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Mode and Tempo of Molecular Evolution in the Nematode Caenorhabditis: Cytochrome Oxidase II and Calmodulin Sequences
Abstract
Through direct sequencing methods, the mitochondrial gene for cytochrome oxidase subunit two (CO II) and the single-copy nuclear gene for calmodulin were compared among strains of Caenorhabidits elegans and two other Caenorhabditis species (C. remanei and C. briggsae). In addition the CO II sequence was determined from a distantly related nematode, Steinernema intermedii. Among the 11 strains of C. elegans tested, there are four types of CO II gene, arising from two major lineages. Levels of intraspecific difference in the CO II gene are low (less than 2.0%) compared to the extraordinary divergence between congeneric species, which is about 50% when corrected for multiple hits. Concordant with the increase in divergence between taxa is a change in the pattern of substitution from a strong transition bias (24 transitions compared to two transversions) within species to a substitution pattern that appears to reflect the base composition of the mitochondrial genome when more divergent nematodes are compared. The base composition of the Caenorhabditis CO II gene is strongly biased toward A + T at all three positions of codons and appears to constrain the amino acid composition of the protein. Both the CO II and calmodulin genes show extreme conservation of amino acid sequences. When the accumulation of changes at silent sites in the two genes is compared among strains, it becomes evident that the mitochondrial gene is changing faster than the nuclear gene.
... Molecular variation in the C. elegans natural lines has been studied using single mitochondrial and nuclear genes (Thomas and Wilson 1991), as well as transposons such as Tc1 (Egilmez, Ebert, and Shmookler Reis 1995;Hodgkin and Doniach 1997). A recent large-scale analysis of nuclear single-nucleotide polymorphism (SNP) patterns shows extensive variation in SNP density among different lines and that many of the lines share SNPs (Koch et al. 2000). ...
... mtDNA base composition was highly stable in all the C. elegans natural isolates: 44.9% to 45.1% T, 9.0% to 9.1% C, 30.7% to 30.9% A, and 15.1% to 15.2% G. Stationarity of base composition, necessary for the phylogenetic analyses presented below, was confirmed using Tree-Puzzle (Schmidt et al. 2002). The pattern of mtDNA variation observed here in the C. elegans natural isolates was consistent with what has previously been observed in C. elegans and other animal species (Thomas and Wilson 1991;Vigilant et al. 1991;Ballard and Kreitman 1994;Xia, Hafner, and Sudman 1996). We explored the nuclear substitution patterns of the C. elegans natural isolates by sequencing 44,111 bp of nuclear DNA from 18 of the isolates (table 2). ...
... Nuclear variable sites were, on average, lower in abundance compared with mtDNA variable sites in the C. elegans natural isolates, as has been previously reported (table 2) (Thomas and Wilson 1991). However, two nuclear loci harbored an extremely large number of variable sites (table 2); these will be considered in-depth further below. ...
This study establishes a phylogenetic framework for the natural geographic isolates of the widely studied nematode species Caenorhabditis elegans. Virtually complete mitochondrial genomes are sequenced from 27 C. elegans natural isolates to characterize mitochondrial divergence patterns and to investigate the evolutionary history of the C. elegans hermaphrodite lineages. Phylogenetic analysis of mitochondrial sequences reveals the presence of two major C. elegans hermaphrodite clades (designated clade I and clade II). Fifty-six nuclear loci, widely distributed across the five autosomes and the X chromosome, are also analyzed in a subset of the C. elegans isolates to evaluate nuclear divergence patterns and the extent of mating between different strains. A comparison of the phylogenetic tree derived from mitochondrial data with the phylogenetic tree derived from nuclear data reveals only one inconsistency in the distribution of isolates into clades I and II, suggesting that mating between divergent C. elegans strains is an infrequent event in the wild.
... The first systematic analysis of codon usage in C. elegans is the study of Stenico et al. (1994), although biased codon patterns were pointed out earlier (Emmons 1988;Thomas and Wilson 1991;Kennedy et al. 1993). It is from this study that most of C. elegans optimal codons were identified (see also Sharp and Bradnam 1997;Duret and Mouchiroud 1999). ...
