When One Is Not Enough: Introgression of Mitochondrial DNA in Drosophila

J. William O. BallardGo,

The Field Museum, Chicago, Illinois

The specific purpose of this study is to investigate alternate processes that may have resulted in the formation of the two distinct mitochondrial haplotypes (maI and maII) of Drosophila mauritiana. The most plausible explanation for the observed data is that there has been introgression of Drosophila simulans mtDNA into D. mauritiana. More generally, this article addresses three important issues concerning resolution of species relationships. First, pooling data from distinct process partitions has the potential to obscure biologically informative patterns of substitution (Bull et al. 1993Citation ; Ballard et al. 1998Citation ). Second, hypothesizing a species phylogeny from a single linkage partition may be problematic (reviewed by Doyle 1992Citation ; Avise 1994Citation ). Third, phylogenetic hypotheses may be influenced by the inclusion of a single representative of a terminal taxon (Omland, Lanyon, and Fritz 1999Citation ). Multiple unlinked loci and multiple individuals from within species that exhibit extensive population subdivision should be included to maximize the potential to fully resolve species relationships.

Slowinski and Page (1999)Citation identified two levels of potential error when inferring species phylogenies from molecular sequence data. First, a gene tree for a set of molecular sequences may be incorrectly inferred if there is sufficient systematic or random error (Swofford et al. 1996Citation ). Second, even if a gene tree is correctly inferred, deep coalescence, retention of ancestral polymorphism, gene duplication, and horizontal gene transfer among different species can produce a gene tree that differs from the species tree (Doyle 1992Citation ; Avise 1994Citation ). This second source of error may be confounded if the nucleotides are linked such that there is a single gene tree, or genealogy. As an example, genes in organelle genomes such as metazoan mtDNA are historically linked with no recombination (but see Awadalla, Eyre-Walker, and Maynard Smith 1999Citation ; Eyre-Walker, Smith, and Maynard Smith 1999Citation ; Hagelberg et al. 1999Citation ). In this case, phylogenetic hypotheses from different mtDNA genes can only infer the mitochondrial genealogy, which may or may not be the same as the true species tree.

The well-corroborated mitochondrial genealogy of the Drosophila melanogaster subgroup implies that D. mauritiana is paraphyletic relative to D. simulans and Drosophila sechellia (Solignac and Monnerot 1986Citation ; Satta and Takahata 1990Citation ; Ballard 2000Citation ). One explanation for this result is that the mtDNA genealogy does not reflect the species relationships. The phylogenetic relationships of the D. melanogaster subgroup are not clear (Caccone, Amato, and Powell 1988Citation ; Hey and Kliman 1993Citation ; Kliman and Hey 1993Citation ; Hey 1994Citation ; Caccone et al. 1996Citation ). One hypothesis is that D. sechellia and D. mauritiana are derived from an ancestral D. simulans population and that many ancient polymorphisms are shared between D. mauritiana and D. simulans (Kliman and Hey 1993Citation ). An alternate explanation for the nonmonophyly of the D. mauritiana mtDNA haplotypes is that D. mauritiana is a complex of sibling species. This alternate explanation is not supported by the morphological data. The consistent morphological differences between members of the D. melanogaster subgroup include the shape of the posterior process of the male genital arch and the number of bristles on the sex comb (Coyne 1983Citation ; True et al. 1997Citation ). The male genital arch from the distinct mitochondrial lineages of D. mauritiana is a slender, fingerlike process that is very different from that observed in all other species. Furthermore, isofemale lines of both D. mauritiana haplotypes have more bristles on the sex comb than do all lines of D. simulans examined.

