Gene flow and gene flux shape evolutionary patterns of variation in Drosophila subobscura

Abstract

Gene flow (defined as allele exchange between populations) and gene flux (defined as allele exchange during meiosis in heterokaryotypic females) are important factors decreasing genetic differentiation between populations and inversions. Many chromosomal inversions are under strong selection and their role in recombination reduction enhances the maintenance of their genetic distinctness. Here we analyze levels and patterns of nucleotide diversity, selection and demographic history, using 37 individuals of Drosophila subobscura from Mount Parnes (Greece) and Barcelona (Spain). Our sampling focused on two frequent O-chromosome arrangements that differ by two overlapping inversions (O_ST and O₃₊₄), which are differentially adapted to the environment as observed by their opposing latitudinal clines in inversion frequencies. The six analyzed genes (Pif1A, Abi, Sqd, Yrt, Atpα and Fmr1) were selected for their location across the O-chromosome and their implication in thermal adaptation. Despite the extensive gene flux detected outside the inverted region, significant genetic differentiation between both arrangements was found inside it. However, high levels of gene flow were detected for all six genes when comparing the same arrangement among populations. These results suggest that the adaptive value of inversions is maintained, regardless of the lack of genetic differentiation within arrangements from different populations, and thus favors the Local Adaptation hypothesis over the Coadapted Genome hypothesis as the basis of the selection acting on inversions in these populations.

Introduction

Chromosomal inversions are a major mechanism shaping the level and distribution of genomic diversity within and between species. Inversion polymorphism has been described in several Drosophila species (Krimbas and Powell, 1992) and has been observed to vary seasonally, and with altitude and latitude (Dobzhansky, 1943; Krimbas, 1993; Kennington et al., 2006). The rich polymorphism in paracentric inversions found in Drosophila subobscura (Krimbas and Powell, 1992; Krimbas, 1993) has had an important role in demonstrating the adaptive role of inversions, as shown by the coinciding latitudinal clines on inversion frequencies found in Palearctic and also in colonizing populations (Krimbas and Loukas, 1980; Prevosti et al., 1988; Balanyà et al., 2003). Moreover, changes in chromosomal polymorphism matching global warming (Solé et al., 2002; Balanyà et al., 2004, 2006) also suggest the adaptive value of inversions in D. subobscura. Despite the evidence for an adaptive role of inversions, the genetic and mechanistic basis underlying their role in adaptation remains unknown.

Several hypotheses have been suggested to explain the maintenance of inversion polymorphism in populations (reviewed in Hoffmann and Rieseberg, 2008). The coadaptation hypothesis (Dobzhansky, 1950) suggests that natural selection maintains favorable combinations of alleles that interact epistatically within and between arrangements in a certain population. The local adaptation hypothesis predicts that inversions will spread in a population at migration-selection balance when they capture at least two advantageous alleles that are individually adapted to local conditions (Kirkpatrick and Barton, 2006). Particularly, it explains that the inversion will establish a cline when interacting populations are distributed along an environmental gradient. In both hypotheses, the reduced recombination between inversion heterokaryotypes avoids gene exchange with other genetic backgrounds, but epistasis is only a requirement in the former one.

The low gene transfer between inversions (gene flux) for genes located inside the inverted region observed in some Drosophila species is in agreement with both hypotheses (Laayouni et al., 2003; Schaeffer et al., 2003; Munté et al., 2005; Hoffmann and Rieseberg, 2008). However, despite the fact that Dobzhansky (1950) detected a lower fitness of heterozygous individuals from different populations of D. pseudoobscura in laboratory experiments, molecular studies failed to detect genetic differentiation within inversions sampled from different populations (Schaeffer et al., 2003). In D. subobscura, high genetic differentiation between European populations was detected when chromosomal arrangements were used as markers, as their frequency widely varies between populations (Krimbas, 1993). However, given that these chromosomal arrangements are under strong selection (Prevosti et al., 1988; Balanyà et al., 2006), gene flow between populations would likely be underestimated using the inversions themselves as makers. Interestingly, low levels of genetic differentiation between European populations of D. subobscura were observed using molecular markers such as restriction fragment-length polymorphisms (Rozas et al., 1995) and microsatellite loci (Pascual et al., 2001). Consequently, gene flow and gene flux could be changing the genetic content of inversions from widely separated populations. Thus, the analysis of candidate genes undergoing selection in D. subobscura could allow contrasting different hypotheses explaining the maintenance of inversion polymorphism in populations.

In the present study we analyze DNA sequence variation and differentiation at six genes across the O-chromosome within and between two populations of D. subobscura from the western and eastern mediterranean: Barcelona (Spain) and Mount Parnes (Greece). Despite being located at approximately the same latitude, these populations differ substantially in inversion frequencies (Krimbas and Loukas, 1980; Krimbas, 1993; Araúz et al., 2009). Our sampling focused on homokaryotypic individuals carrying either of two arrangements, O_ST and O₃₊₄, selected because they are the more common arrangements in both populations and yet show significant latitudinal clines of opposite sign (Prevosti et al., 1988). Furthermore, differential basal expression of the Hsp70 gene, a candidate for thermal adaptation, was detected between carriers of these two arrangements from the same population (Calabria et al., 2012). Thus, the six nuclear genes studied in the present work (Table 1) were chosen, because they are candidates to thermal adaptation (Laayouni et al., 2007) and because of their cytological location across the O-chromosome (Figure 1).

Table 1. Chromosomal location of the six genes (newly determined by in situ hybridization), the sequenced fragment length and primers used in the amplification and sequencing.

