothesis testing in a model-based phylogenetic framework. RAD-seq will undoubtedly prove useful in evaluating other species for male or female heterogamety, particularly the majority of fish, amphibian, and reptile species that lack visibly heteromorphic sex chromosomes, and will significantly accelerate the pace of biological discovery.

Evolutionary stability of sex chromosomes in snakes

“…This supports the hypothesis of the stability of GSD when compared with ESD ('GSD as an evolutionary trap' hypothesis), although ESD might be ancestral for squamates, and maybe all amniotic vertebrates [1,2,3]. The strong evolutionary stability of differentiated sex chromosomes in advanced snakes has important practical and theoretical consequences.…”

“…in viviparous mammals and birds), which led some authors to conclude that the stability versus non-stability of sex chromosomes corresponds to thermal strategies [4]. Nevertheless, cytogenetic data suggest that significant conservation in sex chromosomes can also be widespread in many lineages of ectothermic amniotes [2,3], but molecular data demonstrating the conservation of sex chromosomes comparable with endotherms in both time and taxonomical scale has been presented only recently and to date just for a single group of ectothermic amniotes (in iguanas) [5].…”

Mammalian X homolog acts as sex chromosome in lacertid lizards

“…The case of the therian X and lacertid Z supports this hypothesis. However, it was estimated that sex chromosomes evolved around 35 times just in squamate reptiles (Gamble et al, 2015) and thus probably more than 40 times in amniotes (reviewed in Johnson Pokorná and Kratochvíl, 2016) and we still do not have enough information on the homology of sex chromosomes to enable us to test whether some chromosomes are indeed more likely to evolve into sex chromosomes than others. Taking into account the relatively small number of chromosomes in the ancestral amniote karyotype and the large number of reconstructed independent emergences of sex chromosomes, it cannot yet be rejected whether some chromosomes, such as those homologous to avian Z or mammalian X, evolved repeatedly into sex chromosomes more often than just by chance.…”

“…The ancestral sex-determining system for this important animal clade has not yet been satisfactorily reconstructed. Some authors recently argued that it was likely to be ESD (Pokorná and Kratochvíl, 2009;Johnson Pokorná and Kratochvíl, 2016), and that GSD, and hence sex chromosomes, evolved multiple times within this clade and remained notably stable after their emergence (Pokorná and Kratochvíl, 2009;Johnson Pokorná and Kratochvíl, 2016;Gamble et al, 2015). However, evolutionary transitions from GSD to ESD are theoretically possible and have been experimentally induced in a reptile in the laboratory (Quinn et al, 2007;Holleley et al, 2015).…”

Sex determination by multiple sex chromosomes in Xenopus tropicalis

“…Previous work using the most modern, highly sensitive restriction site-associated DNA (RAD)-tag approach, well-suited to find sex-linked DNA sequence polymorphism and through this define sex chromosomes (16,17), failed to uncover any region in the X. tropicalis genome that shows sexspecific heterozygosity (18) and was unable to provide further information about the genetics of sex determination. Thus, Roco et al (8) had to come back to the more classic tools of genetics.…”