Logo of genbioBioMed CentralBiomed Central Web Sitesearchsubmit a manuscriptregisterthis articleGenome BiologyJournal Front Page
Genome Biol. 2007; 8(11): R242.
Published online Nov 16, 2007. doi:  10.1186/gb-2007-8-11-r242
PMCID: PMC2258195

Quantification of ortholog losses in insects and vertebrates

Abstract

Background

The increasing number of sequenced insect and vertebrate genomes of variable divergence enables refined comparative analyses to quantify the major modes of animal genome evolution and allows tracing of gene genealogy (orthology) and pinpointing of gene extinctions (losses), which can reveal lineage-specific traits.

Results

To consistently quantify losses of orthologous groups of genes, we compared the gene repertoires of five vertebrates and five insects, including honeybee and Tribolium beetle, that represent insect orders outside the previously sequenced Diptera. We found hundreds of lost Urbilateria genes in each of the lineages and assessed their phylogenetic origin. The rate of losses correlates well with the species' rates of molecular evolution and radiation times, without distinction between insects and vertebrates, indicating their stochastic nature. Remarkably, this extends to the universal single-copy orthologs, losses of dozens of which have been tolerated in each species. Nevertheless, the propensity for loss differs substantially among genes, where roughly 20% of the orthologs have an 8-fold higher chance of becoming extinct. Extrapolation of our data also suggests that the Urbilateria genome contained more than 7,000 genes.

Conclusion

Our results indicate that the seemingly higher number of observed gene losses in insects can be explained by their two- to three-fold higher evolutionary rate. Despite the profound effect of many losses on cellular machinery, overall, they seem to be guided by neutral evolution.

Background

The evolution of gene repertoires is mostly driven by gene duplications and gene losses. Duplications can arise by short-range copying of individual genes or of longer multigene DNA segments, or even result from whole genome duplications [1,2]. Copies of single genes are frequently associated with retrotransposition [3], whereas unequal homologous recombination copies DNA segments of varying length. Gene proliferation, on the other hand, is balanced by gene losses, either through acquiring deleterious mutations that eventually disable the genes or as a consequence of unequal homologous recombination.

Massive gene losses of olfactory receptors were reported in human and ape families compared to mice [4], which have been speculated to be linked with the acquisition of full trichromatic vision, lowering the demand for olfaction [5]. Ohlson's 'less-is-more' hypothesis emphasizes that loss-of-function mutations may play a beneficial role in evolution [6]; an example for adaptive gene loss is the near-complete fixation of a null allele of CASP12 in the human lineage [7], presumably to confer protection from severe sepsis. Gene losses have also been implicated in reproductive isolation of Drosophila races [8].

The fast growing number of available vertebrate and insect genomes allows increasingly refined comparisons and the quantification of the major modes of animal genome evolution. The recent sequencing of the honeybee [9] and the Tribolium beetle [10] genomes extends insect genomics from only Dipteran species to the orders of Hymenoptera and Coleoptera, which radiated about 300 million years ago [11]. This allowed us to quantify and date losses of orthologous groups across ten bilaterian species in the first analysis that consistently compares five insects (phylum Arthropoda) and five vertebrates (phylum Chordata). Previous studies of gene losses have been focussed on mammals [12], vertebrates [13], or included only a single insect [14], or two dipterans [15]. Reassuringly, our analysis recovered previously published cases of gene losses, such as the loss of DNA methylation [16], and the heavy rearrangement of the circadian clock [17] in Diptera.

Results

Quantification of ortholog losses

To systematically identify gene losses in vertebrate and insect representatives of Bilaterian species, we delineated orthologous groups based on all-against-all Smith-Waterman comparisons using the official gene sets of five vertebrates (human, mouse, opossum, chicken and pufferfish) and five insects (fruitfly, malaria mosquito, dengue/yellow fever mosquito, honeybee and red flour beetle) (see details in Materials and methods). The species choice aimed to maximize the phylogenetic coverage with similar lineage radiation times in both deuterostomia and protostomia. The fraction of genes with recognized orthology among these species represents about 70-80% of their predicted gene pools. The comparative analysis of the shared content of gene repertoires across these species is discussed in the study presenting the analysis of the first beetle genome, that of Tribolium castaneum [10], and here we focus on the analysis of losses of orthologous genes. According to their phyletic distribution and gene copy-number in each of the species, we considered the following types of orthologous groups reflecting different selection pressures: the universal single-copy orthologs (U); the universal multiple-copy orthologs (N); patchy orthologs (P) that are present in both phyla in at least three species, in single or multiple copies; and insect- or vertebrate-specific orthologs (I and V, respectively). While universal single-copy orthologs (U) are evolving under a distinct pressure for copy-number control, the number of universal multiple-copy orthologs (N) under similarly strict copy-number control is extremely low (only six groups have equal multiple-copy gene number in at least nine species). Although U, N and P orthologs must all have been present in the last common ancestor of insects and vertebrates, the Urbilateria, losses in these fractions occur at different rates.

Figure Figure1b1b shows the size distribution of the orthologous fractions and the number of losses in each species and ortholog category. The tree shown in Figure Figure1a1a illustrates the species phylogeny, which allowed us to infer the number of losses on the internal branches, assuming evolutionary parsimony, which minimizes the number of events required to explain the phyletic gene distribution in each orthologous group. The phylogenetic tree was reconstructed using maximum-likelihood analysis of the concatenated alignment of 1,150 universal single-copy orthologs [10] where the lengths of the branches are proportional to the number of accumulated mutations, allowing us to compare the gene loss rates with the rates of lineage divergence (measured as the rate of protein substitutions). For the branches closest to the root, the numbers of gene losses cannot be inferred without an additional outgroup.

Figure 1
Quantification of orthologous gene losses in insects and vertebrates. (a) The phylogenetic relations among the organisms are illustrated by the tree, with branch length proportional to the rate of amino acid substitutions estimated using the maximum-likelihood ...