Gene symbola	Chromosome location	Length (bp)	Primers
Pif1A (CG42599)	79Db	1820	5′-AATGTATCACAAGGAGAACG-3′c,d,e
			5′-CTCCTGGTAGTACTGCAGAT-3′c,d,e
			5′-GTCCAACTATGGTTGATGCC-3′d
			5′-ACGACTTTACAGCTAGCTGG-3′d
Abi (CG9749)	81Ab	1566	5′-CCTTGTCCGCATAGTAGTCA-3′c,d
			5′-GTGAGTAGTAATTAGGTTCG-3′c,d
			5′-ACTCACGTGGCATACTGCTC-3′d
Sqd (CG16901)	85Db	1436	5′-AACTAACCTTGTTCCTCTCC-3′c,e
			5′-TTACACACGCTTCGTCAGTT-3′c,d,e
			5′-CATTATAGTAGCCACCAGGA-3′d
			5′-TCTTGGTGGTTGTTGCTGTG-3′d
Yrt (CG9764)	86E	911	5′-CTGGACATCATCGAGAAGGA-3′c,d,e
			5′-ACATTGGCCAGCTTCACTTG-3′c,e
			5′-AACTGGAGTCTGGCTGGCGT-3′d
			5′-TACGCCGGATCATCGTTGCT-3′d
Atpα (CG5670)	87C	1490	5′-TCATAAGATCTCTCCTGAGG-3′c,d,e
			5′-GCAATATCCTCAACGGTCTC-3′c,d,e
			5′-CATCATTGAGGCGCGCAGCT-3′d
			5′-CCAGGGCTAGTTCTATCGTA-3′d
Fmr1 (CG6203)	98Ab	1984	5′-ACAGCCAAGTCGTTCTACCA-3′c,d,e
			5′-CCATTCACCAGACCTTCCTT-3′c,d,e
			5′-GGCAAGGTAATCGGCAAGAA-3′d

Abbreviations: Abi, Abelson interacting protein; Atpα; Na pump α-subunit; Fmr1; Fragile X mental retardation; Pif1A, PFTAIRE-interacting factor 1A; Sqd, Squid; Yrt; Yurt.

^aGene symbol of the homologous gene in D. melanogaster and annotation symbol in brackets.

^bMislocated genes in Laayouni et al., 2007.

^cPrimers used in the amplifications.

^dPrimers used for sequencing.

^ePrimers previously designed (Laayouni et al., 2007).

Figure 1.

Top: location of the six gene regions studied in the O₃₊₄ and O_ST arrangements in comparison with the ancestral O₃ arrangement. The O-chromosome is divided in sections SI and SII, where SI is the fragment covered by the overlapped inversions O₃₊₄. Bottom: sequenced fragment for each locus. Exonic regions are identified using gray boxes, and intronic regions are represented by lines. For each gene, the size of the sequenced fragment is given in parentheses.

Materials and methods

Fly samples, DNA isolation and sequencing

D. subobscura isochromosomal lines were established from two distant European populations (Barcelona, Spain, and Mt. Parnes, Greece) following the pattern of genetic crosses described in Mestres et al. (1998). Chromosomal arrangements for each line were determined by analysis of polytene chromosomes of third instar larvae (Figure 2). A total of 25 O₃₊₄ lines (13 from Barcelona and 12 from Mt. Parnes) and 12 O_ST lines (5 from Barcelona and 7 from Mt. Parnes) were non-lethal and sequenced in the present study. The structure of O_ST and O₃₊₄ arrangements is represented in Figure 1. It is worth considering that O₃ and O₄ inversions are never found alone in natural populations. D. madeirensis and D. pseudoobscura were used for interspecific analyses. D. madeirensis sequences were obtained from a laboratory strain (Supplementary Table S1) and D. pseudoobscura sequences were downloaded from Flybase (http://flybase.org).

Figure 2.

Polytene chromosome of third instar larvae preparation of O₃₊₄/O_ST heterokaryotype. The two overlapped inversions (right of the image) are located opposite to the centromere, in region SI. A full color version of this figure is available at the Heredity journal online.

Six genes distributed across the O-chromosome were studied (Figure 1): Pif1A (PFTAIRE-interacting factor 1A), Abi (Abelson interacting protein), Sqd (Squid), Yrt (Yurt), Atpα (Na pump α-subunit) and Fmr1 (Fragile X mental retardation). They were selected because they showed differential expression between laboratory populations maintained at different temperature regimes (Laayouni et al., 2007). Although their cytological location had been previously reported, new in situ hybridizations have been carried out in the present study, following standard protocols (Laayouni et al., 2000). After thorough inspection, four out of six genes proved to be previously mislocalized and the correct locations are given in Table 1. Primers used for amplification and sequencing reaction are also listed in Table 1. Some primers were reported in Laayouni et al. (2007) and others were designed in the present study using Primer Designer v1.01 (1990 Scientific and Educational Software, Durham, NC, USA). Single fly genomic DNA was extracted using Gentra Puregene Cell Kit (Qiagen, Chatsworth, CA, USA).