... However, there is substantial heterogeneity in the levels of diversity across loci and strong dependence on whether global or local population samples are considered (Denver et al. 2003;Barrière and Félix 2005a;Stewart et al. 2005;Cutter 2006). In coding sequences, purifying selection causes the much lower levels of genetic variation observed per site for replacement sites relative to synonymous and noncoding sites (Thomas and Wilson 1991;Koch et al. 2000;Wicks et al. 2001;Graustein et al. 2002;Denver et al. 2003;Jovelin et al. 2003). Nucleotide polymorphism in C. briggsae is of a similar magnitude as for C. elegans, although the more striking population structure in C. briggsae gives rise to two to three times as many differences per kilobase among the haplotypes that derive from different latitudinal regions (Graustein et al. 2002;Cutter, Felix 2006;Hillier et al. 2007;Howe and Denver 2008). ...
... Consequently, mitochondrial sequence is expected to have ;10 times the neutral polymorphism of nuclear loci, on average. Mitochondrial sequences do indeed exhibit higher polymorphism than nuclear loci (Thomas and Wilson 1991;Graustein et al. 2002;Denver et al. 2003). In a reanalysis of nearly complete mitochondrial genome sequences for a global sample of 27 C. elegans strains (Denver et al. 2003), we calculate that synonymous site diversity across mitochondrial genes is p syn 5 0.031 (95% confidence interval [CI] 0.012-0.072), ...
A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.
... A transition bias in nucleotide substitution is common in all animal mtDNA studied to date. This phenomenon has been reported in both vertebrate species (Beckenbach et al., 1990;Brown et al., 1982;Irwin et al., 1991) and invertebrate species (Thomas and Wilson, 1991). Two factors have been suggested to contribute to this: (1) most spontaneous mutations are transitional type substitutions (Li et al., 1984); (2) purifying selection in protein-coding genes can tolerate transition substitutions which tend to yield synonymous mutations rather than transversional mutations, that more frequently lead to amino acid changes. ...
... This was observed in the mtDNA evolution study of Caenorhabditis where a noticeable drop in tsltv ratio was observed between intra-to inter-specific compa.risons (Thomas and Wilson, 1991). ...
... This would not be expected if hermaphroditism facilitated speciation unless hermaphroditism was a recent acquisition in this genus. Molecular data indicate that the hermaphroditic species of Caenorhabditis , C. elegans and C. briggsae, are evolutionarily ancient lineages (Emmons et aI., 1979; Butler et aI., 1981; Prasad and Baillie, 1989; Heschl and Baillie, 1990; Thomas and Wilson, 1991 ). Second, geographically separate populations of C. elegans exhibit a high degree ofgenetic cohesion (Emmons et aI., 1983; Thomas and Wilson, 1991 ), suggesting that the spread of allelic variants within these populations is slow. ...
... Molecular data indicate that the hermaphroditic species of Caenorhabditis , C. elegans and C. briggsae, are evolutionarily ancient lineages (Emmons et aI., 1979; Butler et aI., 1981; Prasad and Baillie, 1989; Heschl and Baillie, 1990; Thomas and Wilson, 1991 ). Second, geographically separate populations of C. elegans exhibit a high degree ofgenetic cohesion (Emmons et aI., 1983; Thomas and Wilson, 1991 ), suggesting that the spread of allelic variants within these populations is slow. Thus, in ...
We have attempted interspecific hybridizations among six species of rhabditid nematodes: Caenorhabditis elegans, Caenorhabditis briggsae, Caenorhabditis remanei, Caenorhabditis sp. v, Rhabditis sp., and Peloderateres. Copulation was observed in all crosses between Caenorhabditis species; however, none resulted in the generation of stable hybrid populations. No copulation was observed in crosses between Caenorhabditis males and Rhabditis or Pelodera females, even when congeneric females were present, suggesting that Caenorhabditis males are able to selectively recognize congeneric females by a short-range stimulus. All pairwise combinations of Caenorhabditis species were isolated to some degree by gametic mechanisms; 7 of 12 combinations were cross infertile and 5 of 12 were cross-fertile but had low brood sizes. In cross-fertile combinations, most hybrid embryos were inviable and arrested prior to gastrulation. Only in crosses of C. briggsae males to C. sp. v females did any hybrids survive embryogenesis. Most of these C. briggsae/C. sp. v hybrids arrested during larval development, and the few that reached adulthood invariably were female. These results are consistent with the presence of at least two lethal factors in the C. briggsae- C. sp. v combination: a maternal lethal factor in the cytoplasm of C. briggsae and a recessive lethal factor on the X chromosome of C. sp. v.
... Our observed high AT content and codon usage analysis bias of nd4 suggest that there is an A+T mutational bias in Heterorhabditis nd4 gene sequence and that the possibility of substitutions from C or G to A or T should always be higher than the opposite direction. A+T mutational bias has been also observed in many nematodes including genus Caenorhabditis elegans [28] and Ascaris suum [29], Meloidogyne hapla [30] and several other nematode species [31,32]. ...