The paraphyly of D. mauritiana mtDNA may have resulted from the retention of ancestral polymorphism or introgression. There is no evidence of recombination among the mtDNA genomes of Drosophila (Ballard 2000Citation ). To test these alternatives, intron 1 of the nuclear Alcohol dehydrogenase-repeated (Adhr) locus was sequenced from the same eight isofemale lines that Ballard (2000)Citation considered in his complete mtDNA analysis. The autosomal and mtDNA data are taken from distinct linkage partitions (Slowinski and Page 1999Citation ); however, it is likely that there is recombination at the Adhr locus (Ballard et al. 1996Citation ). Intron 1 of Adhr was sequenced because it had considerable variation, and the pattern was consistent with a neutrally evolving locus (Sumner 1991Citation ).

This is the first study, to my knowledge, that specifically includes autosomal data from representatives of each species and distinct mitochondrial haplotype in the D. melanogaster subgroup. Inclusion of representatives from each lineage permits the investigation of how incomplete sampling of a species may influence phylogenetic interpretations gleaned from the data. Two isofemale lines of D. melanogaster are included as outgroup taxa—Oregon R and Zimbabwe 53. The Oregon R line was collected in Roseburg, Oreg., around 1925 by D. E. Lancefield. The D. melanogaster Zimbabwe 53 line, referred to here as D. melanogaster Zimbabwe, was collected in 1990 at the Sengwa Wildlife Preserve in Africa by R. R. Ramey and L. Brown. Isofemale lines taken from North America and Zimbabwe have clearly differentiated mtDNA (Rand, Dorfsman, and Kann 1994Citation ), and many nuclear variants are not shared between the two localities (Begun and Aquadro 1993Citation ). Drosophila mauritiana has been collected only from Mauritius (Tsacas and David 1974Citation ; Lachaise et al. 1988Citation ). Two isofemale lines of D. mauritiana are included, one from each distinct haplotype (maI and -II). O. Kitagawa (Tokyo Metropolitan University, Japan) collected D. mauritiana maI BG1 in Mauritius in 1981 and D. mauritiana maII G52 in 1985. There are three geographically subdivided D. simulans haplotypes (Solignac, Monnerot, and Mounolou 1986Citation ; Baba-Aïssa et al. 1988Citation ; James and Ballard 2000Citation ). The siI type is known to occur in New Caledonia, Hawaii, Tahiti, and the Seychelles Islands. The siII type has a worldwide distribution but has not been collected on the Pacific Islands of New Caledonia, Hawaii, and Tahiti. The siIII haplotype has been collected only from Madagascar and Reunion Island, where it is sympatric with the siII type. Three isofemale lines of D. simulans are included. I collected D. simulans siI TT01 in Papeete on Tahiti Nui in 1998. Drosophila simulans siII DSR was collected in 1984 from Riverside, Calif. (DSR) by A. A. Hoffman (LaTrobe University, Melbourne, Australia). I collected D. simulans siIII MD199 in Joffreville, Madagascar, in 1998. Drosophila sechellia has been collected only in the Seychelles Islands (Lachaise et al. 1988Citation ). One isofemale line of D. sechellia is included, because intraspecific variation is low (Hey and Kliman 1993Citation ; Kliman and Hey 1993Citation ; Hey 1994Citation ; unpublished data). H. M. Robertson (University of Illinois, Urbana, Ill.) collected this line in 1980 at Tsacas on Cousin Island, Seychelles.

DNA from all lines was extracted using the PureGene Kit (Gentra) following the isolation from fixed tissue protocol. In all cases, the DNA was extracted from individuals less than 14 days of age. The 501-bp region of intron 1 of Adhr was amplified (Ballard et al. 1996Citation ) and cloned, and a single copy was sequenced (Ballard 2000Citation ). Two to four cycle sequencing reactions were employed to sequence this region. Sequences were imported into the Sequencher program, and the chromatograms were investigated. These sequences have been submitted to GenBank (accession numbers AF201423AF201427, AF201429, AF201436, and AF201447).