PCR amplifications were carried out in a 25-μl total volume with 3.5 μl buffer 10 × , 3 μl deoxyribonucleotide triphosphates (1 mℳ), 0.2 μl Taq DNA Polymerase (Qiagen), 0.5 μl forward primer (10 μℳ), 0.5 μl reverse primer (10 μℳ), 16.3 μl water and 1 μl DNA. Amplification conditions were 4 min at 94 °C of initial denaturation, and 35 cycles with 30 s at 94 °C, 30 s at the required annealing temperature (56 °C for all genes with the exception of Abi and Sqd at 50 °C) and 3 min at 72 °C, and 5 min at 72 °C of final extension. PCR amplification products were purified with ExoI-SAP (New England, BioLabs, Ipswich, MA, USA-Promega, Madison, WI, USA). Sequencing reactions were carried out using the ABI Prism BigDye Terminators 3.1 cycle sequencing kit (Applied Biosystems, Foster City, CA, USA), and sequences read on an ABI 3730 sequencer at the Biotechnology Resource Center of Cornell University. Follow-up PCR and sequencing of some genes was done at the University of Barcelona as follows. PCR amplification reactions were carried out in a 15-μl total volume with 3 μl buffer 10 × , 3 μl deoxyribonucleotide triphosphates (1 mℳ), 0.45 μl dimethyl sulfoxide, 0.3 μl Phire Hot Start DNA Polymerase (Finnzymes, Thermo Scientific, Waltham, MA, USA), 0.75 μl forward primer (10 μℳ), 0.75 μl reverse primer (10 μℳ), 5.75 μl water and 1 μl DNA. Amplification conditions were 30 s at 98 °C of initial denaturation, and 35 cycles with 5 s at 98 °C denaturation, 5 s at the required annealing temperature (56 °C for all genes with the exception of Abi and Sqd at 50 °C) and 90 s at 72 °C, and 7 min at 72 °C for final extension. PCR amplification products were purified and sequenced as before, but at the Serveis Cientifico-Tècnics at Universitat de Barcelona. Sequences were assembled with SeqMan II (DNASTAR) and aligned with Clustal W (Thompson et al., 1994) implemented in BioEdit v7 (Hall, 1999).

Data analysis

The six analyzed genes can be divided into two groups according to their cytological location (Figure 1). The Fmr1 gene is located within inversion O₄ in region SI, which includes the chromosome segment covered by the O₃₊₄ arrangement. The other genes (Pif1A, Abi, Sqd, Yrt and Atpα) are located in region SII, which includes the colinear chromosome segment that can probably freely recombine between arrangements O_ST and O₃₊₄ (Pegueroles et al., 2010a). Distance in base pairs of each gene to the nearest inversion breakpoints was estimated, assuming that all cytological bands contain the same amount of DNA and that the length of the O-chromosome of D. subobscura is equivalent to chromosome 2 of D. pseudoobscura (Pegueroles et al., 2010b). The exonic and intronic regions of each gene sequence were determined by blasting against the genome of D. pseudoobscura, and the resulting expected proteins were compared with the corresponding D. pseudoobscura proteins to ensure the correct assignment of the exons. Exonic and intronic composition of each gene is shown in Figure 1.

Analyses were carried out separately for each gene and also for the concatenated data set. The Abi gene was not included in the final concatenate data set because of the insufficient number of individuals. For this gene, sequencing of some individuals failed because of the presence of a gene duplication (data not shown). Only individuals with sequences for the five remaining genes were used in the concatenation. Gene concatenation was carried out using the Concatenator v1 software (Pina-Martins and Paulo, 2008). DnaSP v5 (Librado and Rozas, 2009) was used to estimate the standard parameters for each population and arrangement.

We estimated the number of haplotypes (h), number of polymorphic sites (S), the number of singletons, nucleotide diversity (π; Nei, 1987), nucleotide diversity in synonymous sites and non-coding positions (π_sil; Nei and Gojobori, 1986) and heterozygosity in silent sites (θ_sil; Watterson, 1975). Comparisons in diversity values were assessed by Wilcoxon matched pairs tests using Statistica v6. Divergence per silent site (K_sil) between D. subobscura and D. madeirensis, or D. pseudoobscura (Nei and Gojobori, 1986), was also obtained. Genetic differentiation was assessed using Dxy (Nei, 1987), F_ST (Hudson et al., 1992) and Snn (Hudson, 2000), and its significance estimated after 10 000 replicates. These analyses were carried out excluding insertion–deletion events (indels).

Tajima's D (Tajima, 1989) and Fu and Li's D (Fu and Li, 1993) were used to test for neutrality. Fu and Li's D was computed using D. pseudoobscura as an outgroup, given the similar θ_sil and K_sil values considering D. madeirensis as the outgroup (see results). Population size changes were determined by the statistic R₂ (Ramos-Onsins and Rozas, 2002) and its significance was assessed by coalescent simulations using 1000 replicates considering either no recombination, free recombination, or level of recombination (ρ) determined from the observed sequence diversity using the composite likelihood method of Hudson (Hudson, 2001) implemented in LDhat v2.1 (http://www.stats.ox.ac.uk/~mcvean/LDhat). Gene genealogies were constructed using the neighbor-joining method with the maximum composite likelihood model implemented in the Mega v4 program (Tamura et al., 2007). Bootstrap values were obtained from 1000 replicates.

The age of inversions was estimated with the Fmr1 gene, as it is located inside the inversions, using two different approaches: using the silent nucleotide diversity of the two most divergent individuals (Rozas and Aguadé, 1994), and using mean silent nucleotide diversity of all individuals (Rozas et al., 1999), except those identified as recombinants. The number of substitutions per site and year was estimated using the divergence per silent site between D. subobscura and D. pseudoosbcura, assuming that the two species diverged 17.7 million years (Myr) ago, based on a large multilocus data set (Tamura et al., 2004), and 8 Myr ago, based on only one gene (Ramos-Onsins et al., 1998) but used for comparison with previous studies.