The analysis identified hundreds of differentially lost Urbilaterian genes of U, N and P orthologs in each of the species (see table of Figure Figure1).1). Overall, about 40% of ancient orthologous groups have been lost in at least one (out of the ten) species, illustrating the extent of the evolutionary flexibility of gene pools. Moreover, there are dozens of genes lost in each of the species that otherwise appear as universal single-copy orthologs. Koonin et al. [14] noted that nearly all pan-eukaryotic single-copy orthologs are subunits of known protein complexes; nevertheless, the observed losses indicate that even seemingly tightly constrained genes are, to a certain degree, dispensable in evolution.

Number of losses correlate with molecular divergence

The inferred distribution of losses over the internal branches of the species phylogeny allowed us to correlate them with the estimated geological time of species radiations and the molecular evolutionary rate in each of the lineages. The molecular rates of evolution were quantified using genome-wide maximum-likelihood analysis of amino acid substitutions in the well aligned regions of single-copy orthologs (see Materials and methods). Figure Figure2a2a displays the correlation of the number of losses of the different types of orthologs plotted versus the protein sequence divergence. Losses of U and N orthologs (Figure (Figure2b)2b) occur only at the terminal branches as the fraction definition requires presence of the orthologous genes in at least nine species, whereas losses of P orthologs (Figure (Figure2c)2c) occur at both internal and terminal branches. Correlations are statistically significant for all categories (see Figure Figure22 legend for details), and there is no distinction between insects and vertebrates. Moreover, although the absolute numbers of insect- and vertebrate-specific losses appear different, they in fact follow the same trend when normalized to the total number of the phylum-specific orthologous groups (Figure (Figure2d;2d; see Additional data file 1 for a graph with absolute numbers). The different slopes of the regression lines reflect the varying stringency of evolutionary constraints that differ between the postulated types of orthologs. Despite the difference in the absolute numbers of lost U and N orthologs, their rates of loss are indistinguishable when normalized to the number of such orthologous groups, indicating the same level of purifying selection (Figure (Figure2b).2b). The data show that P orthologs are about 8-fold less constrained than U and N orthologs; this roughly corresponds to about 20% of the common Bilateria gene pool evolving 8 times faster than the remaining, more constrained fraction. I and V orthologs appear to be about three-fold more constrained than P orthologs, which is not surprising as they may represent a similar mixture of a slower evolving fraction of 80% and a faster evolving minority. The level of correlation between the number of losses and the protein sequence divergence rates (Figure (Figure2)2) is similar to that observed between other genome-wide measures of species divergence [18]. Chicken was excluded from this and all following analyses as a clear outlier (see Discussion).

Figure 2
The number of ortholog losses correlates with the rate of amino acid substitutions. The number of orthologous group (U, N, P, I/V) losses normalized with the total size of the fraction is plotted versus the branch length of the maximum-likelihood phylogenetic ...

Insects evolve two to three times faster than vertebrates

Protein sequence divergence is significantly larger between insects than between vertebrates (see the longer branch lengths in Figure Figure1;1; Mann-Whitney U test, p = 0.009). Similarly, this is reflected in the observation of significantly more frequent gene losses in insects than in vertebrates (Mann-Whitney U test: N orthologs, p = 0.016; P orthologs, p = 0.04). In comparison with vertebrates, the rate of evolution in bee and beetle is about two-fold higher and up to three-fold higher in Diptera. This especially high rate of evolution in Diptera, particularly at the base of the Dipteran radiation, has been noted previously [19].

Lower estimate of the Urbilateria number of genes

Despite inherent dating uncertainties, the correlation between the number of lost orthologous groups and divergence times is significant for U and P orthologs (Spearman rank correlations: U orthologs, rs = 0.84, p = 0.007; N orthologs, rs = 0.58, p = 0.11; P orthologs, rs = 0.57, p = 0.03), indicating that losses of ancient genes occur in a roughly clock-like manner. The good correlation between the rate of losses with molecular rate and time indicates their stochastic nature. Projection of these trends as shown in Figure Figure33 to 600 million years ago (MYA), presumably dating the radiation of insects and vertebrates, suggests that over 1,000 (95% confidence interval 799-1,456) Urbilaterian genes have been lost from insects and only half this number (95% confidence interval 404-678) from vertebrates. This leads to the lower estimate of the number of Urbilaterian genes of just over 7,000 (remarkably, we obtained 7,114 orthologous groups with at least one insect and one vertebrate member). This estimate, however, does not take into account: genes that currently appear as insect- or vertebrate-specific, many of which could be of Urbilaterian origin; closely related Urbilateria paralogs that remain unresolved and are likely grouped together in N groups; as well as fractions of fast diverging genes that escaped our orthology classification.

Figure 3
Extrapolation of number of ancient (U, N and P) orthologs to Urbilateria. The regression lines (and their 90% confidence intervals) are drawn using the number of U, N and P orthologous groups in current species, the estimates for putative ancestors, including ...

Functional load of losses

Recovered known facts as positive controls

Reassuringly, closer inspection of several of the predicted cases of lost genes pointed to recently published findings of lineage-specific biology.

Hedgehog signaling pathway rearrangements in Drosophila

Hedgehog signaling pathway rearrangements in Drosophila have been reported where orthologs of human Sil, Hip and Gas1 are missing from Drosophila [20], and homologs of polaris/TG737 (nompB) and Kif3a (Klp64D) appear to have roles unrelated to hedgehog signaling [21,22].

Sid-1/tag-130 gene loss in all Diptera

Sid-1/tag-130 genes have been lost in all Diptera but are present in bee and Tribolium as reported by Weinstock et al. [9]. Sid-1 is implicated in the cellular import of RNA interference signal and enables passive uptake of double-stranded RNA (yet, Sid-1 is likely to be a Caenorhabditis elegans invention as its inparalog, TAG130, is less derived (Additional data file 2)).

