Conservation and change in the DNA sequences coding for alcohol dehydrogenase in sibling species of Drosophila

Genes Encoding Mammalian Oviductal Proteins Involved in Fertilization are Subjected to Gene Death and Positive Selection

Oviductal proteins play an important role in mammalian fertilization, as proteins from seminal fluid. However, in contrast with the latter, their phylogenetic evolution has been poorly studied. Our objective was to study in 16 mammals the evolution of 16 genes that encode oviductal proteins involved in at least one of the following steps: (1) sperm–oviduct interaction, (2) acrosome reaction, and/or (3) sperm–zona pellucida interaction. Most genes were present in all studied mammals. However, some genes were lost along the evolution of mammals and found as pseudogenes: annexin A5 (ANXA5) and deleted in malignant brain tumor 1 (DMBT1) in tarsier; oviductin (OVGP1) in megabat; and probably progestagen-associated endometrial protein (PAEP) in tarsier, mouse, rat, rabbit, dolphin, and megabat; prostaglandin D2 synthase (PTGDS) in microbat; and plasminogen (PLG) in megabat. Four genes [ANXA1, ANXA4, ANXA5, and heat shock 70 kDa protein 5 (HSPA5)] showed branch-site positive selection, whereas for seven genes [ANXA2, lactotransferrin (LTF), OVGP1, PLG, S100 calcium-binding protein A11 (S100A11), Sperm adhesion molecule 1 (SPAM1), and osteopontin (SPP1)] branch-site model and model-site positive selection were observed. These results strongly suggest that genes encoding oviductal proteins that are known to be important for gamete fertilization are subjected to positive selection during evolution, as numerous genes encoding proteins from mammalian seminal fluid. This suggests that such a rapid evolution may have as a consequence that two isolated populations become separate species more rapidly.

MOLECULAR ANALYSIS OF THE ALLELES OF ALCOHOL DEHYDROGENASE ALONG A CLINE IN DROSOPHILA MELANOGASTER. I. MAINE, NORTH CAROLINA, AND FLORIDA

Clinal variation in natural populations is often assumed to be due to the operation of natural selection. However, for many clines there exist plausible neutralist explanations which suggest that aspects of population structure maintain differences among subpopulations for particular traits. We used a restriction-mapping technique to investigate the contributions of population subdivision and selection to the maintenance of the allozyme polymorphism at the alcohol dehydrogenase (Adh) locus of Drosophila melanogaster. Digestions of genomic DNAs from 270 lines of flies by seven enzymes reveal 15-20% of all possible nucleotide substitutions and virtually all of the insertion/deletion variation in a 2.7-kilobase region containing the Adh structural locus. Analysis of large samples from each of three populations along the east coast of the United States provides evidence of founder effects in the most northerly population. Although there are signs of population differentiation among the samples, similarities between two of the populations indicate that migration among populations is extensive and strengthen the argument that natural selection plays a role in maintaining the cline.

USING HITCHHIKING GENES TO STUDY ADAPTATION AND DIVERGENCE DURING SPECIATION WITHIN THE DROSOPHILA MELANOGASTER SPECIES COMPLEX

Several studies of intraspecific and interspecific DNA sequence variation from Drosophila loci have revealed a pattern of low intraspecific variation from genomic regions of low recombination. The mechanisms consistently invoked to explain these patterns are the selective sweep of advantageous mutations together with genetic hitchhiking of linked loci. To examine the effect of selective sweeps on genetic divergence during speciation, we studied two loci in different genomic regions thought to be subject to selective sweeps. We obtained DNA sequences from 1.1kb pair portions of the fourth chromosome locus cubitus interruptus Dominant (ci^D ) and from the asense locus near the telomere of the X chromosome. At ci^D , we found very low variation among multiple lines of Drosophila mauritiana and D. sechellia. This finding is consistent with an earlier report of very low variation in D. melanogaster and D. simulans at ci^D and supports the conclusion of selective sweeps and genetic hitchhiking on the nonrecombining fourth chromosome. The pattern of variation found at asense suggests that a selective sweep has occurred recently at the tip of the X chromosome in D. simulans, but not in D. melanogaster or D. mauritiana. The data from ci^D and asense are compared with data from three X chromosome loci (period, zeste, and yolk protein 2) that experience normal levels of recombination. By examining estimated genealogies and the rates at which different classes of mutations have accumulated, we conclude that selective sweeps are common occurrences on the fourth chromosome but less common near the tip of the X chromosome. An interesting pattern of low variation at ci^D among D. simulans, D. mauritiana, and D. sechellia suggests that a selective sweep may have occurred among these forms even after divergence into separate species had begun.

RACE FORMATION, SPECIATION, AND INTROGRESSION WITHIN DROSOPHILA SIMULANS, D. MAURITIANA, AND D. SECHELLIA INFERRED FROM MITOCHONDRIAL DNA ANALYSIS

Mitochondrial DNA cleavage maps from three chromosomally homosequential species Drosophila simulans, D. mauritiana, and D. sechellia, were established for 12 restriction enzymes. One isofemale strain was studied in D. sechellia (se), 13 in D. simulans, and 17 in D. mauritiana: in the last two species, respectively, three (siI, II, and III) and two (maI and II) cleavage morphs were found. The evolutionary relationships based on mtDNA cleavage map comparisons show that the maI and se mtDNAs are internal branches of the phylogenetic tree of the D. simulans mtDNA. D. mauritiana and D. sechellia species appear to be derived from a population of D. simulans which carried an ancestral form of the current siI mtDNA type. In addition, two cleavage morphs (siIII [only present in D. simulans from Madagascar] and maI) appeared to be identical, although found in different species. We present a speculative interpretation of data on biogeography and hybridization which is consistent with the hypothesis of a recent introgression of mitochondrial DNA of D. simulans from Madagascar into D. mauritiana.

Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences

A major analytical challenge in computational biology is the detection and description of clusters of specified site types, such as polymorphic or substituted sites within DNA or protein sequences. Progress has been stymied by a lack of suitable methods to detect clusters and to estimate the extent of clustering in discrete linear sequences, particularly when there is no a priori specification of cluster size or cluster count. Here we derive and demonstrate a maximum likelihood method of hierarchical clustering. Our method incorporates a tripartite divide-and-conquer strategy that models sequence heterogeneity, delineates clusters, and yields a profile of the level of clustering associated with each site. The clustering model may be evaluated via model selection using the Akaike Information Criterion, the corrected Akaike Information Criterion, and the Bayesian Information Criterion. Furthermore, model averaging using weighted model likelihoods may be applied to incorporate model uncertainty into the profile of heterogeneity across sites. We evaluated our method by examining its performance on a number of simulated datasets as well as on empirical polymorphism data from diverse natural alleles of the Drosophila alcohol dehydrogenase gene. Our method yielded greater power for the detection of clustered sites across a breadth of parameter ranges, and achieved better accuracy and precision of estimation of clusters, than did the existing empirical cumulative distribution function statistics.

Dubious maternal inheritance of mitochondrial DNA in D. simulans and evolution of D. mauritiana

Within-line heterogeneity has been found in the mitochondrial DNA (mtDNA) in two isofemale lines of D. simulans. The co-existing types, S and M, were typical of the mtDNA in D. simulans and in D. mauritiana, respectively, their nucleotide divergence per site being ca. 2·1%. Segregation analysis confirmed that some individuals in these lines were heteroplasmic and suggested incomplete maternal inheritance of mtDNA in Drosophila. Examination of other lines of D. simulans revealed that the M type of D. mauritiana occurs at 71% in Réunion, 38% in Madagascar and 0% in Kenya. This finding and interspecific sequence comparisons of both M types indicate that D. mauritiana diverged from D. simulans probably less than 240000 years ago.

Sequence variation of alcohol dehydrogenase (Adh) paralogs in cactophilic Drosophila

This study focuses on the population genetics of alcohol dehydrogenase (Adh) in cactophilic Drosophila. Drosophila mojavensis and D. arizonae utilize cactus hosts, and each host contains a characteristic mixture of alcohol compounds. In these Drosophila species there are two functional Adh loci, an adult form (Adh-2) and a larval and ovarian form (Adh-1). Overall, the greater level of variation segregating in D. arizonae than in D. mojavensis suggests a larger population size for D. arizonae. There are markedly different patterns of variation between the paralogs across both species. A 16-bp intron haplotype segregates in both species at Adh-2, apparently the product of an ancient gene conversion event between the paralogs, which suggests that there is selection for the maintenance of the intron structure possibly for the maintenance of pre-mRNA structure. We observe a pattern of variation consistent with adaptive protein evolution in the D. mojavensis lineage at Adh-1, suggesting that the cactus host shift that occurred in the divergence of D. mojavensis from D. arizonae had an effect on the evolution of the larval expressed paralog. Contrary to previous work we estimate a recent time for both the divergence of D. mojavensis and D. arizonae (2.4 +/- 0.7 MY) and the age of the gene duplication (3.95 +/- 0.45 MY).

Isolation and characterization of the genomic region from Drosophila kuntzei containing the Adh and Adhr genes

The nucleotide sequences of the Adh and Adhr genes of Drosophila kuntzei were derived from combined overlapping sequences of clones isolated from a genomic library and from cloned PCR and inverse-PCR fragments. Only a proximal promoter was detected upstream of the Adh gene, indicating that D. kuntzei Adh is regulated by a one-promoter system. Further upstream of the Adh structural gene, an adult enhancer region (AAE) was found that contains most of the regulatory sequences described for AAEs of other Drosophila species. Analysis of the ADH protein showed an amino acid change from valine to threonine in the active site at position 189 which is also found in D. funebris but is otherwise unique among Drosophila. This difference alone may be responsible for the very low ADH activity found in this species and may cause a difference in substrate usage pattern. Codon bias in Adh and Adhr was comparable and found to be very low compared with other species. Phylogenetic analysis showed that D. kuntzei is closest related to D. funebris and D. immigrans. The time of divergence between D. kuntzei and D. funebris was estimated to be 14.2-20.2 Myr and that between D. kuntzei-D. funebris and D. immigrans to be 30.8-44.0 Myr. An analysis of the genetic variation in the Adh gene and upstream sequences of four European strains showed that this gene was highly variable. Overall nucleotide diversity (pi) was 0.0139, which is two times higher than that in D. melanogaster.

Evolution of mitochondrial and ribosomal gene sequences in anophelinae (Diptera: Culicidae): implications for phylogeny reconstruction

In this study, two mitochondrial genes, cyt b and ND5, and the D2 expansion segment of the 28S nuclear ribosomal gene were used to reconstruct a phylogeny of the mosquito subfamily Anophelinae. The ingroup consisted of all three genera of Anophelinae and five of six subgenera of Anopheles. Six genera of Culicinae were used as the outgroup. Extreme conservation at the protein level coupled with rapid saturation of synonymous positions probably accounted for the lack of meaningful phylogenetic signal in the cyt b gene. In contrast, abundant variation at all codon positions of the ND5 gene allowed recovery of the basal and most of the recent relationships. Phylogenetic analysis of D2 produced results consistent with those of ND5. Combined analysis indicated well-supported monophyletic Anophelinae (with Chagasia basal), Anopheles + Bironella, and subgeneric clades within the genus Anopheles. Moreover, subgenera Nyssorhynchus and Kerteszia were supported as a monophyletic lineage. The Kishino-Hasegawa test could not reject the monophyly of Anopheles, whereas the recently proposed hypothesis of close affinity of Bironella to the subgenus Anopheles was rejected by the analyses of ND5 and combined data sets. The lack of resolution of Bironella and Anopheles clades, or basal relationships among subgeneric clades within Anopheles, suggests their rapid diversification. Recovery of relationships consistent with morphology and previous molecular studies provides evidence of substantial phylogenetic signal in D2 and ND5 genes at levels of divergence from closely related species to subfamily in mosquitoes.

Molecular evolution of the histone 3 multigene family in the Drosophila melanogaster species subgroup

Molecular evolution of the histone multigene family was studied by cloning and sequencing regions of the histone 3 gene in the Drosophila melanogaster species subgroup. Analysis of the nucleotide substitution pattern showed that in the coding region synonymous changes occurred more frequently to A or T in contrast to the GC-rich base composition, while in the 3' region the nucleotide substitutions were most likely in equilibrium. These results suggested that the base composition at the third codon position of the H3 gene, i.e., codon usage, has been changing to A or T in the Drosophila melanogaster species subgroup.

