| INVESTIGATION Wolbachia in the Drosophila yakuba Complex: Pervasive Frequency Variation and Weak Cytoplasmic Incompatibility, but No Apparent Effect on Reproductive Isolation Brandon S. Cooper,*,1 Paul S. Ginsberg,* Michael Turelli,* and Daniel R. Matute† *Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, California 95616 and †Biology Department, University of North Carolina, Chapel Hill, North Carolina 27510 ORCID IDs: 0000-0002-8269-7731 (B.S.C.); 0000-0003-1188-9856 (M.T.); 0000-0002-7597-602X (D.R.M.) ABSTRACT Three hybridizing species—the clade [(Drosophila yakuba, D. santomea), D. teissieri]—comprise the yakuba complex in the D. melanogaster subgroup. Their ranges overlap on Bioko and São Tomé, islands off west Africa. All three species are infected with Wolbachia—maternally inherited, endosymbiotic bacteria, best known for manipulating host reproduction to favor infected females. Previous analyses reported no cytoplasmic incompatibility (CI) in these species. However, we discovered that Wolbachia from each species cause intraspecific and interspecific CI. In D. teissieri, analyses of F1 and backcross genotypes show that both host genotype and Wolbachia variation modulate CI intensity. Wolbachia-infected females seem largely protected from intraspecific and interspecific CI, irrespective of Wolbachia and host genotypes. Wolbachia do not affect host mating behavior or female fecundity, within or between species. The latter suggests little apparent effect of Wolbachia on premating or gametic reproductive isolation (RI) between host species. In nature, Wolbachia frequencies varied spatially for D. yakuba in 2009, with 76% (N = 155) infected on São Tomé, and only 3% (N = 36) infected on Bioko; frequencies also varied temporally in D. yakuba and D. santomea on São Tomé between 2009 and 2015. These temporal frequency fluctuations could generate asymmetries in interspecific mating success, and contribute to postzygotic RI. However, the fluctuations in Wolbachia frequencies that we observe also suggest that asymmetries are unlikely to persist. Finally, we address theoretical questions that our empirical findings raise about Wolbachia persistence when conditions fluctuate, and about the stable coexistence of Wolbachia and host variants that modulate Wolbachia effects. KEYWORDS frequency variation; hybridization; host-microbe interactions; mutualism; reproductive isolation NDOSYMBIOTIC Wolbachia bacteria infect about half for their effects on host reproduction (Laven 1951; Yen and Eof all insect species (Werren and Windsor 2000; Zug Barr 1971; Rousset et al. 1992; O’Neill et al. 1997), which, and Hammerstein 2012), as well as many other arthro- in Drosophila, includes cytoplasmic incompatibility (CI) and pods (Bouchon et al. 1998; Jeyaprakash and Hoy 2000; male killing (Hoffmann et al. 1986; Hoffmann and Turelli Hilgenboecker et al. 2008; Weinert et al. 2015). Hosts can 1997; Hurst and Jiggins 2000). Because host females verti- acquire Wolbachia horizontally from distantly related taxa, cally transmit Wolbachia, natural selection favors Wolbachia cladogenically from common ancestors, or through introgres- variants that enhance host fitness (Prout 1994; Turelli 1994; sion (O’Neill et al. 1992; Lachaise et al. 2000; Raychoudhury Haygood and Turelli 2009). Many Wolbachia infections et al. 2009; Hamm et al. 2014). Wolbachia gained attention do not appreciably manipulate host reproduction—wAu in D. simulans, wSuz in D. suzukii, and wMel in D. melanogaster Copyright © 2017 by the Genetics Society of America (Hoffmann 1988; Hoffmann et al. 1996; Kriesner et al. 2013; doi: 10.1534/genetics.116.196238 Hamm et al. 2014). These infections presumably persist Manuscript received July 25, 2016; accepted for publication October 24, 2016; fi published Early Online November 7, 2016. through positive effects on host tness (Hoffmann and Turelli Supplemental material is available online at http://www.genetics.org/cgi/content/ 1997) that are mostly not understood, although viral protec- full/genetics.116.196238/DC1. 