DNA-methyltransferases DNMT1 and DNMT3B lost in the Coleoptera/Diptera ancestor

DNA-methyltransferases DNMT1 and DNMT3B have been lost in the Coleoptera/Diptera ancestor, consistent with their loss reported in Diptera [23] and their surprising presence in honeybee [9,16].

A candidate insect telomerase reverse transcriptase

A candidate insect telomerase reverse transcriptase (TERT) is present in honeybee and Tribolium but absent in all Dipterans. The absence of TERT in Diptera seems to be correlated with the loss of telomeric TTAGG repeats [24].

Sterol metabolism, NAD biosynthesis, and other losses

Sterol metabolism, NAD biosynthesis, and other losses proposed earlier from the comparison of the fly and the mosquito genomes [23] seem to have been lost in all insects sequenced so far, that is, before the appearance of holometabolous insects. Exceptions are a dihydroxyacetone kinase 1 lost from both Drosophila and Anopheles, a C-5 sterol desaturase and a histidine ammonia-lyase present in only Tribolium and two genes present in only honeybee, an ornithine carbamoyltransferase and a malonyl-CoA decarboxylase.

Novel case stories

Below we describe some of the identified losses that are likely to have had an impact on the functional divergence of the lineages, exemplifying losses of different types of orthologs, from the most conserved single-copy genes to orthologs with a highly patchy phylogenetic distribution. It has been suggested that secondary gene losses can be driven by the losses of key players of particular pathways or complexes that disable their functionality [25-27]. Hence, we mapped losses to the characterized biochemical pathways annotated for human orthologs; the results for Tribolium and its ancestor are overviewed in Table Table1.1. However, having low numbers of losses per pathway [26], we concentrated more on providing examples of losses of directly interacting genes, reported for Drosophila from protein-protein interaction screens [28] and literature co-citations via human orthologs [29].

Table 1
Losses in Tribolium and its (Coleoptera/Diptera) ancestor mapped to pathways using human orthologs

Losses of universal single-copy orthologs

An example of a universal single-copy ortholog missing in Drosophila is a 35 kDa protein associated with U11 snRNPs. U11 and U12 are components of the minor spliceosome responsible for the splicing of a small number of U12-type introns (<1% in both humans and flies) [30]. The minor spliceosome is widely conserved from plants to humans, including most insects but absent from C. elegans. Lack of a clear ortholog of U11 snRNA and the associated 35 kDa protein has been initially proposed [31], but Schneider et al. [32] identified a highly divergent U11 snRNA. The 31 kDa and 35 kDa proteins seem to be missing from all Drosophila species and a 25 kDa protein is absent from Diptera [33]. Interestingly, the loss of U11/U12 spliceosomal proteins in Drosophila is accompanied by the loss of the majority of U12-type introns [33,34].

Another example of a universal gene that seems to be missing from the Drosophila genome is sortilin-related receptor LR11 (also known as SorLA), a member of the low-density lipoprotein receptor family. LR11 binds low-density lipoprotein, the major cholesterol-carrying lipoprotein of plasma, and transports it into cells by endocytosis. Human LR11 also regulates trafficking of amyloid precursor protein and its expression is decreased in the brain of Alzheimer's disease patients [35].

Losses of universal multi-copy orthologs

An example is the Cdc7 kinase and its regulatory subunit Dbf4 implicated in triggering DNA replication in G1 phase through phosphorylation of Mcm proteins [36]. Cdc7 is essential in yeast in contrast to mice where homozygous null mutants for the Cdc7 ortholog Nr2c2 show impaired spermatogenesis [37]. Cdc7 is a universal single-copy gene with two fly paralogs whereas Dbf4 is present in two copies in humans and opossum. We confirmed the loss of both genes in Tribolium by tBlastn search and phylogenetic analysis (Additional data file 3). Cdc7 is also missing from the current Anopheles annotation but tBlastn searches identified a Cdc7 candidate in the genome. Dbf4 appears to be missing from the Anopheles and Tetraodon genomes. Interestingly, in yeast an allele of the gene MCM5 (CDC46) has been identified that bypasses the requirement for CDC7/DBF4 [38]. Although the Tribolium MCM5 ortholog TC_09146 does not feature the same mutation, P86L, it is conceivable that a similar mutation has rendered CDC7/DBF4 disposable in Tribolium.

Another example of a loss of an otherwise universal gene is the Tribolium ortholog of human ATP-binding cassette transporter A1 (ABCA1). ABCA1 is a cholesterol efflux transporter and is also required for engulfment of apoptotic cells by macrophages in mice and C. elegans [39,40]. In humans, the turnover of ABCA1 is regulated by Alpha1-syntrophin [41], and both genes encoding these proteins appear to be missing from the beetle genome.

Losses of patchy and insect-specific orthologs

We observed numerous losses in Diptera, many of which seem to be involved in the ubiquitin cycle, DNA repair (also reported in [31]), actin cytoskeleton and transcription control (Additional data file 4), which may point to substantial rearrangements of the ancestral pathways. An intriguing example is the BRCC complex, a complex with ubiquitin E3 ligase activity known to be involved in DNA repair, cell cycle regulation and homology-directed repair in human that has lost BRCA1, RBBP-8 and BRCC3 in the Dipteran lineage.

An example of insect-specific orthologous groups lost in Diptera are genes associated with oxidoreductase activity, including Aldo/keto reductases and several FAD dependent oxidoreductases; this category of genes was enriched among the 160 Diptera gene losses in a comparative Gene Ontology (GO) analysis with the Tribolium genome (Additional data file 5).