Structure-function relationships in Drosophila melanogaster alcohol dehydrogenase allozymes ADH(S), ADH(F) and ADH(UF), and distantly related forms

Drosophila melanogaster alcohol dehydrogenase (ADH), a paradigm for gene-enzyme molecular evolution and natural selection studies, presents three main alleloforms (ADHS, ADHF and ADHUF) differing by one or two substitutions that render different biochemical properties to the allelozymes. A three-dimensional molecular model of the three allozymes was built by homology modeling using as a template the available crystal structure of the orthologous D. lebanonensis ADH, which shares a sequence identity of 82.2%. Comparison between D. lebanonensis and D. melanogaster structures showed that there is almost no amino-acid change near the substrate or coenzyme binding sites and that the hydrophobic active site cavity is strictly conserved. Nevertheless, substitutions are not distributed at random in nonconstricted positions, or located in external loops, but they appear clustered mainly in secondary structure elements. From comparisons between D. melanogaster allozymes and with D. simulans, a very closely related species, a model based on changes in the electrostatic potential distribution is presented to explain their differential behavior. The depth of knowledge on Drosophila ADH genetics and kinetics, together with the recently obtained structural information, could provide a better understanding of the mechanisms underlying molecular evolution and population genetics.

A quantitative genetic analysis of male sexual traits distinguishing the sibling species Drosophila simulans and D. sechellia

A quantitative trait locus (QTL) genetic analysis of morphological and reproductive traits distinguishing the sibling species Drosophila simulans and D. sechellia was carried out in a backcross design, using 38 markers with an average spacing of 8.4 cM. The direction of QTL effects for the size of the posterior lobe was consistent across the identified QTL, indicating directional selection for this trait. Directional selection also appears to have acted on testis length, indicating that sexual selection may have influenced many reproductive traits, although other forms of directional selection cannot be ruled out. Sex comb tooth number exhibited high levels of variation both within and among isofemale lines and showed no evidence for directional selection and, therefore, may not have been involved in the early speciation process. A database search for genes associated with significant QTL revealed a set of candidate loci for posterior lobe shape and size, sex comb tooth number, testis length, tibia length, and hybrid male fertility. In particular, decapentaplegic (dpp), a gene known to influence the genital arch, was found to be associated with the largest LOD peak for posterior lobe shape and size.

Paleo-demography of the Drosophila melanogaster subgroup: application of the maximum likelihood method

The species divergence times and demographic histories of Drosophila melanogaster and its three sibling species, D. mauritiana, D. simulans, and D. yakuba, were investigated using a maximum likelihood (ML) method. Thirty-nine orthologous loci for these four species were retrieved from DDBJ/EMBL/GenBank database. Both autosomal and X-linked loci were used in this study. A significant degree of rate heterogeneity across loci was observed for each pair of species. Most loci have the GC content greater than 50% at the third codon position. The codon usage bias in Drosophila loci is considered to result in the high GC content and the heterogenous rates across loci. The chi-square, G, and Fisher's exact tests indicated that data sets with 11, 23, and 9 pairs of DNA sequences for the comparison of D. melanogaster with D. mauritiana, D. simulans, and D. yakuba, respectively, retain homogeneous rates across loci. We applied the ML method to these data sets to estimate the DNA sequence divergences before and after speciation of each species pair along with their standard deviations. Using 1.6 x 10(-8) as the rate of nucleotide substitutions per silent site per year, our results indicate that the D. melanogaster lineage split from D. yakuba approximately 5.1 +/- 0.8 million years ago (mya), D. mauritiana 2.7 +/- 0.4 mya, and D. simulans 2.3 +/- 0.3 mya. It implies that D. melanogaster became distinct from D. mauritiana and D. simulans at approximately the same time and from D. yakuba no earlier than 10 mya. The effective ancestral population size of D. melanogaster appears to be stable over evolutionary time. Assuming 10 generations per year for Drosophila, the effective population size in the ancestral lineage immediately prior to the time of species divergence is approximately 3 x 10(6), which is close to that estimated for the extant D. melanogaster population. The D. melanogaster did not encounter any obvious bottleneck during the past 10 million years.

Cloning and characterization of a cDNA encoding a male-specific serum protein of the Mediterranean fruit fly, Ceratitis capitata, with sequence similarity to odourant-binding proteins

Male-specific serum proteins (MSSPs) are low molecular weight proteins which accumulate in high amounts in the haemolymph of adult males of the medfly Ceratitis capitata. By screening an expression library with anti-MSSP antibodies, we have isolated and determined the nucleotide sequence of a cDNA clone coding for one of the male-specific polypeptides (MSSP-alpha). The MSSP-alpha mRNA encodes a polypeptide of 144 amino acids with a secretory signal sequence of sixteen amino acids. Southern analysis indicated that there are multiple copies of MSSP genes in the medfly genome. Northern analysis showed that the MSSP mRNAs are synthesized only in adult males. The accumulation pattern of these mRNAs during development suggests that the expression of the MSSP genes is developmentally regulated at both transcriptional and translational levels. The predicted peptide sequence of MSSP-alpha shows significant similarity to a group of pheromone- and general odourant-binding proteins of insects.

A microsatellite-based multilocus phylogeny of the Drosophila melanogaster species complex

Uncovering the genealogy of closely related species remains a major challenge for phylogenetic reconstruction. It is unlikely that the phylogeny of a single gene will represent the phylogeny of a species as a whole [1], but DNA sequence data across a large number of loci can be combined in order to obtain a consensus tree [2]. Long sequences are needed, however, to minimize the effect of (infrequent) base substitutions, and sufficient individuals must be sequenced per species to account for intraspecific polymorphisms, an overwhelming task using current DNA sequencing technology. By contrast, microsatellites are easy to type [3], allowing the analysis of many loci in multiple individuals. Despite their successful use in mapping [4,5], behavioural ecology [6] and population genetics [7], their usefulness for the phylogenetic reconstruction of closely related taxa has never been demonstrated, even though microsatellites are often conserved across species [8-10]. One drawback to microsatellite use is their high mutation rate (10(-4)-10(-2)), combined with an incomplete understanding of their mutation patterns. Many microsatellites are available for Drosophila melanogaster, and they are distributed throughout the genome [11]. Most can be amplified in the D. melanogaster species complex [12,13] and have low mutation rates [14, 15]. We show that microsatellite-specific distance measurements [16] correlate with other multilocus distances, such as those obtained from DNA-DNA hybridization data. Thus microsatellites may provide an ideal tool for building multilocus phylogenies. Our phylogenetic reconstruction of the D. melanogaster complex provides strong evidence that D. sechellia arose first, followed by a split between D. simulans and D. mauritiana.