The Adhr data were aligned without ambiguity against the previously published sequence of Cohn et al. (1984)Citation and Ballard et al. (1996)Citation in CLUSTAL X (Higgins and Sharp 1988Citation ). The eight insertion/deletion events ranged in size from 2 to 10 nt. The mtDNA data were obtained from GenBank (accession numbers AF200828AF200832, AF200834, AF200841, and AF200852) and aligned following Ballard (2000)Citation . The mtDNA sequences were not easily alignable at positions 5535–5584 and 6022–6047. Consequently, 74 bp of mtDNA were deleted from the analyses. The region between positions 5535 and 5584 forms the majority of an intervening sequence between COIII and the glycine tRNA. The region between positions 6022 and 6047 is located in an intervening sequence between ND3 and the alanine tRNA. A single data set consisting of the aligned autosomal and mitochondrial data was constructed in PAUP* (Swofford 1998Citation ). In both the mitochondrial and the autosomal data sets, each presumed insertion/deletion event was parsimoniously scored by inserting a "1" into the matrix at appropriate sites.

The most appropriate method for analyzing independently acquired data sets, in this case the mtDNA and Adhr data, is vigorously debated in the phylogenetic literature. Kluge (1989)Citation suggested that all data sets should be analyzed simultaneously according to a total-evidence or simultaneous-analysis (Nixon and Carpenter 1993Citation ) procedure to maximize informativeness. This approach seeks a single best-fitting hypothesis that, in cladistics, involves maximizing character congruence. If the Drosophila mtDNA and autosomal data are pooled, parsimony analysis generates a single tree that has the same topology as that generated by the mtDNA data set alone (see fig. 1A). The procedure of simultaneous analysis does not consider whether each data set may be subject to distinct biological forces. Bull et al. (1993)Citation suggested that subsets of characters that are evolving under demonstrably different rules should be defined a priori, and the null hypothesis that each partition is evolving under homogeneous processes should be explicitly tested. In this study, the mitochondrial and autosomal data are distinct linkage partitions (Slowinski and Page 1999Citation ), and distinct evolutionary processes may be acting. To investigate whether these linkage partitions are significantly associated, the incongruence length difference (ILD) test (Farris et al. 1995Citation ) was employed to test the null hypothesis that the mitochondrial genome and Adhr are evolving under homogeneous biological processes. This random-partitioning test is an extension of a measure originally reported by Mickevich and Farris (1981)Citation and is based on the null hypothesis of congruence. The mtDNA and intron 1 of Adhr are not evolving under the same processes, as determined by the ILD test (1,425 steps; P = 0.01) implemented in PAUP* (Swofford 1998Citation ). There is a single difference between the mitochondrial genomes of D. simulans siIII and D. mauritiana maI (fig. 1A ): an insertion/deletion event at position 13252 of the aligned sequence. In contrast, the data from the nuclear locus suggest that the two isofemale lines of D. mauritiana are sister taxa (fig. 1B ). This result is robustly supported, with 97% of bootstrap pseudosamples (Efron 1982Citation ; Felsenstein 1985Citation ) supporting this node. Kliman and Hey (1993)Citation and Hey and Kliman (1993)Citation also found that the D. mauritiana alleles are monophyletic at the period, yolk protein 2 and zeste loci.



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Fig. 1.—Parsimony analysis using PAUP* of the eight taxa included in this study. Drosophila melanogaster is the designated outgroup. The Drosophila simulans haplotypes are shown as siI, siII, and siIII, respectively. A, The mitochondrial data. The mtDNA sequences are A+T-rich (mean base frequency of A = 0.39, C = 0.13, G = 0.10, and T = 0.38) and have sequence divergences that are in the range of 0%–4%. The chi-square test of homogeneity of base frequencies across taxa does not suggest that there is any heterogeneity among taxa ({chi}221 = 2.62, P = 1.0). Of the 14,958 characters included, 385 variable characters are parsimony-uninformative, while 736 are parsimony-informative. A single most-parsimonious tree of 1,370 steps was found (consistency index [CI] = 0.86). B, The Adhr data. The aligned sequences are A+T-rich (mean base frequency of A = 0.30, C = 0.19, G = 0.18, and T = 0.33) and have sequence divergences that are in the range of 8%–19%. The chi-square test of homogeneity of base frequencies across taxa does not suggest that there is any heterogeneity among taxa ({chi}221 = 1.406, P = 1.0). Of the 501 characters included, 23 variable characters are parsimony-uninformative, while 27 are parsimony-informative. Three equally parsimonious trees of 55 steps were found (CI = 0.93). The bootstrap proportions from 1,000 pseudosamples are shown in circles. Branch lengths are recorded above each line