Extreme cases: exclusive insect models of human genes

At extremes, each novel insect genome sequence uncovers previously invisible orthologous gene relationships to human genes (see [10] for venn diagram that shows how many new orthologous relations are uncovered by the honeybee and beetle genomes). For example, we identified 45 orthologous groups shared between honeybee and at least one vertebrate but lost in the Coleoptera/Diptera ancestor, for example, an ortholog of RAD18 (GB-14468) that is an E3 ubiquitin-protein ligase involved in postreplication repair of UV-damaged DNA.

To complement the initial analysis of the Tribolium genome, we further identified 62 genes that are present in all vertebrates and Tribolium but lost from the other four insect genomes. Examples include Yipf3, a natural killer cell-specific antigen expressed during embryonic hematopoiesis in humans, and CENP-S, which in humans is a component of a centromeric protein complex, CENPA-CAD [42], that replaces histones in centromeres. In Tribolium, the orthologs of the other five complex members [42] seem to be absent from the genome, indicating a different mode of action. CRLF3, a cytokine receptor-like factor 3, has also been lost in all insects but Tribolium, as well as a regulator of the NF-κB pathway, Tgf, which positively regulates I-kappaB kinase. Because of structural and functional similarities in the mode of activation between insect and vertebrate NF-κB/Rel transcription factors, they are thought to have countered infections in Urbilateria [43]. Another Tribolium gene, TC_04309, absent in all sequenced arthropods, is an ortholog of the human F-box only gene 7 (Fbxo7). The tBlastn search and phylogenetic analysis of FBXO7 confirmed the lack of clear orthologs in other insects (Additional data files 6 and 7). FBXO7 is a component of modular E3 ubiquitin protein ligases called SCFs and functions in phosphorylation-dependent ubiquitination [44]. Human FBXO7 was also reported to positively regulate the activity of cyclin D/CDK6 in order to facilitate entry into the cell cycle [45]. In Drosophila, the cyclin D/CDK6 complex stimulates cell growth as well as proliferation [46,47]. Amniotes have two cdk4 orthologs due to a gene duplication (cdk4 and cdk6) and two cyclin D orthologs. Tribolium also encodes a cdk4 ortholog and two cyclin D orthologs, in contrast to the other insects, which have only one cyclin D ortholog (Additional data file 8). It is tempting to speculate that the presence of FBXO7 and a second cyclin D in the beetle are functionally linked. TC_04309 is expressed in limbs and the hindgut of Tribolium embryos (Figure (Figure4).4). The function of TC_04309 is unknown but, taken together, it is conceivable that it controls cell proliferation in a tissue-specific manner as in mammals.

Figure 4
Expression pattern of the F-box gene during embryogenesis of the beetle T. castaneum. (a) F-box gene TC_04309 is initially expressed in the germ rudiment at the rims of the invaginating mesoderm, a position where activated Map-kinase is also seen [76]. ...

Robustness of estimates

Several factors can lead to an overestimation of gene losses: incomplete annotations, genome sequence gaps and the limited sensitivity of protein sequence comparison methods. Reassuringly, our estimates of number of gene losses for Drosophila and human, the two most extensively studied and curated model organisms, are similar to that of automatically annotated species, indicating a fairly good quality of genome annotations and their relative completeness. The chicken genome, however, shows exceptionally high numbers of losses in all categories that are likely to be overestimates due to an incomplete genome sequence that was estimated to be missing 5-10% of the genes [48], and, therefore, it was not taken into account in the analysis presented above. A closer inspection of 'missing' Tribolium genes from the universal single-copy and insect-specific fraction allowed us to correct about 30 Tribolium genes overlooked by the automatic annotation and some 150 merged genes. Nevertheless, most 'missing' genes were confirmed to be absent from the genome using tBlastn searches, indicating that the Tribolium annotation is nearly complete for evolutionarily conserved genes. Orthology misclassifications can also lead to inflated estimates when orthologous groups are wrongly split up, or to underestimates when several orthologous groups are spuriously pooled together, 'hiding' losses. We compared the results of our analysis with an independently derived and hand curated set of about 100 gene losses in Diptera (Hugh Robertson, personal communication). Detailed phylogenetic examination revealed only two to three cases of likely errors in our high throughput orthology identification pipeline and a few complicated cases that could not be resolved even using phylogenetic methods as the proteins were too short or too divergent.

Discussion

We present here the quantification of losses of orthologous groups in five vertebrate and five insect genomes. Lineage-specific gene duplications result in multi-copy orthologous groups or fine-grained gene families. Here we focused on complete losses of such gene families (requiring all orthologous genes to be lost in a lineage). Members of an orthologous group are likely to share overlapping functions, and a complete loss of all representatives is more likely to have biological consequences [49,50] than a loss of a specific gene member. The parsimonious interpretation of the losses in the context of the species phylogeny suggests hundreds of gene losses on each branch of the tree. Diptera species lost the most genes, and placentals the least.

We show that the higher numbers of lost genes in insects can be explained by their higher rates of evolution as the loss rate is positively correlated with the molecular rate of evolution for each ortholog category and branch of the phylogeny. Interestingly, losses normalized for evolutionary rate and total number of orthologous groups are similar between insects and vertebrates, even for I and V orthologs. Therefore, one can not exclude that gene losses are mainly driven by neutral evolution [51,52], which should be taken as the null hypothesis until proven otherwise. Our data also suggest that about 20% of the gene repertoire evolves 8 times faster than the rest. The fact that the overall number of losses of orthologous groups is in agreement with the model of neutral evolution does not, of course, mean that all losses are selectively neutral. In that respect, it is noteworthy that some of the lost genes we discuss, such as Cdc7/Dbf4 or Fboxo7, seem to act as positive regulators.