Initiation binding repressor, a factor that binds to the transcription initiation site of the histone h5 gene, is a glycosylated member of a family of cell growth regulators [corrected]

Initiation binding repressor [corrected] (IBR) is a chicken erythrocyte factor (apparent molecular mass, 70 to 73 kDa) that binds to the sequences spanning the transcription initiation site of the histone h5 gene, repressing its transcription. A variety of other cells, including transformed erythroid precursors, do not have IBR but a factor referred to as IBF (68 to 70 kDa) that recognizes the same IBR sites. We have cloned the IBR cDNA and studied the relationship of IBR and IBF. IBR is a 503-amino-acid-long acidic protein which is 99.0% identical to the recently reported human NRF-1/alpha-Pal factor and highly related to the invertebrate transcription factors P3A2 and erected wing gene product (EWG). We present evidence that IBR and IBF are most likely identical proteins, differing in their degree of glycosylation. We have analyzed several molecular aspects of IBR/F and shown that the factor associates as stable homodimers and that the dimer is the relevant DNA-binding species. The evolutionarily conserved N-terminal half of IBR/F harbors the DNA-binding/dimerization domain (outer limits, 127 to 283), one or several casein kinase II sites (37 to 67), and a bipartite nuclear localization signal (89 to 106) which appears to be necessary for nuclear targeting. Binding site selection revealed that the alternating RCGCRYGCGY consensus constitutes high-affinity IBR/F binding sites and that the direct-repeat palindrome TGCGCATGCGCA is the optimal site. A survey of genes potentially regulated by this family of factors primarily revealed genes involved in growth-related metabolism.

Evolution of the LINE-like I element in the Drosophila melanogaster species subgroup

LINE-like retrotransposons, the so-called I elements, control the system of I-R (inducer-reactive) hybrid dysgenesis in Drosophila melanogaster. I elements are present in many Drosophila species. It has been suggested that active, complete I elements, located at different sites on the chromosomes, invaded natural populations of D. melanogaster recently (1920-1970). But old strains lacking active I elements have only defective I elements located in the chromocenter. We have cloned I elements from D. melanogaster and the melanogaster subgroup. In D. melanogaster, the nucleotide sequences of chromocentral I elements differed from those on chromosome arms by as much as 7%. All the I elements of D. mauritiana and D. sechellia are more closely related to the chromosomal I elements of D. melanogaster than to the chromocentral I elements in any species. No sequence difference was observed in the surveyed region between two chromosomal I elements isolated from D. melanogaster and one from D. simulans. These findings strongly support the idea that the defective chromocentral I elements of D. melanogaster originated before the species diverged and the chromosomal I elements were eliminated. The chromosomal I elements reinvaded natural populations of D. melanogaster recently, and were possibly introduced from D. simulans by horizontal transmission.

Structural evolution of the Drosophila 5S ribosomal genes

We compare the 5S gene structure from nine Drosophila species. New sequence data (5S genes of D. melanogaster, D. mauritiana, D. sechellia, D. yakuba, D. erecta, D. orena, and D. takahashii) and already-published data (5S genes of D. melanogaster, D. simulans, and D. teissieri) are used in these comparisons. We show that four regions within the Drosophila 5S genes display distinct rates of evolution: the coding region (120 bp), the 5'-flanking region (54-55 bp), the 3'-flanking region (21-22 bp), and the internal spacer (149-206 bp). Intra- and interspecific heterogeneity is due mainly to insertions and deletions of 6-17-bp oligomers. These small rearrangements could be generated by fork slippages during replication and could produce rapid sequence divergence in a limited number of steps.

Amino acids important in enzyme activity and dimer stability for Drosophila alcohol dehydrogenase

We have determined the nucleotide sequences of eight ethyl methanesulphonate-induced mutants in Drosophila alcohol dehydrogenase (ADH), of which six were previously characterized by Hollocher and Place [(1988) Genetics 116, 253-263 and 265-274]. Four of these ADH mutants contain a single amino acid change: glycine-17 to arginine, glycine-93 to glutamic acid, alanine-159 to threonine, and glycine-184 to aspartic acid. Although these mutants are inactive, three mutants (Gly17Arg, Gly93Glu and Gly184Asp) form stable homodimers, as well as heterodimers with wild-type ADH, in which the wild-type ADH subunit retains full enzyme activity [Hollocher and Place (1988) Genetics 116, 265-274]. Interestingly, the Ala159Thr mutant does not form either stable homodimers or heterodimers with wild-type ADH, suggesting that alanine-159 is important in stabilizing ADH dimers. The mutations were analysed in terms of a three-dimensional model of ADH using bacterial 20 beta-hydroxysteroid dehydrogenase and rat dihydropteridine reductase as templates. The model indicates that mutations in glycine-17 and glycine-93 affect the binding of NAD+. It also shows that alanine-159 is part of a hydrophobic anchor on the dimer interface of ADH. Replacement of alanine-159 with threonine, which has a larger side chain and can hydrogen bond with water, is likely to reduce the strength of the hydrophobic interaction. The three-dimensional model shows that glycine-184 is close to the substrate binding site. Replacement of glycine-184 with aspartic acid is likely to alter the position of threonine-186, which we propose hydrogen bonds to the carboxamide moiety of NAD+. Also, the negative charge on the aspartic acid side chain may interact with the substrate and/or residues in the substrate binding site. These mutations provide information about ADH catalysis and the stability of dimers, which may also be useful in understanding homologous dehydrogenases, which include the human 17 beta-hydroxysteroid, 11 beta-hydroxysteroid and 15-hydroxyprostaglandin dehydrogenases.