... However, these ratios have been reduced when performing intra-specific comparison, H. contortus and H. placei (1.1) [32]. Similar case of rapid drop of si/sv ratio was observed by Thomas and Wilson [28] when moving from intrato inter-specific comparison in Caenorhabditis. Thus, it is important to use only the most closely related species in order to infer the substitution patterns correctly in nematodes due to the transitional change saturation on the con-generic species level and the transversional changes plateau on the con-familial genera [32]. ...
We investigated the potential of the mitochondrial gene nd4 in molecular differentiation and phylogenetic relationship inference among Heterorhabditis strains. Partial nd4 gene sequences of mitochondrial DNA were determined from 20 strains of Heterorhabditis representing six different species collected from different geographic regions all over the world. Thirteen hap- lotypes were observed with a diversity index of 0.853 and standard deviation of 0.08 while the nucleotide diversity was only 0.05087. The overall average of pairwise distance among Heterorhabditis strains was only 5%. No nd4 gene sequence- and ND4 amino acid-based phenetic and phylogenetic trees completely resolved the phylogenetic relationships among species of Heterorhabditis. We conclude that nd4 is not an ideal target for reconstruction of phylogeny or molecular differentiation among Heterorhabditis species.
... The mtDNA cox-2 fragments showed little variation among sites of C. pelagicum. The intraspecific variability of 1-2% found is in accordance with literature data for Nematodes (THOMAS; WILSON, 1991;GARBIN et al., 2013). In the last 20 years, genetic analysis has been used as an important tool in the identification of sibling species, as well as larval stages of Contracaecum (NASCETTI et al., 1993;ORECCHIA et al., 1994;MATTIUCCI et al., 2002;LI et al., 2005;GARBIN et al., 2013). ...
... The small intraspecific variation and the greater interspecific variation found in this study, show how the mtDNA cox-2 region can be a valuable tool for the identification of species in the genus. The AT rich composition found has already been reported in literature for Nematode mtDNA cox-2 region (THOMAS; WILSON, 1991;NADLER;HUDSPETH, 2000;JEX et al., 2008). Mattiucci et al. (2008) and Garbin et al. (2013) found values of AT bases frequencies that were very similar to the ones found in this C. pelagicum study. ...
Three new sequences of Mitochondrial cytochrome c-oxidase subunit 2 (mtDNA cox-2) from C. pelagicum parasite of Spheniscus magellanicus, the Magelanicus penguin, were determined from Brazilian waters. The sequences presented 99 and 98% of similarity with C. pelagicum sequences from Argentina, deposited on GenBank for the same genetic region and with a strong statistical support inferred from the phylogenetic tree. The morphological and ultrastructural studies that were carried out confirmed the genetic analysis.
... These messages are similarly trans-spliced very close to the initiator codon, with four nucleotides separating SL1 from coding sequence in Cbg1 and 7 nucleotides in Crg1-2. Past studies have indicated that C. elegans, C. remanei , and C. briggsae have existed as separate species long enough such that unconstrained sequences have diverged considerably, and most highly conserved sequences are actively transcribed or represent functional regulatory elements (Heine and Blumenthal 1986; Heschl and Baillie 1990; Kennedy et al. 1993; Prasad and Baillie 1989; Thomas and Wilson 1991; Zucker-Aprison and Blumenthal 1989 ). Comparison of the 3 untranslated sequences of these globin genes provides an opportunity to identify potential regulatory elements. ...
... The finding of two divergent alleles in Caenorhabditis would be unexpected as most strains used in laboratories are known inbred lines. In addition, a study of calmodulin-like genes from 11 different strains of C. elegans collected around the world showed no sequence differences, even in introns (Thomas and Wilson 1991). Our finding of two divergent alleles in C. remanei suggest that the C. remanei species may exhibit a more variable population structure than that of C. elegans. ...
Globin genes from theCaenorhabditis speciesbriggsae andremanei were identified and compared with a previously describedC. elegans globin gene. The encoded globins share between 86% and 93% amino acid identity, with most of the changes in or just before
the putative B helix.C. remanei was found to have two globin alleles,Crg1-1 andCrgl-2. The coding sequence for each is interrupted by a single intron in the same position. The exons of the two genes are only
1 % divergent at the nucleotide level and encode identical polypeptides. In contrast, intron sequence divergence is 16% and
numerous insertions and deletions have significantly altered the size and content of both introns. Genetic crosses show thatCrg1-1 andCrgl-2 segregate as alleles. Homozygous lines for each allele were constructed and northern analysis confirmed the expression of
both alleles. These data reveal an unusual situation wherein two alleles encoding identical proteins have diverged much more
rapidly in their introns than the silent sites of their coding sequences, suggesting multiple gene conversion events.