Several hypotheses have been put forward to explain differences in evolutionary rates across species [53]. A high evolutionary rate might simply reflect differences in mutation rates. The known contributors to the rate of mutations, metabolic rate [54] and generation time [55], are clearly different between dipterans and mammals. In addition, differences in DNA methylation, fidelity of DNA-repair mechanisms or the production of DNA-damaging agents have also been suggested to explain different mutation rates in different species [53,56]. We found a number of genes implicated in DNA repair missing from Diptera. Although the functional consequences of these losses in Diptera are unknown, they might contribute to an increased mutation rate. A second hypothesis is that the efficiency of selection against deleterious mutants varies across species, due to differences in effective population size and/or mode of reproduction. Finally, rate variation across lineages could be caused by species-specific differences in the timing and frequency of adaptive evolution. Indeed, theoretical models [57,58] have proposed that evolvability is a selectable trait.

Conclusion

We showed that the gene loss rate correlates well with rates of molecular evolution, explaining the significantly higher number of gene losses in insects. The data also can not reject that gene losses are dominated by neutral evolution.

The hundreds of lost genes we identified along the phylogenetic tree suggest common rearrangements and rewiring of ancient pathways and signaling cascades. Such global approaches are suitable for generating further experimentally testable hypotheses, and will lead to a better understanding of global evolutionary trends and detailed functional differences among lineages.

Materials and methods

Orthology classification

Protein sets were retrieved from Ensembl for Drosophila, Anopheles and all vertebrates as of 4 August 2006. Tribolium and Apis proteins were retrieved from Baylor College of Medecine and Aedes proteins from VectorBase. The assignment to orthologous groups was performed as described earlier [9,59,60]. Namely, we retained the longest open reading frame per locus and performed all-against-all comparisons using the Smith-Waterman algorithm as implemented in ParAlign [61] with default parameters. The orthologous groups were then assembled from the best reciprocal hits (BRHs; reciprocally best maching genes in between-genome-comparisons) applying a COG-like [62] procedure to join BRHs across three or more species, going from the best scoring ones until an E-value cut-off of 10-6, and keeping single BRH pairs only with E-values less than 10-10. Furthermore, the orthologous groups were expanded by genes that are more similar to each other within a proteome than to any gene in any of the other species, and by very similar copies that share over 97% sequence identity, which were identified initially using CD-hit [63]. All proteins in a group were required to have aligned regions overlapping by at least 20 residues to avoid the 'domain walking' effect.

Species tree

A maximum likelihood species tree was calculated using the concatenated multiple alignments of 1,150 orthologs present in exactly one copy in all the organisms studied here. Multiple protein alignments were produced using muscle [64] and confidently aligned regions were extracted using Gblocks [65] with default settings. Individual protein alignments were concatenated into a 336,069 amino acid superalignment that was then subjected to maximum-likelihood analysis using the JTT model (G4+I+F) as implemented in PhyML [66] and we used Tree-Puzzle [67] to join separate bootstrap analyses. All shown branchings have at least 99% bootstrap support estimated from 500 replicates.

Quantification of losses and correlation with other traits

Species radiation dates were taken from the literature: for insects from [18] and for vertebrates from [68,69]. We used MatLab version 7.2 (MathWorks, Natick MA, USA) for statistical analysis and data plotting. Regression lines were required to cross the origin. For each category of orthologs, the slopes of the regression lines for insects and vertebrates were compared based on a Student's t-distribution and were found not to be significantly different. Because traits were not normally distributed, we used non-parametric Spearman's correlation coefficients and Mann-Whitney U tests. Chicken data were excluded from graphs and statistical tests (see Discussion).

Manual analysis of case studies

Selected orthologous groups were examined manually as follows. The absence of Tribolium proteins was verified by screening the Tribolium proteome, genome (assembled and single reads) and expressed sequence tags using the Baylor College of Medicine blast server [70]. All sufficiently similar sequences, including members of other orthologous groups, were aligned using muscle v3.6 [64] with default settings and all positions containing gaps were trimmed from conserved blocks using Gblocks [65]. Phylogenetic trees were constructed using maximum likelihood as implemented in PhyML [66] using the JTT model of amino acid substitution, a gamma distribution of rates over four rate categories and 100 bootstraps.

Pathway mapping and database searches

We used pathway annotations from the KEGG database [71], mapping genes to Biocarta and co-citation analysis using Webgestalt [29] web interface. For data mining we used Ensembl [72], Swiss-prot/UniProt [73], Flybase [74], the Interactive Fly [22] and Online Mendelian Inheritance in Man [75] annotations.

Abbreviations

ABCA1, ATP-binding cassette transporter A1; BRH, best reciprocal hit; CRLF3, cytokine receptor-like factor 3; GO, Gene Ontology; I, insect-specific orthologs; MYA, million years ago; N, universal multiple-copy orthologs; P, patchy orthologs; TERT, insect telomerase reverse transcriptase; U, universal single-copy orthologs; V, vertebrate-specific orthologs.

Authors' contributions

SW and EMZ analyzed the data and wrote the manuscript. EK contributed the orthology data and the species phylogeny. RS and TK contributed experimental characterization of exclusive Tribolium and honeybee orthologs of human genes. EMZ supervised the project.

Additional data files

The following additional data are available with the online version of this paper. Additional data file 1 is a graph showing the correlation between the absolute number of lost orthologous groups and and the rate of amino acid substitutions. Additional data files 2 and 3 provide the phylogenetic analysis of SID-1 and CDC7, respectively. Additional data file 4 is a table listing GO analysis of insect-specific orthologous groups lost in all Dipterans. Additional data file 5 is a table listing functionally linked genes coeliminated in the Diptera and Drosophila lineages. Additional file 6 provides the phylogenetic analysis of Fboxo7/cdk4/cyclin D. Additional data file 7 is a figure showing the alignment of Fboxo7 proteins.

Supplementary Material

Additional data File 1:

Correlation between the absolute number of lost orthologous groups and the rate of amino acid substitutions.

Additional data File 2:

Phylogenetic analysis of SID-1 proteins.

Additional data File 3:

Phylogenetic analysis of CDC7 proteins.

Additional data File 4:

GO analysis of insect-specific orthologous groups lost in all Dipterans.