ADH evolution and the phylogenetic footprint

The evolution of any given protein reflects the interplay between proximal selective forces involving the conservation of protein structure and function and more general populational factors that shape the action and efficiency of natural selection. In an attempt to address that interplay, we have analyzed patterns of amino acid replacement within a well-conserved molecule, alcohol dehydrogenase (ADH), in the Drosophilidae. A sliding window, moved along the protein sequence in order to quantify the extent of change at each amino acid position, reveals heterogeneous amounts of replacement across the molecule when all ADH sequences are analyzed simultaneously. Surprisingly, the replacement profile for ADH differs significantly in the melanogaster, mulleri, and Hawaiian subgroups, reflecting the imprint of the differing evolutionary histories of each of these assemblages on the evolution of this conservative molecule.

The evolutionary genetics of the hobo transposable element in the Drosophila melanogaster complex

Hobo elements are a family of transposable elements found in Drosophila melanogaster and its three sibling species: D. simulans, D. mauritiana and D. sechellia. Studies in D. melanogaster have shown that hobo may be mobilized, and that the genetic effects of such mobilizations included the general features of hybrid dysgenesis: mutations, chromosomal rearrangements and gonadal dysgenis in F1 individuals. At the evolutionary level some hobo-hybridizing sequences have also been found in the other members of the melanogaster subgroup and in many members of the related montium subgroup. Surveys of older collected strains of D. melanogaster suggest that complete hobo elements were absent prior to 50 years ago and that they have recently been introduced into this species by horizontal transfer. In this paper we review our findings and those of others, in order to precisely describe the geographical distribution and the evolutionary history of hobo in the D. melanogaster complex. Studies of the DNA sequences reveal a different level of divergence between the group D. melanogaster, D. simulans and D. mauritiana and the fourth species D. sechellia. The hypothesis of multiple transfers in the recent past into the D. melanogaster complex from a common outside source is discussed.

Evolution of the mitochondrial ATPase 6 gene in Drosophila: unusually high level of polymorphism in D. melanogaster

We have determined 1990 bp mitochondrial DNA sequence which extends from 3' end of the cytochrome oxidase subunit I (COI) gene to 5' end of the COIII gene from two sibling species of Drosophila, D. simulans and D. mauritiana. Analyses of the sequences and part of the NADH dehydrogenase subunit 2 gene and the COI gene together with those from D. melanogaster and D. yakuba revealed that amino-acid substitution rate of the ATPase 6 gene seems to be higher in some strains of D. melanogaster than in the other species. High level of amino-acid polymorphism in this gene was observed in D. melanogaster. Synonymous substitution rate is relatively constant in all the genes examined, suggesting that mutation rate is not higher in the ATPase 6 gene of D. melanogaster. The amino-acid substitutions found specifically in D. melanogaster are at the sites which are not conserved among mammals, yeast and E. coli. These sites of the ATPase 6 gene might lose the selective constraint in D. melanogaster, and the amino-acid substitutions can be explained by neutral mutations and random genetic drift.

Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size

The number of amino acid replacement substitutions and that of synonymous substitutions are examined by using DNA sequences of the Adh locus of Drosophila. The ratio of replacement to synonymous substitutions is higher in sequence comparisons between species than in polymorphisms within species. The ratio for the between-species comparisons is highest in the Hawaiian group and lowest in the obscura group. These observations suggest that amino acid substitutions are facilitated by small population size. The result is in accord with the nearly neutral theory of molecular evolution.

Evolutionary genetics of the Drosophila alcohol dehydrogenase gene-enzyme system

Evolutionary genetics embodies a broad research area that ranges from the DNA level to studies of genetic aspects in populations. In all cases the purpose is to determine the impact of genetic variation on evolutionary change. The broad range of evolutionary genetics requires the involvement of a diverse group of researchers: molecular biologists, (population) geneticists, biochemists, physiologists, ecologists, ethologists and theorists, each of which has its own insights and interests. For example, biochemists are often not concerned with the physiological function of a protein (with respect to pH, substrates, temperature, etc.), while ecologists, in turn, are often not interested in the biochemical-physiological aspects underlying the traits they study. This review deals with several evolutionary aspects of the Drosophila alcohol dehydrogenase gene-enzyme system, and includes my own personal viewpoints. I have tried to condense and integrate the current knowledge in this field as it has developed since the comprehensive review by van Delden (1982). Details on specific issues may be gained from Sofer and Martin (1987), Sullivan, Atkinson and Starmer (1990); Chambers (1988, 1991); Geer, Miller and Heinstra (1991); and Winberg and McKinley-McKee (1992).

Sequence analysis of the indirect flight muscle actin-encoding gene of Drosophila simulans

A genomic clone of the Drosophila simulans indirect flight muscle actin-encoding gene (Act88F) has been isolated, and the sequence of a 3358-nucleotide segment corresponding to the Drosophila melanogaster Act88F transcription unit is presented. The ACt88F homologs in these two sibling species encode identical proteins and the general genomic organization of the Act88F locus is highly conserved, including the location of the transcription start point, and the size and position of intron/exon junctions. Substitutions within the 5' flanking region, however, are clearly nonuniform and the regions of lowest divergence coincide with regions that have been implicated in transcript accumulation and the regulation of tissue-specific expression. Silent substitutions within the coding regions have been compared to five other gene homologs in these sibling species. The rate of silent substitution at these loci varies more than threefold, suggesting selection at the codon level.

cis-diol dehydrogenases encoded by the TOL pWW0 plasmid xylL gene and the Acinetobacter calcoaceticus chromosomal benD gene are members of the short-chain alcohol dehydrogenase superfamily

In the aerobic degradation of benzoate by bacteria, benzoate is first dihydroxylated by a ring-hydroxylating dioxygenase to form a cis-diol (1,2-dihydroxycyclohexa-3,4-diene carboxylate) which is subsequently transformed to a catechol by an NAD(+)-dependent cis-diol dehydrogenase. The structural gene for this dehydrogenase, encoded on TOL plasmid pWW0 of Pseudomonas putida (xylL) and that encoded on the chromosome of Acinetobacter calcoaceticus (benD), were sequenced. They encode polypeptides of about 28 kDa in size. These proteins are similar to each other, exhibiting 58% sequence identity. They are also similar to other proteins of at least 20 different functions, which are members of the short-chain alcohol dehydrogenase family. The alignment of these proteins suggest two amino acids, lysine and tyrosine, as catalytically important residues.

