Helena and BS: Two Travellers between the Genera Drosophila and Zaprionus

Abstract

The frequency of horizontal transfers of transposable elements (HTTs) varies among the types of elements according to the transposition mode and the geographical and temporal overlap of the species involved in the transfer. The drosophilid species of the genus Zaprionus and those of the melanogaster, obscura, repleta, and virilis groups of the genus Drosophila investigated in this study shared space and time at some point in their evolutionary history. This is particularly true of the subgenus Zaprionus and the melanogaster subgroup, which overlapped both geographically and temporally in Tropical Africa during their period of origin and diversification. Here, we tested the hypothesis that this overlap may have facilitated the transfer of retrotransposons without long terminal repeats (non-LTRs) between these species. We estimated the HTT frequency of the non-LTRs BS and Helena at the genome-wide scale by using a phylogenetic framework and a vertical and horizontal inheritance consistence analysis (VHICA). An excessively low synonymous divergence among distantly related species and incongruities between the transposable element and species phylogenies allowed us to propose at least four relatively recent HTT events of Helena and BS involving ancestors of the subgroup melanogaster and ancestors of the subgenus Zaprionus during their concomitant diversification in Tropical Africa, along with older possible events between species of the subgenera Drosophila and Sophophora. This study provides the first evidence for HTT of non-LTRs retrotransposons between Drosophila and Zaprionus, including an in-depth reconstruction of the time frame and geography of these events.

Fig. 1.

—Evolutionary scenario and historical biogeography of drosophilid in the Old World with emphasis on the subgroup melanogaster (melanogaster group, Sophophora subgenus, genus Drosophila) and the subgenus Zaprionus (Zaprionus genus). The ages (numbers in My) of the African continent colonization of the melanogaster subgroup and Zaprionus subgenus, migrations (arrows) and lineages diversification in each region are indicated (Okada and Carson 1983, Jeffs et al. 1994, Russo et al. 1995, Yassin et al. 2008, Lachaise and Silvain 2004).

Fig. 2.

—Calibrated tree of Helena sequences mirrored by a phylogenetic species tree reconstructed with sequences of the gene Amyrel. (A) The Helena tree was reconstructed with partial sequences of the reverse transcriptase gene using the Bayesian phylogenetic inference method and the Tamura-Nei nucleotide substitution model (Tamura and Nei 1993). The analysis involved 78 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were 397 positions in the final alignment. Branch support values >0.7 are indicated by black circles at the root of each clade, with the age estimated for each branching. Asterisks indicate sequences retrieved from sequenced genomes, and apostrophes indicate the PCR amplified sequences. The Helena sequences of the subgenus Zaprionus and the subgroup melanogaster are shown in red and blue, respectively. The branch with 11 sequences of the non-LTR elements Doc (1), Jockey (9), and TART (1), used as outgroup, was collapsed. The evolutionary analyses were conducted in BEAST v16.1 (Drummond et al. 2012). (B) The species tree was inferred by using the Maximum Likelihood method based on the Tamura 3-parameter substitution model. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 21 nucleotide sequences with 1,489 positions in the final alignment. Branch support values >0.7 are indicated by black circles. The ages of divergence of the melanogaster group and complexes indicated in the branches follow Lachaise and Silvain (2004), and those of the Zaprionus subgroups follow Yassin et al. (2008). Evolutionary analyses were conducted in MEGA 7 (Kumar et al. 2016).

Fig. 3.

—Calibrated tree of BS sequences mirrored by a phylogenetic species tree reconstructed with sequences of the gene Amyrel. (A) The BS tree was reconstructed with partial sequences of the reverse transcriptase gene using the Bayesian phylogenetic inference method and the Kimura 2-parameter substitution model (Kimura 1980). The analysis involved 86 nucleotide sequences. All ambiguous positions were removed for each sequence pair, leaving 762 positions in the final alignment. Branch support values >0.7 are indicated by black circles at the root of each clade, with the age estimated for each branching. Asterisks indicate BS sequences obtained from sequenced genomes, and apostrophes indicate the PCR amplified sequences The BS sequences of the subgenus Zaprionus and subgroup melanogaster are represented in red and blue, respectively. The branch with seven sequences of the non-LTR elements Doc (1), Jockey (5), and TART (1), used as outgroup, was collapsed. Evolutionary analyses were conducted in BEAST v16.1 (Drummond et al. 2012). (B) The species tree is inferred by using the Maximum Likelihood method based on the Tamura 3-parameter model. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 15 nucleotide sequences with 1,489 positions in the final alignment. Branch support values >0.7 are indicated by black circles. The ages of divergence of the melanogaster group and complexes indicated in the branches follow Lachaise and Silvain (2004), and those of the Zaprionus subgroups follow Yassin et al. (2008). Evolutionary analyses were conducted in MEGA 7 (Kumar et al. 2016).