Additional data File 5:

Coeliminiation of functionally linked genes in the Diptera and Drosophila lineages.

Additional data File 6:

Phylogenetic analysis of Fboxo7, cdk4 and cyclin D.

Additional data File 7:

Alignment of Fboxo7 proteins.

Acknowledgements

We thank Hugh Robertson for sharing unpublished data, Peer Bork for stimulating discussions, and Robert M Waterhouse for help with the manuscript. Swiss National Science Foundation is acknowledged for funding (SNF 3100A0-112588 to EMZ).

References

  • Samonte RV, Eichler EE. Segmental duplications and the evolution of the primate genome. Nat Rev Genet. 2002;3:65–72. doi: 10.1038/nrg705. [PubMed] [Cross Ref]
  • Zhang J. Evolution by gene duplication: an update. Trends Ecol Evol. 2003;18:292–298. doi: 10.1016/S0169-5347(03)00033-8. [Cross Ref]
  • Brosius J. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene. 1999;238:115–134. doi: 10.1016/S0378-1119(99)00227-9. [PubMed] [Cross Ref]
  • Niimura Y, Nei M. Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates. J Human Genet. 2006;51:505–517. doi: 10.1007/s10038-006-0391-8. [PMC free article] [PubMed] [Cross Ref]
  • Gilad Y, Wiebe V, Przeworski M, Lancet D, Paabo S. Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. PLoS Biol. 2004;2:E5. doi: 10.1371/journal.pbio.0020005. [PMC free article] [PubMed] [Cross Ref]
  • Olson MV. When less is more: gene loss as an engine of evolutionary change. Am Human Genet. 1999;64:18–23. doi: 10.1086/302219. [PMC free article] [PubMed] [Cross Ref]
  • Wang X, Grus WE, Zhang J. Gene losses during human origins. PLoS Biol. 2006;4:e52. doi: 10.1371/journal.pbio.0040052. [PMC free article] [PubMed] [Cross Ref]
  • Greenberg AJ, Moran JR, Fang S, Wu CI. Adaptive loss of an old duplicated gene during incipient speciation. Mol Biol Evol. 2006;23:401–410. doi: 10.1093/molbev/msj045. [PubMed] [Cross Ref]
  • Weinstock GM, Robinson GE, Gibbs RA, Worley KC, Evans JD, Maleszka R, Robertson HM, Weaver DB, Beye M, Bork P, et al. Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006;443:931–949. doi: 10.1038/nature05260. [Cross Ref]
  • Consortium TGS. The first genome sequence of a beetle, Tribolium castaneum, a model for insect development and pest biology. Nature.
  • Grimaldi D, Engel M. Evolution of the Insects. Cambridge: Cambridge University Press; 2005.
  • Demuth JP, Bie TD, Stajich JE, Cristianini N, Hahn MW. The evolution of Mammalian gene families. PLoS ONE. 2006;1:e85. doi: 10.1371/journal.pone.0000085. [PMC free article] [PubMed] [Cross Ref]
  • Blomme T, Vandepoele K, De Bodt S, Simillion C, Maere S, Van de Peer Y. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 2006;7:R43. doi: 10.1186/gb-2006-7-5-r43. [PMC free article] [PubMed] [Cross Ref]
  • Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 2004;5:R7. doi: 10.1186/gb-2004-5-2-r7. [PMC free article] [PubMed] [Cross Ref]
  • Hughes AL, Friedman R. Differential loss of ancestral gene families as a source of genomic divergence in animals. Proc Biol Sci. 2004;271(Suppl 3):S107–109. doi: 10.1098/rsbl.2003.0124. [PMC free article] [PubMed] [Cross Ref]
  • Wang Y, Jorda M, Jones PL, Maleszka R, Ling X, Robertson HM, Mizzen CA, Peinado MA, Robinson GE. Functional CpG methylation system in a social insect. Science. 2006;314:645–647. doi: 10.1126/science.1135213. [PubMed] [Cross Ref]
  • Rubin EB, Shemesh Y, Cohen M, Elgavish S, Robertson HM, Bloch G. Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock. Genome Res. 2006;16:1352–1365. doi: 10.1101/gr.5094806. [PMC free article] [PubMed] [Cross Ref]
  • Zdobnov EM, Mering C, Letunic I, Bork P. Consistency of genome-based methods in measuring Metazoan evolution. FEBS Lett. 2005;579:3355–3361. doi: 10.1016/j.febslet.2005.04.006. [PubMed] [Cross Ref]
  • Savard J, Tautz D, Richards S, Weinstock GM, Gibbs RA, Werren JH, Tettelin H, Lercher MJ. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res. 2006;16:1334. doi: 10.1101/gr.5204306. [PMC free article] [PubMed] [Cross Ref]
  • Glise B, Miller CA, Crozatier M, Halbisen MA, Wise S, Olson DJ, Vincent A, Blair SS. Shifted, the Drosophila ortholog of Wnt inhibitory factor-1, controls the distribution and movement of Hedgehog. Dev Cell. 2005;8:255–266. doi: 10.1016/j.devcel.2005.01.003. [PubMed] [Cross Ref]
  • Kernan M, Cowan D, Zuker C. Genetic dissection of mechanosensory transduction: mechanoreception-defective mutations of Drosophila. Neuron. 1994;12:1195–1206. doi: 10.1016/0896-6273(94)90437-5. [PubMed] [Cross Ref]
  • The Interactive Fly http://www.sdbonline.org/fly/segment/shifted4.htm
  • Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science. 2002;298:149–159. doi: 10.1126/science.1077061. [PubMed] [Cross Ref]
  • Robertson HM, Gordon KHJ. Canonical TTAGG-repeat telomeres and telomerase in the honey bee, Apis mellifera. Genome Res. 2006;16:1345. doi: 10.1101/gr.5085606. [PMC free article] [PubMed] [Cross Ref]
  • Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc Natl Acad Sci USA. 1999;96:4285–4288. doi: 10.1073/pnas.96.8.4285. [PMC free article] [PubMed] [Cross Ref]
  • Aravind L, Watanabe H, Lipman DJ, Koonin EV. Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci USA. 2000;97:11319–11324. doi: 10.1073/pnas.200346997. [PMC free article] [PubMed] [Cross Ref]
  • Barker D, Pagel M. Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. Plos Comput Biol. 2005;1:24–31. doi: 10.1371/journal.pcbi.0010003. [PMC free article] [PubMed] [Cross Ref]
  • Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006;34:D535–539. doi: 10.1093/nar/gkj109. [PMC free article] [PubMed] [Cross Ref]
  • Zhang B, Kirov S, Snoddy J. WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005;33:W741–W748. doi: 10.1093/nar/gki475. [PMC free article] [PubMed] [Cross Ref]
  • Will CL, Luhrmann R. Splicing of a rare class of introns by the U12-dependent spliceosome. Biol Chem. 2005;386:713–724. doi: 10.1515/BC.2005.084. [PubMed] [Cross Ref]
  • Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF. The Genome Sequence of Drosophila melanogaster. Science. 2000;287:2185. doi: 10.1126/science.287.5461.2185. [PubMed] [Cross Ref]
  • Schneider C, Will CL, Brosius J, Frilander MJ, Luhrmann R. Identification of an evolutionarily divergent U11 small nuclear ribonucleoprotein particle in Drosophila. Proc Natl Acad Sci USA. 2004;101:9584–9589. doi: 10.1073/pnas.0403400101. [PMC free article] [PubMed] [Cross Ref]
  • Mount SM, Gotea V, Lin CF, Hernandez K, Makalowski W. Spliceosomal small nuclear RNA genes in 11 insect genomes. RNA. 2007;13:5–14. doi: 10.1261/rna.259207. [PMC free article] [PubMed] [Cross Ref]
  • Sheth N, Roca X, Hastings ML, Roeder T, Krainer AR, Sachidanandam R. Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res. 2006;34:3955–3967. doi: 10.1093/nar/gkl556. [PMC free article] [PubMed] [Cross Ref]
  • Spoelgen R, von Arnim CA, Thomas AV, Peltan ID, Koker M, Deng A, Irizarry MC, Andersen OM, Willnow TE, Hyman BT. Interaction of the cytosolic domains of sorLA/LR11 with the amyloid precursor protein (APP) and beta-secretase beta-site APP-cleaving enzyme. J Neurosci. 2006;26:418–428. doi: 10.1523/JNEUROSCI.3882-05.2006. [PubMed] [Cross Ref]
  • Bell SP, Dutta A. DNA replication in eukaryotic cells. Annu Rev Biochem. 2002;71:333–374. doi: 10.1146/annurev.biochem.71.110601.135425. [PubMed] [Cross Ref]
  • Mu X, Lee YF, Liu NC, Chen YT, Kim E, Shyr CR, Chang C. Targeted inactivation of testicular nuclear orphan receptor 4 delays and disrupts late meiotic prophase and subsequent meiotic divisions of spermatogenesis. Mol Cell Biol. 2003;24:5887–5899. doi: 10.1128/MCB.24.13.5887-5899.2004. [PMC free article] [PubMed] [Cross Ref]
  • Hardy CFJ, Dryga O, Seematter S, Pahl PMB, Sclafani RA. mcm5/cdc46-bob1 bypasses the requirement for the S phase activator Cdc7p. Proc Natl Acad Sci USA. 1997;94:3151–3155. doi: 10.1073/pnas.94.7.3151. [PMC free article] [PubMed] [Cross Ref]
  • Hamon Y, Broccardo C, Chambenoit O, Luciani MF, Toti F, Chaslin S, Freyssinet JM, Devaux PF, McNeish J, Marguet D. ABC1 promotes engulfment of apoptotic cells and transbilayer redistribution of phosphatidylserine. Nat Cell Biol. 2000;2:399–406. doi: 10.1038/35017029. [PubMed] [Cross Ref]
  • Sheps JA, Ralph S, Zhao ZY, Baillie DL, Ling V. The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes. Genome Biol. 2004;5:R15. doi: 10.1186/gb-2004-5-3-r15. [PMC free article] [PubMed] [Cross Ref]
  • Munehira Y, Ohnishi T, Kawamoto S, Furuya A, Shitara K, Imamura M, Yokota T, Takeda S, Amachi T, Matsuo M. {alpha} 1-Syntrophin modulates turnover of ABCA1. Biol Chem. 2004;279:15091–15095. doi: 10.1074/jbc.M313436200. [PubMed] [Cross Ref]
  • Foltz DR, Jansen LE, Black BE, Bailey AO, Yates JR, 3rd, Cleveland DW. The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol. 2006;8:458–469. doi: 10.1038/ncb1397. [PubMed] [Cross Ref]
  • Hoffmann JA, Reichhart JM. Drosophila innate immunity: an evolutionary perspective. Nat Immunol. 2002;3:121–126. doi: 10.1038/ni0202-121. [PubMed] [Cross Ref]
  • Hsu JM, Lee YC, Yu CT, Huang CY. Fbx7 functions in the SCF complex regulating Cdk1-cyclin B-phosphorylated hepatoma up-regulated protein (HURP) proteolysis by a proline-rich region. Biol Chem. 2004;279:32592–32602. doi: 10.1074/jbc.M404950200. [PubMed] [Cross Ref]
  • Laman H, Funes JM, Ye H, Henderson S, Galinanes-Garcia L, Hara E, Knowles P, McDonald N, Boshoff C. Transforming activity of Fbxo7 is mediated specifically through regulation of cyclin D/cdk6. EMBO J. 2005;24:3104–3116. doi: 10.1038/sj.emboj.7600775. [PMC free article] [PubMed] [Cross Ref]
  • Datar SA, Jacobs HW, de la Cruz AFA, Lehner CF, Edgar BA. The Drosophila cyclin D-cdk4 complex promotes cellular growth. EMBO J. 2000;19:4543–4554. doi: 10.1093/emboj/19.17.4543. [PMC free article] [PubMed] [Cross Ref]