Results

Nucleotide variation

Genetic variability levels of the six genes within each arrangement (O₃₊₄ and O_ST) and for each population are presented in Table 2. In all cases, the number of haplotypes detected approached the number of sequences analyzed. No significant differences between populations were obtained neither in nucleotide diversity (π: Z=0.58, P=0.56) nor in the number of polymorphic sites (S: Z=0.04, P=0.97). When comparing the two arrangements within populations, no significant differences were detected for π (Z=0.31, P=0.75 for Barcelona population and Z=1.36, P=0.17 for Mt. Parnes population). The number of polymorphic sites within each arrangement was similar for all genes, except for Pif1A. This gene presented the highest nucleotide diversity, probably because of its larger proportion of intronic regions (Figure 1). Thus, nucleotide diversity, heterozygosity per site and divergence were subsequently analyzed using only synonymous sites and non-coding positions. The mean highest π_sil and K_sil values found in the Yrt gene (π_sil=0.036, K_sil-mad=0.078, K_sil-pseu=0.325) suggest that this gene might have a higher substitution rate. Genetic divergence from D. subobscura was always higher for D. pseudoobscura than for D. madeirensis, as expected from their phylogenetic relationships (Table 2).

Table 2. Nucleotide variation and divergence for each gene and arrangement (O₃₊₄ and O_ST) in MP and BC populations.

	Pif1A		Abi		Sqd		Yrt		Atpα		Fmr1
	MP	BC	MP	BC	MP	BC	MP	BC	MP	BC	MP	BC
O3+4
n	12	12	12	7	12	10	12	12	12	12	11	10
h	12	12	12	7	12	10	12	12	12	11	11	10
S	120	114	32	24	25	21	33	35	22	27	38	28
Singletons	55	42	20	15	16	14	18	21	9	16	25	18
π	0.021	0.022	0.005	0.006	0.005	0.005	0.010	0.010	0.005	0.005	0.005	0.004
πsil	0.023	0.023	0.012	0.014	0.006	0.006	0.034	0.035	0.015	0.016	0.009	0.008
θsil	0.026	0.024	0.017	0.015	0.008	0.007	0.042	0.041	0.013	0.019	0.012	0.010
Ksil-mad	0.034	0.032	0.013	0.013	0.030	0.028	0.078	0.078	0.018	0.018	0.025	0.025
Ksil-pseu	0.191	0.190	0.173	0.173	0.116	0.115	0.327	0.326	0.208	0.209	0.151	0.151
OST
n	5	7	2	3	5	6	5	6	5	6	4	6
h	5	7	2	3	5	5	5	6	4	6	4	6
S	82	95	11	16	11	9	23	27	17	12	26	34
Singletons	57	49	11	16	8	5	20	22	7	7	16	18
π	0.022	0.023	0.007	0.007	0.004	0.003	0.011	0.011	0.006	0.003	0.007	0.007
πsil	0.023	0.024	0.017	0.017	0.005	0.004	0.037	0.037	0.014	0.011	0.014	0.014
θsil	0.024	0.025	0.017	0.017	0.005	0.004	0.040	0.043	0.013	0.011	0.014	0.014
Ksil-mad	0.032	0.038	0.012	0.013	0.031	0.030	0.077	0.078	0.018	0.015	0.020	0.023
Ksil-pseu	0.190	0.194	0.173	0.173	0.116	0.115	0.322	0.326	0.208	0.207	0.149	0.149

Abbreviations: Abi, Abelson interacting protein; Atpα; Na pump α-subunit; BC, Barcelona; Fmr1, Fragile X mental retardation; h, number of haplotypes; K_sil-pseu, divergence per silent site between D. subobscura and D. pseudoobscura; K_sil-mad, divergence per silent site between D. subobscura and D. madeirensis; MP, Mount Parnes; n, sample size; Pif1A, PFTAIRE-interacting factor 1A; S, number of polymorphic sites; Sqd, Squid; Yrt; Yurt; π, nucleotide diversity including all sites; π_sil, nucleotide diversity in synonymous sites and non-coding positions; θ_sil, heterozygosity in silent sites.

Genetic differentiation between populations and arrangements

When comparing populations for the same arrangement, the Snn values were always not significantly different from zero (Table 3). Between arrangements, significant differences and fixed mutations were only found for Fmr1 (Supplementary Table S2). This result is consistent with the cytological location of Fmr1 within inversion O₄ (Figure 1). F_ST values were small for all the comparisons, with the exception of Fmr1 when comparing the two arrangements. Moreover, there were significant differences between arrangements for the concatenated data set considering all genes, but the analysis of the concatenated data set excluding Fmr1 showed small and non-significant values (Table 3). The highest Dxy values were detected for Pif1A, (Table 3), which could be explained by its large portion of intronic content resulting in higher variability levels.

Table 3. Genetic differentiation between O ₃₊₄ and O_ST arrangements from MP and BC.

	Pif1A	Sqd	Yrt	Atpα	Fmr1	4Conca	5Concb
O3+4 MP vs O3+4 BC
Dxy	0.021	0.004	0.010	0.005	0.004	0.010	0.009
Fst	−0.017	−0.050	−0.008	−0.044	0.028	−0.0214	−0.015
P(Snn)	NS	NS	NS	NS	NS	NS	NS
OST MP vs OSTBC
Dxy	0.022	0.003	0.01	0.005	0.007	0.011	0.010
Fst	−0.014	−0.048	−0.117	0.079	−0.100	0.038	0.013
P(Snn)	NS	NS	NS	NS	NS	NS	NS
O3+4 MP vs OST MP
Dxy	0.020	0.004	0.010	0.005	0.011	0.010	0.010
Fst	−0.053	−0.031	−0.028	0.035	0.466	−0.054	0.094
P(Snn)	NS	NS	NS	NS	***	NS	**
O3+4 BC vs OST BC
Dxy	0.022	0.004	0.010	0.004	0.011	0.010	0.011
Fst	0.018	0.011	−0.070	−0.048	0.497	0.022	0.155
P(Snn)	NS	NS	NS	NS	***	NS	**
O3+4 MP vs OST BC
Dxy	0.022	0.004	0.010	0.004	0.012	0.010	0.011
Fst	0.006	−0.021	−0.06	−0.037	0.487	0.021	0.153
P(Snn)	NS	NS	NS	NS	***	NS	*
O3+4 BC vs OST MP
Dxy	0.021	0.004	0.010	0.006	0.011	0.010	0.010
Fst	−0.031	0.025	−0.047	0.089	0.487	−0.026	0.116
P(Snn)	NS	NS	NS	NS	**	NS	*

Abbreviations: Abi, Abelson interacting protein; Atpα; Na pump α-subunit; BC, Barcelona; Fmr1; Fragile X mental retardation; MP, Mount Parnes; NS, not significant; Pif1A, PFTAIRE-interacting factor 1A; Sqd, Squid; Yrt; Yurt.