Fig. 4.

—Phylogenetic network reconstruction for the non-LTR retrotransposon Helena of Zaprionus and Drosophila species with emphasis on the relationships between the sequences of Zaprionus and the species of the melanogaster complex. The network was constructed with partial amino acid sequences of the reverse transcriptase gene using the median-joining algorithm implemented in Network 5.0.0.1 (Bandelt et al. 1999). The size of each circle denotes the number of sequences grouped together, and the branch lengths are proportional to the number of substitutions between two nodes. Small empty circles represent the ancestor vectors, black circles represent sequences that do not belong to the melanogaster group, and grey circles represent sequences that belong to the melanogaster group from the Oriental region. The sequences from the melanogaster subgroup are represented by cool colors (blue to green), and Zaprionus sequences are represented by warm colors (red to purple). Z. cam: Z. camerounensis, Z. sep: Z. sepsoides, Z. ind: Z. indianus, Z. gab: Z. gabonicus, Z. ine: Z. inermis, Z. orn: Z. ornatus, Z. dav: Z. davidi, Z. tub: Z. tuberculatus, Z. nig: Z. nigranus, D. mau: D. mauritiana, D. sec: D. sechellia, D. sim: D. simulans, D. mel: D. melanogaster, D. yak: D. yakuba, D. tei: D. teissieri, D. ore: D. orena, D. ere: D. erecta, D. bip: D. bipectinata, D. ana: D. ananassae, D. vir: D. virilis, D._moj: D. mojavensis, D. buz: D. buzzatii, D. koe: D. koepferae. In this analysis, 86 codons and 65 sequences were used.

Fig. 5.

—Phylogenetic network reconstruction for the non-LTR retrotransposon BS of Zaprionus and Drosophila species with emphasis on the relationships between the sequences of Zaprionus and the species of the melanogaster complex. The network was constructed with amino acid sequences of the reverse transcriptase gene using the median-joining algorithm implemented in Network 5.0.0.1 (Bandelt et al. 1999). The size of each circle denotes the number of sequences grouped together, and the branch lengths are proportional to the number of substitutions between two nodes. Small empty circles represent the ancestor vectors, black circles represent sequences that do not belong to the melanogaster group, and grey circles represent sequences that belong to the melanogaster group from the Oriental region. The sequences from the melanogaster subgroup are represented by cool colors (blue to green), and Zaprionus sequences are represented by warm colors (red to purple). Z. ind: Z. indianus, Z. gab: Z. gabonicus, Z. afr: Z. africanus, Z. sep: Z. sepsoides, Z. dav: Z. davidi, Z. orn: Z. ornatus, D. mel: D. melanogaster, D. sim: D. simulans, D. sec: D. sechellia, D. ere: D. erecta, D. bip: D. bipectinata, D. fic: D. ficusphila, D. per: D. persimilis, D. pse: D. pseudoobscura, and D. moj: D. mojavensis. This analysis used 227 codons and 67 sequences.

Fig. 6.

—ENC–dS correlation graph obtained from the comparison between D. simulans versus Z. indianus, D. simulans versus D. yakuba, and D. sechellia versus Z. gabonicus representing inferences of HT and VT. Black empty circles represent the 30 host genes used as controls for vertically transmitted genetic information, red solid triangles represent the Helena and BS ENC–dS plotted against the vertically inherited host genes, the dotted black lines represent the predicted distribution of the ENC–dS correlation between host genes derived from the observed data, and the dotted red lines represent the variance of the observed measurements. If the TE ENC–dS red triangle is plotted within the variance of the host data, then it is not significantly different from the host genes and is considered vertically transmitted. In contrast, if it is plotted far from the dotted red line, then it is significantly different from the host genes, and therefore, will be considered horizontally transferred between the two species. dS is the number of synonymous substitutions per synonymous site, and ENC is the effective number of codons (according to Wallau et al. 2016).