Kinetic interpretations of active site topologies and residue exchanges in Drosophila alcohol dehydrogenases

1. A comparison of full and partly sequenced Adhs from various Drosophila species reveal that 127 of their 253-255 positions are identical (50% identity). 2. Fifty-six of the 115 C-terminal amino acids building up the alcohol binding region differ. In spite of the large differences in primary structure of the alcohol binding region in the Adh enzyme in distantly related Drosophila species, the substrate specificity and stereospecificity have been retained. The topology of the alcohol binding region has been largely conserved during evolution. 3. The primary structures of the alcohol dehydrogenases (Adh) in the Sophophora subgenus is distinguished by few amino acid exchanges, and kinetic and activity parameters show that those at positions 14, 82, 192 and 214 are directly or indirectly involved in coenzyme binding. 4. In these non-metallo Adhs, a tyrosine has been tentatively identified as a nucleophilic catalyst of the hydride transfer step. The three tyrosines at positions 63, 152 and 178 are conserved among the Drosophila alcohol dehydrogenases.

The alcohol dehydrogenase polymorphism in natural populations of Drosophila melanogaster: restriction map variation in the region of the Adh locus in populations from two hemispheres

Restriction endonuclease variation in the 12 kb region surrounding the Adh locus was measured in seven Australian and six Chinese populations of Drosophila melanogaster. There is a higher level of nucleotide-substitution variation in the Australian populations than in the Chinese, which is possibly a reflection of their origins. None of the restriction site polymorphisms, nor any of the insertions, showed a significant association with latitude. A 0.2 kb deletion varied with latitude in the Chinese populations. In accordance with previous studies, a majority of the insertions were located in a region 1.5-3.5 kb 3' from the Adh coding region, and a majority of the deletions were at a site 3 kb 5' to the Adh coding region. Two of the insertions shared homologies with known mobile elements. Overall, the data suggest that restriction endonuclease variation in the Adh region is not related to the cline in Adhs frequencies.

The urate oxidase gene of Drosophila pseudoobscura and Drosophila melanogaster: evolutionary changes of sequence and regulation

The urate oxidase (UO) transcription unit of Drosophila pseudoobscura was cloned, sequenced, and compared to the UO transcription unit from Drosophila melanogaster. In both species the UO coding region is divided into two exons of approximately equal size. The deduced D. pseudoobscura and D. melanogaster UO peptides have 346 and 352 amino acid residues, respectively. The nucleotide sequences of the D. pseudoobscura and D. melanogaster UO protein-coding regions are 82.2% identical whereas the deduced amino acid sequences are 87.6% identical with 42 amino acid changes, 33 of which occur in the first exon. Although the UO gene is expressed exclusively within the cells of the Malpighian tubules in both of these species, the temporal patterns of UO gene activity during development are markedly different. UO enzyme activity, UO protein, and UO mRNA are found in the third instar larva and adult of D. melanogaster but only in the adult stage of D. pseudoobscura. The intronic sequences and the extragenic 5' and 3' flanking regions of the D. pseudoobscura and D. melanogaster UO genes are highly divergent with the exception of eight small islands of conserved sequence along 772 bp 5' of the UO protein-coding region. These islands of conserved sequence are possible UO cis-acting regulatory elements as they reside along the 5' flanking DNA of the D. melanogaster UO gene that is capable of conferring a wild-type D. melanogaster pattern of UO regulation on a UO-lacZ fusion gene.

Evidence for interspecific transfer of the transposable element mariner between Drosophila and Zaprionus

The transposable element mariner occurs widely in the melanogaster species group of Drosophila. However, in drosophilids outside of the melanogaster species group, sequences showing strong DNA hybridization with mariner are found only in the genus Zaprionus. The mariner sequence obtained from Zaprionus tuberculatus is 97% identical with that from Drosophila mauritiana, a member of the melanogaster species subgroup, whereas a mariner sequence isolated from Drosophila tsacasi is only 92% identical with that from D. mauritiana. Because D. tsacasi is much more closely related to D. mauritiana than is Zaprionus, the presence of mariner in Zaprionus may result from horizontal transfer. In order to confirm lack of a close phylogenetic relationship between the genus Zaprionus and the melanogaster species group, we compared the alcohol dehydrogenase (Adh) sequences among these species. The results show that the coding region of Adh is only 82% identical between Z. tuberculatus and D. mauritiana, as compared with 90% identical between D. tsacasi and D. mauritiana. Furthermore, the mariner gene phylogeny obtained by maximum likelihood and maximum parsimony analyses is discordant with the species phylogeny estimated by using the Adh genes. The only inconsistency in the mariner gene phylogeny is in the placement of the Zaprionus mariner sequence, which clusters with mariner from Drosophila teissieri and Drosophila yakuba in the melanogaster species subgroup. These results strongly suggest horizontal transfer.

Evolution of the dec-1 eggshell locus in Drosophila. I. Restriction site mapping and limited sequence comparison in the melanogaster species subgroup

We have analyzed approximately 18 kb of DNA in and upstream of the defective chorion-1 (dec-1) locus of the eight known species of the melanogaster species subgroup of Drosophila. The restriction maps of D. simulans, D. mauritiana, D. sechellia, D. erecta, and D. orena are shown to have basically the restriction map of D. melanogaster, whereas the maps of D. teissieri and D. yakuba were more difficult to align. However, the basic amount of DNA and sequence arrangement appear to have been conserved in these species. A small deletion of varying length (65-200 bp) is found in a repeated sequence of the central transcribed region of D. melanogaster, D. simulans, and D. erecta. Restriction site mapping indicated that the dec-1 gene is highly conserved in the melanogaster species subgroup. However, sequence comparison revealed that the amount of nucleotide and amino acid substitution in the repeated region is much larger than in the 5' translated region. The 5' flanking region showed noticeable restriction site polymorphisms between species. Based on calculations from the restriction maps a dendrogram was derived that supports earlier published phylogenetic relationships within the melanogaster species subgroup except that the erecta-orena pair is placed closer to the melanogaster complex than to D. teissieri and D. yakuba.