1Corresponding author: Division of Biological Sciences, 32 Campus Dr., University of tion and nutritional supplementation have been documented Montana, Missoula, MT 59812. E-mail: [email protected] (Hedges et al. 2008; Teixeira et al. 2008; Brownlie et al. Genetics, Vol. 205, 333–351 January 2017 333 2009; Martinez et al. 2014; Cattel et al. 2016a). Similarly, interactions between Wolbachia and their hosts. Wolbachia even for the best understood CI systems, it is unknown how that cause CI in D. recens become male killers when intro- Wolbachia increase host fitness so that infections tend to gressed into certain strains of the sister species D. subquinaria spread from low frequencies. For example, the spread of (Jaenike 2007). Wolbachia from D. melanogaster that cause wRi in D. simulans has been studied for decades, and was limited CI in their natural host induce nearly complete CI thought to have “bistable” dynamics, in which strong CI in D. simulans (Poinsot et al. 1998), and complete CI in counteracted the effects of imperfect maternal transmission Ae. aegypti (Walker et al. 2011). Thus, the fitness effects and negative fitness effects, such that infection frequencies of Wolbachia may fluctuate across abiotic and genetic envi- tended to rise only once a threshold frequency was passed ronments, altering predictions about the spread and mainte- (Turelli and Hoffmann 1991, 1995). However, more recent nance of Wolbachia infections. data suggest that wRi must have a net positive effect on Three hybridizing species—D. yakuba, D. santomea, and D. simulans fitness, allowing it to systematically increase D. teissieri—comprise the yakuba complex within the D. mel- from low frequencies (Kriesner et al. 2013). anogaster subgroup (Lachaise et al. 2000). The human Simple models describe Wolbachia infection frequency commensal D. yakuba is widely distributed throughout sub- dynamics. The spread and maintenance of CI-inducing Wol- Saharan Africa and on the islands of Bioko and São Tomé bachia depend primarily on the proportion of uninfected ova in west Africa. D. yakuba’s sister species, D. santomea, is en- produced by infected females (m), the relative hatch rate of demic to the volcanic island São Tomé. On São Tomé, uninfected eggs fertilized by infected males (H), and the rel- D. yakuba occurs at low elevations (below 1450 m), and ative fecundity—or any factors that affect host fitness—of D. santomea occurs in higher altitude mist forests (between infected females relative to uninfected females (F) (Caspari 1153 and 1800 m), but D. yakuba and D. santomea occasion- and Watson 1959; Hoffmann et al. 1990). When Wolbachia ally hybridize in the midlands of the extinct volcano of Pico de produce F(12m) , 1, infections tend to decrease in fre- São Tomé (Llopart et al. 2005a,b)—hybrids represent about quency when rare, and require stochastic effects for initial 3% of flies sampled between 1000 and 1600 m (Comeault establishment (Jansen et al. 2008). If F(12m) , 1, but et al. 2016). The third species of this clade, D. teissieri [sister F(12m) . H, Wolbachia frequencies will tend to increase to the pair (D. yakuba, D. santomea)], has a fragmented dis- once the infection is sufficiently common, such that infected tribution throughout tropical Africa produced by the loss of males lower the effective fecundity of uninfected females rain forests. D. teissieri occurs on Bioko, but is absent from below that of infected females. CI-causing infections that São Tomé (Lachaise et al. 1981; Devaux and Lachaise 1988; generate H , F(12m) , 1 lead to “bistable” dynamics Joly et al. 2010). Crosses between D. yakuba and D. santomea with stable equilibria at 0, and at a higher frequency denoted produce fertile F1 females; and, despite diverging from this ps, where 0.50 , ps # 1 (Barton and Turelli 2011). Bist- species pair at least 1 MYA (Monnerot et al. 1990; Long ability applies to Aedes aegypti mosquitoes transinfected with and Langley 1993; Bachtrog et al. 2006; Obbard et al. wMel Wolbachia from D. melanogaster that are being re- 2012), D. teissieri also produces fertile F1 females with both leased as a biocontrol of the dengue virus (McMeniman species in the laboratory (Turissini et al. 2015). Hence, hy- et al. 2009; Hoffmann et al. 2011; Walker et al. 2011; bridization with D. teissieri is possible, but its frequency in M. Turelli and N. H. Barton, unpublished results), but seems nature remains unclear. Mitochondrial genetic and genomic not to apply to natural Wolbachia infections (Fenton et al. analysis suggest that pervasive introgression has led to 2011; Kriesner et al. 2013; Hamm et al. 2014; Kriesner et al. shared cytoplasms in the yakuba complex (Lachaise et al. 2016). 2000; Llopart et al. 2005b; Bachtrog et al. 2006; Llopart The fitness effects of Wolbachia on their hosts depend on et al. 2014). However, the most recent analyses of introgres- environmental conditions, and on interactions with hosts. sion using whole genome data rely substantially on IMa2 For example, the fidelity of maternal transmission of wRi by analyses (Llopart et al. 2014), known to produce false posi- D. simulans increases under laboratory conditions (Turelli tives for migration when there are few loci, or when there is and Hoffmann 1995). In very low and in very high iron en- little genomic variation (Becquet and Przeworski 2009; vironments, wMel-infected D. melanogaster have higher fe- Cruickshank and Hahn 2014; Hey et al. 2015); both limita-