Statistical significance was assessed using the P-value of the Snn statistic (*0.01<P<0.05; **0.001<P<0.01; ***P<0.001).

^aConcatenated data set of genes Pif1A, Sqd, Yrt and Atpα.

^bConcatenated data set with the addition of Fmr1 gene.

Distance trees for the concatenated data set or only for Fmr1 were carried out using D. madeirensis and D. pseudoobscura as outgroups (Figure 3). In both phylogenetic trees, sequences from different populations randomly clustered. In the tree of the concatenated data set, both populations and arrangements were randomly distributed (Figure 3a), and although some sequences from the same arrangements were grouped together, their bootstrap values were below 30%. Nonetheless, it is worth noting that in the Fmr1 genealogy (Figure 3b), the O₃₊₄ sequences grouped with a high bootstrap value (97%), though the clustering of the remaining sequences (all belonging to the O_ST arrangement) was not statistically supported. By visual inspection of the Fmr1 sequences (Supplementary Table S1) we detected four recombinant sequences for the O_ST arrangement (asterisks show the recombinant individuals in Figure 3b), but none was detected for the O₃₊₄ arrangement. The regions affected by recombination (more likely gene conversion due to their short size) were approximately 161 bp for MP19 and FBC58, and 10 bp for MP28 and BC55 individuals. When excluding these recombinant individuals, nine fixed differences were observed between both arrangements combining sequences from both populations (Supplementary Table S1). Furthermore, the phylogenetic reconstruction after excluding these recombinants showed monophyly for the two arrangements with more than 89% bootstrap support.

Figure 3.

Neighbor-joining gene genealogy based on total nucleotide variation in (a) the concatenated data set of the five genes (Pif1A, Sqd, Yrt, Atpα and Fmr1) and in (b) the Fmr1 gene alone. D. madeirensis and D. pseudoobscura were used as outgroups. Only bootstrap values above 70% are shown. (Δ) O₃₊₄ from Mt. Parnes, (▵) O₃₊₄ from Barcelona, (◊) O_ST from Mt. Parnes and (♦) O_ST from Barcelona. Asterisks indicate recombinant individuals.

Population demography and selection

Tajima's D and Fu and Li's D test presented negative, although non-significant, values for the concatenated data set as well as for each gene separately, with the exception of the Atpα gene in Mt. Parnes (Table 4). Negative D statistic values correspond to an excess of low-frequency polymorphism, which could be due to either demography or selection. To further elucidate this issue, the R₂ statistic (Ramos-Onsins and Rozas, 2002), which is a test for recent population expansion, was estimated because it is more suitable for small sample sizes presenting recombination. R₂ estimates ranged between 0.09 and 0.18, and significance was assayed considering three alternative recombination scenarios, as rejection of the null hypothesis of constant population size depends on the level of recombination implemented (Table 4). Most of the comparisons were non-significant assuming no recombination, although they were significant when incorporating for each gene the rate of recombination (ρ) estimated using the composite likelihood method of Hudson (2001). Very similar results were obtained assuming free recombination. As the fraction of coding region varies among genes, to compare estimates previously described tests were also calculated using only silent sites (Supplementary Table S3). In general, the same patterns were detected when comparing different recombination levels with the number of significant R₂ estimates being always higher in Mt. Parnes than in Barcelona. Finally, when considering population growth within arrangements for gene Fmr1 gene, which is the only gene showing signals of significant genetic differentiation, the null hypothesis of constant size was only rejected for the O₃₊₄ arrangement (Table 4).

Table 4. Neutrality tests and test of population expansion for each gene separately and all combined genes using Ramos-Onsins and Rozas (2002) R₂.

	Tajima's D	Fu and Li's D	R2	ρ	P-value a	P-value b	P-value c
Mount Parnes
Pif1A	−0.723	−1.142	0.101	100	0.129	0.000	0.000
Abi	−1.099	−0.603	0.091	69	0.034	0.010	0.008
Sqd	−1.017	−1.299	0.092	81	0.062	0.035	0.028
Yrt	−0.871	−0.109	0.096	100	0.079	0.019	0.019
Atpα	0.942	1.104	0.176	13	0.881	0.945	0.990
Fmr1	−1.100	−0.753	0.088	27	0.033	0.008	0.000
Concatenate d	−0.799	−0.670	0.100	100	0.070	0.000	0.000
Barcelona
Pif1A	−0.326	−0.475	0.116	100	0.340	0.101	0.101
Abi	−0.908	−1.569	0.087	68	0.003	0.003	0.002
Sqd	−0.776	−1.335	0.104	62	0.113	0.093	0.079
Yrt	−0.833	−0.418	0.099	100	0.137	0.033	0.033
Atpα	−0.648	−1.033	0.102	79	0.151	0.091	0.069
Fmr1	−0.619	−0.896	0.109	17	0.179	0.133	0.051
Concatenate d	−0.518	−0.810	0.110	100	0.197	0.000	0.000
Fmr1 O3+4e	−1.696	−1.947	0.062	62	0.001	0.000	0.000
Fmr1 OST f	−0.585	−0.831	0.135	67	0.072	0.227	0.354

Abbreviations: Abi, Abelson interacting protein; Atpα; Na pump α-subunit; Fmr1; Fragile X mental retardation; Pif1A, PFTAIRE-interacting factor 1A; Sqd, Squid; Yrt; Yurt.