The study of variation in the human genome

Regions of the genome showing high evolutionary stability are often conserved as a result of functional constraints. Conversely, more variable regions are likely to represent DNA with no functional or structural importance. However, as in the case of immunologically important regions, sequence divergence does not always indicate lack of functional importance. There is thus a wealth of information from both a functional and an evolutionary point of view that comes from studies of DNA sequence variation, a neglected aspect of the genome endeavor. Naturally, one cannot sequence hundreds of individuals in full, but a useful compromise is to use less expensive methods and to limit the more expensive types of analysis to an appropriately chosen sample of loci. The sample could be determined after careful consideration of categories of DNA segments with respect to individual variation. The study of such categories of DNA variation patterns can help in the understanding of the role of each gene and vice versa. One other important application requiring a study of DNA variation in different human populations is forensic DNA typing. This study requires a knowledge of allele frequencies in different human populations. Evidence of a match between two DNA samples is meaningless if the approximate population frequency of the DNA pattern is not known. It has been suggested (E. Lander) that one use the highest frequency for the most common allele as a baseline frequency estimate. Obviously, systems in which this is employed require an extensive analysis of population-specific allele frequencies. In general, the best way of studying interindividual variation when detecting or describing new polymorphisms is to include interethnic variation.(ABSTRACT TRUNCATED AT 250 WORDS)

Adaptive protein evolution at the Adh locus in Drosophila

Proteins often differ in amino-acid sequence across species. This difference has evolved by the accumulation of neutral mutations by random drift, the fixation of adaptive mutations by selection, or a mixture of the two. Here we propose a simple statistical test of the neutral protein evolution hypothesis based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus. If the observed substitutions are neutral, the ratio of replacement to synonymous fixed differences between species should be the same as the ratio of replacement to synonymous polymorphisms within species. DNA sequence data on the Adh locus (encoding alcohol dehydrogenase, EC 1.1.1.1) in three species in the Drosophila melanogaster species subgroup do not fit this expectation; instead, there are more fixed replacement differences between species than expected. We suggest that these excess replacement substitutions result from adaptive fixation of selectively advantageous mutations.

Secondary structure constraints on the evolution of Drosophila 28 S ribosomal RNA expansion segments

Eukaryotic ribosomal RNA genes contain rapidly evolving regions of unknown function termed expansion segments. We present the comparative analysis of the primary and secondary structure of two expansion segments from the large subunit rRNA gene of ten species of Drosophila and the tsetse fly species Glossina morsitans morsitans. At the primary sequence level, most of the differences observed in the sequences obtained are single base substitutions. This is in marked contrast with observations in vertebrate species in which the insertion or deletion of repetitive motifs, probably generated by a DNA-slippage mechanism, is a major factor in the evolution of these regions. The secondary structure of the two regions, supported by multiple compensatory base changes, is highly conserved between the species examined and supports the existence of a general folding pattern for all eukaryotes. Intriguingly, the evolutionary rate of expansion segments is very slow relative to other genic and non-genic regions of the Drosophila genome. These results suggest that the evolution of expansion segments in the rDNA multigene family is a balance between the homogenization of new mutations by unequal crossing over and a combination of selection against some such mutations per se and selection for subsequent compensatory mutations, in order to maintain a particular RNA secondary structure.

The Adh genomic region of Drosophila ambigua: evolutionary trends in different species

The study of individual genes is essential to a comprehensive understanding of genome evolution. The wealth of information on alcohol dehydrogenase (Adh) in Drosophila makes this gene particularly suitable for such analysis. We have characterized more than 4 kb of the genomic Adh region in Drosophila ambigua and compared this region to Drosophila mauritiana and Drosophila pseudoobscura. The presence of two genes, Adh and 3'ORF (open reading frame), has been confirmed and some of their essential features have been inferred from primary structural analysis. Inter- and intraspecific comparisons have led us to support that both genes may have diverged from an ancient precursor. They appear to be evolving independently, and show a species-specific pattern. The Adh in the obscura group species lacks amino acids three and four when compared to the species of the melanogaster group and has accumulated most of its amino acid replacements in the third exon. Neither characteristic is observed when any other group species are compared, which suggests that these may be particular features of the evolution of the obscura group. The 3'ORF is highly conserved among the three species analyzed, although variability in the length of the third exon and the nucleotide substitution rate, which is much higher than in Adh, are worth noting. According to our data, both mutation/fixation rates and the distribution of mutations vary over time, which makes it difficult to predict the evolutionary dynamics of specific genome regions.

Processed pseudogenes in Drosophila

Two species of Drosophila, D. yakuba and D. teissieri, possess pseudogenes of Adh. These pseudogenes lack introns and map to chromosome arm 3R, rather than to chromosome arm 2L, wherein are located the functional Adh genes. Their structure suggests that the pseudogenes arose from reverse transcripts. Because the pseudogenes map to homologous sites in both species, they presumably arose before these species diverged. Remarkably, the pattern of base substitution in the pseudogenes differs between sites that correspond to degenerate and non-degenerate codon positions in their functional paralogs.

Informational redundancy of tRNA(4Ser) and tRNA(7Ser) genes in Drosophila melanogaster and evidence for intergenic recombination

Variant tRNA genes have been widely observed in multicellular eukaryotes. Recent biochemical studies have shown that some of them are expressed in a tissue- or a stage-specific manner. These findings would thus imply that certain modified tRNAs may be crucial for the development of the organism. Using Drosophila melanogaster as a model, we have taken a combined genetic and molecular approach to examine critically the possible biological functions of tRNA(4, 7Ser) genes. We showed that at least 50% of the total templates can be deleted from the genome without inducing abnormal phenotypes such as Minute, or a decrease in viability. In addition, two of the tRNASer variant genes that are unique in sequence are also completely dispensable. This strongly implies that even though they may be expressed in vivo, they play no essential role in the development of the fruitfly. By comparison with some of the corresponding tRNA genes in another sibling species, Drosophila erecta, our results suggest strongly that the variants are products non-reciprocal exchanges among the tRNA(4, 7Ser), genes. Such intergenic recombination events may have a major influence in the concerted evolution of the two gene families.