... Studies of the mitochondrial genome of other filarial nematode parasites may be useful in resolving this issue. Previous studies have suggested that, as in many other organisms, the rate of nucleotide change in the mitochondrial genome of nematodes is greater than that seen in nuclearly encoded sequences [34]. This has been exploited to differentiate strains of C. elegans [34], to survey the level of intra-and inter-population diversity in the cattle nematode parasite Ostertagia osteragi [35], and to distinguish individual female A. suum [36]. ...
... Previous studies have suggested that, as in many other organisms, the rate of nucleotide change in the mitochondrial genome of nematodes is greater than that seen in nuclearly encoded sequences [34]. This has been exploited to differentiate strains of C. elegans [34], to survey the level of intra-and inter-population diversity in the cattle nematode parasite Ostertagia osteragi [35], and to distinguish individual female A. suum [36]. Furthermore, the results presented above suggest that the mitochondrial genome of O. 6ol6ulus may evolve even more rapidly than that of C. elegans and A. suum. ...
The complete DNA sequence of the mitochondrial genome of Onchocerca volvulus is described. The O. volvulus mitochondrial genome is 13 747 bp, slightly smaller than the mitochondrial genomes of the nematodes Ascaris suum and Caenorhabditis elegans, and the smallest metazoan mitochondrial DNA molecule reported to date. The O. volvulus mitochondrial genome contains genes for two ribosomal RNAs, 22 transfer RNAs and 12 proteins. Consistent with the small size of the genome, four gene pairs overlap and eight contain no intergenic regions. Only 17 intergenic regions are found, ranging in size from 1 to 46 bp. As in C. elegans and A. suum, the O. volvulus mitochondrial genome lacks an open reading frame encoding ATPase subunit 8, and all genes are apparently transcribed in the same direction. However, the mitochondrial gene order of O. volvulus differs from that of A. suum, C. elegans and other metazoan mitochondrial genomes. A total of 20 of the 22 transfer RNAs encoded in the O. volvulus mitochondrial genome have the potential to fold into secondary structures lacking the TψC arm, as has been reported in other nematodes. The genome exhibits a striking codon bias, with 15/20 amino acids having a single codon preference of >70%.
... Distinguishing among nematode species can be difficult due to morphological similarities, variation in morphological characters with habitat and food source (Anderson, 1968;Boström and Gydemo, 1983;Schiemer, 1982), and a generally underde-veloped taxonomy. The existence of cryptic nematode species that are morphologically indistinguishable yet genetically divergent (Butler et al., 1981;Emmons et al., 1979;Thomas and Wilson, 1991) suggests that morphologically defined species such as S. lindsayae may represent multiple, reproductively isolated and evolutionarily unique entities. An important fundamental question concerns the potential genetic isolation of S. lindsayae populations. ...
... These 12 haplotypes can be linked together into a minimal evolutionary framework by single mutational steps (Fig. 4). There are a minimum of 11 nucleotide substitutions, of which nine (82%) are transitions, a bias typical of mitochondrial evolution (Thomas and Wilson, 1991). ...
A nematode, Scottnema lindsayae, is the dominant metazoan found in soils of the McMurdo Dry Valleys, Antarctica. The distribution of S. lindsayae is patchy within and between these dry valleys; nevertheless, it is unclear to what extent these populations are genetically isolated. We investigated genetic diversity in this nematode using nuclear and mitochondrial gene sequences that encode ribosomal RNA. In 169 nematodes surveyed, only one variable site was found in each of two different expansion segments of nuclear rRNA. While most nematodes have only one sequence type, some nematodes were found to contain a mixture of both sequences. No fixed differences in nuclear sequences were observed between populations. This pattern of nuclear variation is most consistent with a single species of nematode defined morphologically as S. lindsayae. For mitochondrial DNA sequences, we found 10 variable positions defining 12 haplotypes among 188 nematodes surveyed. While all observed haplotypes are closely related, significant differences in haplotype frequencies were observed between geographically defined populations. The nuclear and mitochondrial variation suggests populations of S. lindsayae represent a single polymorphic species with some restriction of gene flow between geographic populations.