For the Fmr1 gene, neutrality and demographic tests were calculated within arrangement after removing recombinant individuals.

^aP-values were obtained by coalescent simulations without recombination.

^bP-values were obtained by coalescent simulations with estimated levels (ρ) of recombination.

^cP-values were obtained by coalescent simulations with free recombination.

^dGenes Pif1A, Sqd, Yrt, Atpα and Fmr1 included in the concatenate data set. P<0.05 are in bold.

^eBarcelona and Mount Parnes individuals are included in the analysis.

^fBarcelona and Mount Parnes after excluding recombinant individuals.

Age of inversions

Sequences from Fmr1 were used for estimating the age of the inversions, as it is the only gene analyzed, which is located in section SI, in which both arrangements differ (Figure 1). Recombinant individuals were excluded because, only a variation originated by mutation is useful for this analysis (Figure 3). The ages of inversions were estimated for each population separately and combining them, as their origin should be unique (Table 5). As older divergence times lead to estimate smaller mutation rates, the ages of the inversions estimated using Tamura et al. (2004) divergence time are sensitively older than using Ramos-Onsins et al. (1998) divergence time (Table 5). In addition, older estimates were obtained using the information from the two more distant individuals, in relation to the values obtained using the mean silent nucleotide diversity. Within each approach, the age estimates for O₃₊₄ and O_ST were quite similar. Nonetheless, older coalescent times were detected for O₃₊₄ when using the most divergent individuals (1.01 and 2.24 Myr for both divergence times when mixing populations, and 0.87 and 1.93 Myr for Barcelona population; see Table 5), whereas older coalescent time were detected for O_ST with the mean nucleotide diversity excluding recombinants (0.49 and 1.09 Myr for both divergence times when mixing populations, and 0.48 and 1.06 Myr for Barcelona population; see Table 5).

Table 5. Silent nucleotide diversity and age of the different gene arrangements using the Fmr1 gene.

	Estimates from the two most divergent individuals			Estimates from all individuals but recombinants
	πsil	Age (Myr)a	Age (Myr)b	πsil	Age (Myr)a	Age (Myr)b
O3+4 c	0.019	2.24	1.01	0.008	0.98	0.44
OST c	0.015	1.71	0.77	0.009	1.09	0.49
O3+4 MP	0.014	1.70	0.77	0.009	1.00	0.45
O3+4 BC	0.016	1.93	0.87	0.008	0.90	0.41
OST BC	0.014	1.59	0.72	0.009	1.06	0.48

Abbreviation: Myr, million years.

The least biased estimate is indicated in bold (see discussion).

^aAge estimation assuming that the species diverged 17.7 Myr ago (Tamura et al., 2004).

^bAge estimation assuming that D. subobscura and D. pseudoobscura diverged 8 Myr ago (Ramos-Onsins et al., 1998).

^cIndividuals from both populations combined.

Discussion

Patterns of nucleotide variation and demographic effects

The present study focuses on the analysis of six genes in the context of two different arrangements: the O_ST and the O₃₊₄. Five of these genes are located outside the inverted region and only one (Fmr1) was located inside the O₄ inversion and approximately 1.3 Mb from the nearest breakpoint. In terms of nucleotide variability, lower nucleotide diversity values are expected in markers located close to the inversion breakpoint (Andolfatto et al., 2001, Stevison et al., 2011). In D. buzzatii, a correlation between nucleotide diversity and distance to the breakpoint was observed (Laayouni et al., 2003). However, Fmr1 does not present the lowest levels of π_sil, despite being located inside and close to the inversion breakpoint. Similarly, no reduction of the variation was observed in D. subobscura for genes located close to the inversion breakpoints (Munté et al., 2005). Mutation and recombination (including gene conversion) could both have contributed to recover variability levels within the inverted regions. In fact, the variability for Fmr1 gene in O_ST was increased because of the presence of four putative recombinant individuals, despite this gene is closely located to O₄ inversion breakpoint. The presence of recombinants only among O_ST lines could arise from differences in the frequency of both arrangements in the two populations. According to data from Araúz et al. (2009), in Barcelona and Mt. Parnes it is more likely to find O_3+4+X homozygous (35% and 74%, respectively) than O_ST/O_3+4+X heterozygous (13% and 18%, respectively) or O_ST homozygous (1.3% and 1.1%, respectively), where X includes non-overlapped inversions that can freely recombine in region SI with O₃₊₄ (Figure 1). Therefore, the probability of sampling a recombinant O_ST chromosome is higher than that for a recombinant O_3+4+X. Similarly, a previous study concluded that the frequency of heterozygote hybrids between D. pseudoobscura and D. persimilis determines the frequency of genetic exchange in the population (Stevison et al., 2011).