ADH and phylogenetic relationships of Drosophila lebanonesis (Scaptodrosophila)

Increasing data on Drosophila alcohol dehydrogenase (ADH) sequences have made it possible to calculate the rate of amino acid replacement per year, which is 1.7 x 10(-9). This value makes this protein suitable for reconstructing phylogenetic relationships within the genus for those species for which no molecular data are available such as Scaptodrosophila. The amino acid sequence of Drosophila lebanonensis is compared to all of the already known Drosophila ADHs, stressing the unique characteristic features of this protein such as the conservation of an initiating methionine at the N-terminus, the unique replacement of a glycine by an alanine at a very conserved position in the NAD domain of all dehydrogenases, the lack of a slow-migrating peptide, and the total conservation of the maximally hydrophilic peptide. The functional significance of these features is discussed. Although the percent amino acid identity of the ADH molecule in Drosophila decreases as the number of sequences compared increases, the conservation of residue type in terms of size and hydrophobocity for the ADH molecule is shown to be very high throughout the genus Drosophila. The distance matrix and parsimony methods used to establish the phylogenetic relationships of D. lebanonensis show that the three subgenera, Scaptodrosophila, Drosophila, and Sophophora separated at approximately the same time.

Genetic basis of the difference in alcohol dehydrogenase expression between Drosophila melanogaster and Drosophila simulans

Drosophila melanogaster and its sibling species, Drosophila simulans, differ in expression of the enzyme alcohol dehydrogenase (ADH). Adult melanogaster flies that are homozygous for the Slow allozyme have approximately twice the level of ADH activity and crossreacting material as simulans adults. There is no corresponding difference in ADH mRNA, however, so this difference in ADH protein level is evidently due to a difference in the rate of translation of the two RNAs and/or to a difference in protein stability. Here we report an interspecific gene-transfer experiment, using P-element transformation, to determine whether this expression difference is due to genetic background differences between the species (trans-acting modifiers) or to cis-acting factors within the Adh gene. When the Adh genes from D. melanogaster and D. simulans are put into the same genetic background, there is no detectable difference in their level of expression. The level is relatively high in the melanogaster background and relatively low in the simulans background. Therefore, the interspecific difference in Adh expression is due entirely to trans-acting modifiers, in spite of the many sequence differences between the Adh genes of the two species, which include two amino acid substitutions.

Molecular similarity of Drosophila melanogaster alcohol dehydrogenase thermostable alleles from populations on different continents

Allele specific oligonucleotide probes have been used to show that DNA, amplified by the polymerase chain reaction, from eleven thermostable Adh alleles extracted from populations on different continents contains the triplet TCC, which distinguishes AdhFChD (Fast Chateau Douglas) from AdhF (Fast). The molecular similarity of Adh thermostable alleles suggests that they had a common origin, and it is argued that the mutation probably occurred in China where high frequencies of AdhFChD are found.

Functional elements and domains inferred from sequence comparisons of a heat shock gene in two nematodes

Caenorhabditis elegans and Caenorhabditis briggsae are two closely related nematode species that are nearly identical morphologically. Interspecific cross-hybridizing DNA appears to be restricted primarily to coding regions. We compared portions of the hsp-3 homologs, two grp 78-like genes, from C. elegans and C. briggsae and detected regions of DNA identity in the coding region, the 5' flanking DNAs, and the introns. The hsp-3 homologs share approximately 98% and 93% identity at the amino acid and nucleotide levels, respectively. Using the nucleotide substitution rate at the silent third position of the codons, we have estimated a lower limit for the date of divergence between C. elegans and C. briggsae to be approximately 23-32 million years ago. The 5' flanking DNAs and one of the introns contain elements that are highly conserved between C. elegans and C. briggsae. Some of the regions of nucleotide identity in the 5' flanking DNAs correspond to previously detected identities including viral enhancer sequences, a heat shock element, and an element present in the regulatory regions of mammalian grp78 and grp94 genes. We propose that a comparison of C. elegans and C. briggsae sequences will be useful in the detection of potential regulatory and structural elements.

Cloning and characterization of the white and topaz eye color genes from the sheep blowfly Lucilia cuprina

Clones carrying the white and topaz eye color genes have been isolated from genomic DNA libraries of the blowfly Lucilia cuprina using cloned DNA from the homologous white and scarlet genes, respectively, of Drosophila melanogaster as probes. On the basis of hybridization studies using adjacent restriction fragments, homologous fragments were found to be colinear between the genes from the two species. The nucleotide sequence of a short region of the white gene of L. cuprina has been determined, and the homology to the corresponding region of D. melanogaster is 72%; at the derived amino acid level the homology is greater (84%) due to a marked difference in codon usage between the species. A major difference in genome organization between the two species is that whereas the DNA encompassing the D. melanogaster genes is free of repeated sequences, that encompassing their L. cuprina counterparts contains substantial amounts of repeated sequences. This suggests that the genome of L. cuprina is organized on the short period interspersion pattern. Repeated sequence DNA elements, which appear generally to be short (less than 1 kb) and which vary in repetitive frequency in the genome from greater than 10(4) copies to less than 10(2) copies, are found in at least two different locations in the clones carrying these genes. One type of repeat structure, found by sequencing, consists of tandemly repeating short sequences. Restriction site and restriction fragment length polymorphisms involving both the white and topaz gene regions are found within and between populations of L. cuprina.

The Adh gene promoters of Drosophila melanogaster and Drosophila orena are functionally conserved and share features of sequence structure and nuclease-protected sites

The sibling species Drosophila melanogaster and D. orena show similar patterns of alcohol dehydrogenase expression, both spatially and temporally. These two species diverged from a common ancestor 6 million to 15 million years ago, and the DNA sequences of the promoter regions of their Adh genes show a mosaic pattern of conservation and change. By interspecific transformation of D. orena sequences into D. melanogaster, we demonstrate a functional equivalence between these sequences. Using both D. melanogaster embryo extracts and purified transcription factor Adf-1, we compare the protection of these promoter sequences from nuclease, demonstrating considerable conservation.