 
These data suggest that there has been introgression of D. simulans siIII mtDNA into D. mauritiana. This hypothesis is supported by the known distribution of the maternally inherited alpha-proteobacteria Wolbachia and by introgression experiments. James and Ballard (2000)Citation noted that both siIII and maI may be infected with the wMa strain of Wolbachia. However, no Wolbachia-infected lines of the maII haplotype were detected. Aubert and Solignac (1990)Citation introduced single virgin D. simulans females (initial frequency 0.03) into D. mauritiana populations. The flies were allowed to mate freely and were then transferred to a new bottle. Populations were followed for at least 6 generations, and some were reexamined after 20, 25, and 33 generations. Drosophila simulans females were usually inseminated (39/40) and, on average, the F1 progeny accounted for 14% of the total population. As the F1 males are sterile (Robertson 1983Citation ), the F1 hybrid females must have backcrossed to the pure D. mauritiana males in the bottles. The offspring of this backcross accounted for about 63% of the population. In subsequent generations, the D. simulans mtDNA went to fixation in virtually all populations. In the reciprocal experiments, only a few D. mauritiana females were inseminated, and in all cases the mtDNA of the immigrant D. mauritiana went to extinction. In Mauritius, D. mauritiana is a generalist, domestic species with a broad ecological niche similar to that of the cosmopolitan D. simulans. Drosophila simulans has not been collected from Mauritius, but is present on other nearby islands in the Indian Ocean (David et al. 1989Citation ). As a consequence of the observed distribution of D. simulans, Aubert and Solignac (1990)Citation suggested that D. simulans may have been introduced in Mauritius, but the nuclear and mitochondrial gene pools have been absorbed in D. mauritiana by introgressive hybridization. Although less likely, three lines of evidence support the alternate possibility that there has been introgression of D. mauritiana mtDNA into D. simulans following paternal leakage. First, Kondo et al. (1990)Citation backcrossed 331 lines for 10 generations and observed that four lines from the interspecific cross D. simulans (siII female) x D. mauritiana (maI male) showed clear evidence of paternal leakage of mtDNA. Second, Satta et al. (1988)Citation observed that 2 of 25 wild-caught lines from Reunion Island were heteroplasmic for siII and siIII mtDNA. Third, the maI lineage is in the majority in D. mauritiana (88%; Solignac, Monnerot, and Mounolou 1986Citation ), while the siIII lineage is in the minority in D. simulans (about 33% in Madagascar and Reunion; James and Ballard 2000Citation ).

An alternative to introgression across species boundaries is the retention of an ancestral mitochondrial genome. This alternative is considered less likely because of the recent divergence of the D. simulans siIII and D. mauritiana maI genomes compared with nuclear genes. If there has been introgression of siIII mtDNA into D. mauritiana, it is predicted that the estimated divergence time of the mitochondrial data will be more recent than the divergence time estimated from nuclear data. This presupposes that the nuclear locus was not subject to recent introgression, deep coalescence, retention of ancestral polymorphisms, or strong selection. If it assumed that members of the simulans clade diverged from D. melanogaster about 2.5 MYA (Powell 1997Citation ; Li, Satta, and Takahata 1999Citation ) the divergence times can be estimated from the number of silent changes. The estimated divergence time of the siIII and maI genomes is about 4,500 years, while the estimated divergence time of siII and maII mtDNA is around 1.75 Myr. To place an upper bound on the divergence of siIII and maI with 95% confidence, i.e., the time at which the probability that one or fewer changes has occurred (recall that there is a single nucleotide difference in 15,034 bp) is 0.05 = exp(-2knt) + 2knt exp(-2knt), where k is the substitution rate per site per year, n is the number of silent sites, and t is the time since divergence. The calibration of substitution rates in Drosophila is difficult, but if k = 1.6 x 10-8 for silent sites (Li, Satta, and Takahata 1999Citation ) and n = 6,279, the divergence time of the siIII and maI mitochondrial haplotypes is unlikely to be longer than 24,000 years ago. In contrast, the divergence time of D. simulans and D. mauritiana estimated from Adh is 0.86–1.45 Myr (Stephens and Nei 1985Citation ), and that estimated from the zeste and yolk protein 2 loci is 580,000–860,000 years ago (Hey and Kliman 1993Citation ). Thus, even if the siIII and maI haplotypes diverged as long as 50,000 years ago and D. simulans and D. mauritiana diverged as recently as 500,000 years ago, there is still an order of magnitude difference between the divergence times. The simplest explanation for this difference is introgression between the mitochondrial haplotypes.