It has been previously suggested that recombination should be higher in central parts of the inversion, because genes located in this region could be influenced by double crossovers and gene conversion, whereas genes close to inversions breakpoints should be mainly influenced by gene conversion (Navarro et al., 1997). Nevertheless, double recombinants have been observed close to the breakpoints when analyzing the offspring of heterokaryotypic females, indicating that recombination close to the breakpoint can occur, although in very low frequency (Pegueroles et al., 2010a). As recombination between heterokaryotypes is reduced inside inverted regions (Navarro et al., 1997; Stump et al., 2007, Pegueroles et al., 2010a), higher diversity levels are expected outside inverted regions than inside them. In the region where genes can freely recombine between both arrangements (SII region, Figure 1), estimates of π_sil ranged from 0.004 to 0.024 for the O_ST arrangement and from 0.006 to 0.023 for O₃₊₄, after excluding Yrt, as it could act as an outlier for the nucleotide variability (see Results section). The π_sil values for nine genes located inside the inverted region between the two assayed arrangements (SI region, Figure 1), combining results of a previous study (Munté et al., 2005) and the present work, ranged from 0.004 to 0.013 for the O_ST arrangement, and from 0.008 to 0.013 for the O₃₊₄ arrangement, after excluding the Acph-1 gene, which also acted as a mutation outlier. The ranges of nucleotide variability mostly overlap for genes located inside and outside the inverted regions, and non-significant differences were detected when performing a Mann–Whitney U-test (O_ST P=0.142, O₃₊₄ P=0.457), although the highest values were found outside the inversions. Reduced diversity within inversions has been found in the D. persimilis lineage, indicative of a recent fixation process, despite inversions may have arisen long ago (McGaugh and Noor, 2012). Our results suggest that despite the studied inversions are maintained by selection (Prevosti et al., 1988, Balanyà et al., 2006), recombination could also contribute in some extent to recover variability inside reasonably old polymorphic inversions.

The trend in the excess of rare alleles detected by the Tajima's D in Barcelona and Mt. Parnes populations is similar to that observed for genes located inside the inverted regions in previous studies (Rozas et al., 1999; Munté et al., 2005). The hypothesis of a recent population expansion was further supported by the R₂ statistic. The number of significant R₂ estimates is higher in Mt. Parnes than in Barcelona, suggesting that Mt. Parnes had a larger population expansion in accordance with its estimated larger effective population size (Araúz et al., 2009, 2011). When considering expansion within arrangements, the null hypothesis of constant size was only rejected for O₃₊₄ arrangement. As this arrangement is considered to be warm adapted (Balanyà et al., 2004), the inferred expansion in the O₃₊₄ arrangement could be the result of its increase in frequency because of selection after the Pleistocenic glaciations. Interestingly, this arrangement shows increased frequency worldwide, matching recent global warming (Balanyà et al., 2006).

Divergence time of inversions

The age of inversions can be estimated considering their likely unique origin (Powell, 1997). These estimates can be inferred from the time of coalescence of the sequences, taking into account that variability accumulated in the sequences is proportional to its origin. Divergence was initially estimated using two species of the obscura group as outgroups (D. madeirensis and D. pseudoobscura). On one hand, D. madeirensis is more closely related to D. subobscura, as their divergence time was estimated at about 0.63 Myr ago by Ramos-Onsins et al. (1998). This species is endemic of Madeira Island and has a small effective population size. However, its nucleotide diversity is similar to D. subobscura, and therefore not showing the lower levels of variation typically found in an island (Ramos-Onsins et al., 1998; Khadem et al., 2001). On the other hand, D. pseudoobscura divergence time with respect to D. subobscura was estimated to be 17.7 Myr (Tamura et al., 2004) or around 8 Myr (Ramos-Onsins et al., 1998). D. pseudoobscura is a native species from North America and its effective size could be quite similar to D. subobscura (Pascual et al., 2000). For the Abi and Atpα genes, values of silent nucleotide diversity were quite similar to the divergence between D. subobscura and D. madeirensis. Thus, we have used the more divergent outgroup, D. pseudoobscura, to estimate the age of the inversions.

Ages were calculated using two divergence times between D. subobscura and D. pseudoobscura. The divergence time obtained by Tamura et al. (2004) is more reliable, as it is based on a large multilocus data set; nonetheless, the time estimate by Ramos-Onsins et al. (1998), although only based on the rp49 gene, allows the comparison with previous studies (see below). The age of inversions estimated using the two most divergent sequences seems more sensitive to differences in sample size or to differences in the genetic content between populations, as observed by the higher fluctuation of the estimated ages when mixing populations (1.01–2.24 Myr) or estimating ages for each population separately (0.77–1.70 and 0.87–1.93 Myr for Barcelona and Mt. Parnes, respectively, see Table 5). To avoid this potential bias, we suggest using the mean π_sil and considering individuals from a unique population (bold values in Table 5). The age estimates obtained in the present study (0.48 Myr for O_ST and 0.41 Myr for O₃₊₄) are slightly older than those based on genes Acph-1 (0.26 Myr for O_ST and 0.31 Myr for O₃₊₄ in Navarro-Sabaté et al., 1999) and rp49 (0.24 Myr for O_ST and 0.33 Myr for O₃₊₄ in Rozas et al., 1999), despite using the same divergence time (Ramos-Onsins et al., 1998). Differences could be due to intrinsic characteristics of the different genes and to their distinct genetic location. The genes Acph-1 and rp49 are closely located inside inversion O₃ near its distal breakpoint (Munté et al., 2005), whereas the Fmr1 gene is located far away from them, inside inversion O₄ near the distal breakpoint. However, in the three studies the age distance between the two arrangements is reduced, differing in 0.05 Myr in (Navarro-Sabaté et al., 1999), in 0.09 Myr in (Rozas et al., 1999), and in 0.07 Myr in the present study. As genes can differ in their selective pressure, mutation rates, or rate of recombination, each of which can affect estimates of their coalescence time, a multilocus approach as in Tamura et al. (2004) is preferred to more precisely infer the age of inversions. Thus, considering all data available we can conclude that the two arrangements arose approximately at the same time.