  • Meyer CA, Jacobs HW, Datar SA, Du W, Edgar BA, Lehner CF. Drosophila Cdk4 is required for normal growth and is dispensable for cell cycle progression. EMBO J. 2000;19:4533–4542. doi: 10.1093/emboj/19.17.4533. [PMC free article] [PubMed] [Cross Ref]
  • Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME, et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004;432:695–716. doi: 10.1038/nature03154. [PubMed] [Cross Ref]
  • Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 2003;421:231–237. doi: 10.1038/nature01278. [PubMed] [Cross Ref]
  • Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, Li WH. Role of duplicate genes in genetic robustness against null mutations. Nature. 2003;421:63–66. doi: 10.1038/nature01198. [PubMed] [Cross Ref]
  • Kimura M, Takahata N. Selective constraint in protein polymorphism: study of the effectively neutral mutation model by using an improved pseudosampling method. Proc Natl Acad Sci USA. 1983;80:1048–1052. doi: 10.1073/pnas.80.4.1048. [PMC free article] [PubMed] [Cross Ref]
  • Ohta T. Slightly deleterious mutant substitutions in evolution. Nature. 1973;246:96–98. doi: 10.1038/246096a0. [PubMed] [Cross Ref]
  • Pál C, Papp B, Lercher MJ. An integrated view of protein evolution. Nat Rev Genet. 2006;7:337–348. doi: 10.1038/nrg1838. [PubMed] [Cross Ref]
  • Rand DM, Kann LM. Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol Biol Evol. 1996;13:735–748. [PubMed]
  • Kohne DE. Evolution of higher-organism DNA. Quart Rev Biophys. 1970;3:327–375. [PubMed]
  • Kumar S. Molecular clocks: four decades of evolution. Nat Rev Genet. 2005;6:654–662. doi: 10.1038/nrg1659. [PubMed] [Cross Ref]
  • Wagner A. Does evolutionary plasticity evolve? Evolution. 1996;50:1008–1023. doi: 10.2307/2410642. [Cross Ref]
  • Earl DJ, Deem MW. Evolvability is a selectable trait. Proc Natl Acad Sci USA. 2004;101:11531–11536. doi: 10.1073/pnas.0404656101. [PMC free article] [PubMed] [Cross Ref]
  • Kriventseva EV, Rahman N, Espinosa O, Zbodnov EM. OrthoDB: the hierarchical catalog of eukaryotic orthologs. Nucleic Acids Res. 2007 doi:10.1093/nar/gkm845. [PMC free article] [PubMed]
  • Zdobnov EM, Bork P. Quantification of insect genome divergence. Trends Genet. 2007;23:16–20. doi: 10.1016/j.tig.2006.10.004. [PubMed] [Cross Ref]
  • Saebo PE, Andersen SM, Myrseth J, Laerdahl JK, Rognes T. PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology. Nucleic Acids Res. 2005;33:W535–539. doi: 10.1093/nar/gki423. [PMC free article] [PubMed] [Cross Ref]
  • Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997;278:631–637. doi: 10.1126/science.278.5338.631. [PubMed] [Cross Ref]
  • Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–1659. doi: 10.1093/bioinformatics/btl158. [PubMed] [Cross Ref]
  • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. doi: 10.1093/nar/gkh340. [PMC free article] [PubMed] [Cross Ref]
  • Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17:540–552. [PubMed]
  • Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696–704. doi: 10.1080/10635150390235520. [PubMed] [Cross Ref]
  • Schmidt HA, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002;18:502–504. doi: 10.1093/bioinformatics/18.3.502. [PubMed] [Cross Ref]
  • Kumar S, Hedges SB. A molecular timescale for vertebrate evolution. Nature. 1998;392:917–920. doi: 10.1038/31927. [PubMed] [Cross Ref]
  • Hedges SB. The origin and evolution of model organisms. Nat Rev Genet. 2002;3:838–849. doi: 10.1038/nrg929. [PubMed] [Cross Ref]
  • Baylor College of Medicine Blast Server: T. castaneum http://www.hgsc.bcm.tmc.edu/blast/blast.cgi?organism=Tcastaneum
  • Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28:27–30. doi: 10.1093/nar/28.1.27. [PMC free article] [PubMed] [Cross Ref]
  • Hubbard TJP, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. Ensembl 2007. Nucleic Acids Res. 2007;35:D610–617. doi: 10.1093/nar/gkl996. [PMC free article] [PubMed] [Cross Ref]
  • Bairoch A, Bougueleret L, Altairac S, Amendolia V, Auchincloss A, Puy GA, Axelsen K, Baratin D, Blatter MC, Boeckmann B, et al. The universal protein resource (UniProt). Nucleic Acids Res. 2007;35:D193–D197. doi: 10.1093/nar/gkl929. [Cross Ref]
  • Crosby MA, Goodman JL, Strelets VB, Zhang PL, Gelbart WM. FlyBase: genomes by the dozen. Nucleic Acids Res. 2007;35:D486–D491. doi: 10.1093/nar/gkl827. [PMC free article] [PubMed] [Cross Ref]
  • Online Mendelian Inheritance in Man http://www.ncbi.nlm.nih.gov/omim
  • Schoppmeier M, Schröder R. Maternal torso signaling controls body axis elongation in a short germ insect. Curr Biol. 2005;15:2131–2136. doi: 10.1016/j.cub.2005.10.036. [PubMed] [Cross Ref]

Articles from Genome Biology are provided here courtesy of BioMed Central
PubReader format: click here to try

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...