In this study, multiple individuals of D. mauritiana and D. simulans were included. Inclusion of multiple individuals within a species is common for morphological studies but rare in systematic studies based on molecular data. Data presented here show that it is important to sample multiple representatives of terminal taxa when there is population subdivision. Inclusion of a single representative of a species may directly influence the phylogenetic hypotheses by affecting (1) evidence for introgression, (2) species relationships, (3) inferred support for monophyly of an assemblage, and (4) inferences of evolutionary rate. For example, if the maI line were not sampled, there would be no evidence of introgression between D. mauritiana and D. simulans. As a second example, consider the effect of sampling the maI isofemale line and just one of the three D. simulans haplotypes. If the siI line were sampled, D. simulans and D. sechellia would be sister taxa. However, if either the siII or the siIII line were sampled, D. simulans and D. mauritiana would be sister taxa. Omland, Lanyon, and Fritz (1999)Citation also found that it was important to sample more than one individual to accurately infer species relationships in New World orioles. Moreover, they noted that adding subspecies, even to monophyletic groups, increased the bootstrap support for a clade.

Data presented here address three important issues concerning resolution of the phylogenetic relationships of closely related species. First, pooling data from distinct process partitions has the potential to obscure biologically informative patterns of substitution (Bull et al. 1993Citation ; Ballard et al. 1998Citation ). In this study, pooling the autosomal and the mtDNA data would obscure the fact that the topologies derived from the two process partitions were not congruent. Second, hypothesizing a species phylogeny from a single linkage partition may be problematic, because the effects of reticulation may be retained through subsequent generations. Including unlinked loci can corroborate phylogenetic hypotheses (Slowinski and Page 1999Citation ). Third, inclusion of single representatives of a taxon may directly influence the phylogenetic hypotheses of closely related species. Adding taxa and characters may break long branches and result in a more robust phylogeny (Hillis 1996Citation ; Poe and Swofford 1999Citation ). Furthermore, the inclusion of multiple individuals from within a species opens the door to the wealth of statistical tests that have been developed in a population genetic framework (reviewed in Ballard and Kreitman 1995Citation ).


    Acknowledgements
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 Acknowledgements
 literature cited
 
I thank Kirrie Ballard and Andrew Berry for help in collecting flies, ICIPE for assistance in obtaining collection permits, and Jeremy Kirchman for help with sequencing. Dick Hudson and two anonymous reviewers made constructive comments. All sequencing was done in the Pritzker Laboratory of Molecular Systematics and Evolution, Field Museum. Funds were provided by National Science Foundation (NSF) grant number DEB-9702824 and the Field Museum Marshall Field Fund.


    Footnotes
 
Ross Crozier, Reviewing Editor

1 Keywords: mtDNA introgression Drosophila Back

2 Address for correspondence and reprints: J. William O. Ballard, The Field Museum, 1400 South Lake Shore Drive, Chicago, Illinois 60605. E-mail: ballard{at}fmnh.org Back


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Accepted for publication April 11, 2000.