Gene flux is not homogeneously distributed across the chromosomal arrangement

Gene flux is defined as the probability of allele exchange during meiosis in heterokaryotypic females, including both crossing over and gene conversion (Navarro et al., 1997). For the five genes located outside the inversions, no significant genetic differentiation between the O_ST and O₃₊₄ chromosomal arrangements was observed in the present study, suggesting extensive gene flux between them. High levels of gene flux between arrangements were also found in other Drosophila species, such as D. pseudoobscura (Schaeffer and Anderson, 2005) and D. buzzatii (Laayouni et al., 2003). Despite the extensive exchange found outside the inverted region, significant genetic differentiation was found within the inverted region. For the Fmr1 gene, the F_ST values were similar to those obtained in previous studies using other genes located within the studied inverted region (Rozas et al., 1999; Munté et al., 2005). The adaptive value of inversions in D. subobscura has been supported by many observations, such as the latitudinal clines for some chromosomal arrangements (Prevosti et al., 1988; Balanyà et al., 2006) or their seasonal fluctuations (Rodríguez-Trelles et al., 1996). In particular, O_ST and O₃₊₄ present opposite latitudinal clines, with O_ST being more frequent in northern Europe and O₃₊₄ being more frequent in the south (Solé et al., 2002; Balanyà et al., 2004). However, none of the nine genes located across the O₃₊₄ arrangement studied so far show any non-synonymous changes differentiating the two arrangements (Munté et al., 2005 and present study), despite the Fmr1 gene was a candidate gene to be involved in thermal adaptation. Knowing that selective pressure could focus on regulatory regions instead of coding regions (Torgerson et al., 2009), the differential basal expression for the thermal candidate gene Hsp70 among O₃₊₄ and O_ST arrangements (Calabria et al., 2012) may be due to changes in regulatory sequences. Transcriptome variation in Drosophila has been shown to be driven by both cis- and trans-regulatory elements, (Genissel et al., 2008); thus, future studies should focus on the sequencing of the regulatory regions of Fmr1 or other thermal candidate genes in the SI region and study their pattern of expression among different chromosomal arrangements.

High gene flow between populations despite the adaptive value of the inversions

The two populations selected for the present study had been previously observed to differ significantly in frequency of chromosomal inversions (Araúz et al., 2009). For instance, the O₃₊₄ arrangement constituted 28% of the Barcelona population, but its frequency was 52% in Mt. Parnes. Furthermore, inversions that did not appear or had very low frequency in one population showed a moderate frequency in the other (15% O₃₊₄₊₇, 24% O₃₊₄₊₈ and 4% O₃₊₄₊₁ in Barcelona vs 0% O₃₊₄₊₇, 3% O₃₊₄₊₈ and 14% O₃₊₄₊₁ in Mt. Parnes). These differences could reflect historical processes with these two populations representing separate Pleistocene refugia (Taberlet et al., 1998; Hewitt, 1999), with subsequent low levels of gene flow and/or differential selection to local environments (Kovacevic and Schaeffer, 2000).

Low levels of gene flow can be ruled out, as in the present work no significant DNA sequence differentiation was detected comparing the same arrangement between populations independently of the gene location. Similarly, in D. pseudoobscura (Schaeffer et al., 2003), no genetic differentiation was found between populations within arrangements using genes located in the inverted region. In D. subobscura, no significant DNA sequence differentiation was found among three European populations (one from Holland and two from Spain) when analyzing restriction length polymorphism in O_ST and O₃₊₄ arrangements (Rozas et al., 1995). No significant DNA sequence differentiation was found between El Pedroso (Spain) and Bizerte (Tunisia) for the O[₃₊₄] group (including O₃₊₄₊₇ and O₃₊₄₊₈), despite in these group different overlapping inversions were included (Sánchez-Gracia and Rozas 2011). Furthermore, the same sequence associated to the O₃₊₄₊₁ chromosomal arrangement was found on the Odh gene in Barcelona and Mt. Parnes populations (Araúz et al. 2011). An independent origin of this association in both populations seems unlikely and the more parsimonious explanation is gene flow between them. Overall, these results suggest that gene flow between populations of D. subobscura is high, and agree with several studies detecting non-negligible gene flow between natural European populations of this species (Latorre et al., 1992; Pascual et al., 2001; Zivanovic et al., 2007). High gene flow between distant populations could be attributed to migration, both by passive transportation associated to human activities (Pascual et al., 2007) and to the active dispersal capabilities of D. subobscura (Serra et al., 1987). Thus, in European populations, if the gene flow is extensive, the clinal frequencies of some inversions are likely to be maintained by strong selection (Prevosti et al., 1988; Balanyà et al., 2006). Nonetheless, comparisons between introduced (American) and ancestral (European) populations would lead to genetic differentiation within arrangement due to the founder effect, as observed for the Odh gene (Mestres et al., 2004; Gómez-Baldó et al., 2008; Araúz et al., 2011).

In summary, despite using candidate genes for thermal adaptation (which are suspected to be selected in the chromosome inversions where they are located), we observed no differences between populations within arrangement, although it would be useful to include other thermal candidate genes located in the SI region. Moreover, no fitness differences were observed when comparing heterokaryotypes carrying both chromosomes belonging to the same or to different populations (Pegueroles et al., 2010a). Thus, we conclude that the adaptive value of inversions can be maintained, regardless of the lack of genetic differentiation within arrangements from different populations. These results do not agree with the expectation of the coadaptation model that predicts genetic differentiation between populations, but do support the local adaptation hypothesis of Kirkpatrick and Barton (2006).

Data archiving

Sequence data have been submitted to GenBank: accession numbers JN882376-JN882575.

The authors declare no conflict of interest.