... Transition bias in nucleotide substitution is a ubiquitous phenomenon in animal mitochondrial DNA (mtDNA), having been reported in both vertebrate species (Aquadro and Greenberg 1983;Bechkenbach et al. 1990;Brown and Simpson 1982;Edwards and Wilson 1990;Irwin et al. 1991;Thomas and Beckenbach 1989) and invertebrate species (DeSalle et al. 1987;Satta et al. 1987;; Thomas and Wilson 1991). Although the phenomenon of transition bias is poorly understood, two contributing factors have been suggested. ...
... In recent years, the number of studies on the mtDNA of PWN gradually increased, although its utilization mainly involved comparing Bursaphelenchus xylophilus with close relative species (Pereira et al., 2013;Sultana et al., 2013;Moreira et al., 2014). In Nematode, it has been widely confirmed that there are intraspecific mutations in mitogenomes (Thomas and Wilson, 1991), and intraspecific mutations are also recognized in some genes of pinewood nematodes (Valadas et al., 2013). In the present research, intraspecific variation surveys were quantitatively evaluated by the mitochondrial genome scale. ...
Mitogenomic diversity and genetic population structure of the pinewood nematode (PWN) Bursaphelenchus xylophilus inhabiting Kyushu, Japan were analyzed. A method for performing long PCR using single nematodes and sequencing nematode mitochondrial genomes individually is presented here. About 8 kb (∼55%) of the complete mitochondrial genome was successfully obtained from 285 individuals collected from 12 populations. The 158 single nucleotide polymorphisms detected corresponded to 30 haplotypes, clearly classified into two clades. Haplotype diversity was 0.83, evidencing a remarkable high diversity within Kyushu. The high genetic differentiation among the 12 populations (0.331) might be due to past invasion and expansion routes of PWN in northeastern and southeastern Kyushu. The distinct genetic composition of populations within the northwestern, central western, and southwestern Kyushu seems to be mostly related to the extinction of pine forests and long-range migration of PWN due to human activity. Overall, direct long PCR and sequencing of single nematode individuals are effective methods for investigating mitochondrial polymorphisms, and these are effective tools for PWN population genetics and other intraspecific studies.
... [60], Caenorhabditis spp. [61] and Baylisascaris spp. [62]. ...
Background:
Whipworms (Nematoda: Trichuridae), among the most common soil-transmitted helminths (STHs), can cause the socioeconomically important disease trichuriasis in various mammalian hosts including humans and non-human primates. For many years, Trichuris from non-human primates has been assigned to the same species as the one infecting humans Trichuris trichiura. More recently, several molecular reports challenged this assumption following recognition of a Trichuris species complex observed in humans and non-human primates. A refined concept for species limits within Trichuris contributes to an understanding of diversity and the potential (zoonotic) transmission among humans and non-human primates. In this study, we expanded previous investigations by exploring the diversity of Trichuris among eight primates including three Asian autochthonous species (i.e. Rhinopithecus roxellana, Rhinopithecus bieti and Nomascus leucogenys). Species-level identification, whether novel or assignable to known lineages of Trichuris, was based on analyses of nuclear internal transcribed spacers (ITS) and mitochondrial cytochrome c oxidase subunit 1 (cox1) genes.
Results:
In total, seven genetically distinct subgroups of whipworms were determined to be present among the primates sampled. Most Trichuris lineages, including Subgroups 1, 1', 3, 5 and 6, showed a broad host range and were not restricted to particular primate species; in addition to T. trichiura, a complex of Trichuris species was shown infecting primates. Furthermore, it was assumed that Trichuris spp. from either N. leucogenys and P. hamadryas or R. roxellana and R. bieti, respectively, were conspecific. Each pair was indicated to be a discrete lineage of Trichuris, designated, respectively, as Subgroups 1 or 1' and 2, based on integrated genetic and phylogenetic evidence.
Conclusion:
These results emphasise that the taxonomy and genetic variations of Trichuris are more complicated than previously acknowledged. These cumulative molecular and phylogenetic data provide a better understanding of the taxonomy, genetics and evolutionary biology of the whipworms.
... Within-and between-species variation in the genus as a whole lends itself to comparative studies of disease. Species within the genus differ in fundamental ways such as mating system (Kiontke and Fitch, 2005;Kiontke et al., 2011), genome size (Fierst et al., 2015), genetic variation (Thomas and Wilson, 1991;Graustein et al., 2002;Jovelin et al., 2003), life span (McCulloch and Gems, 2003), ecology (Kiontke and Sudhaus, 2006), and body size (Woodruff et al., 2017). These different taxa nonetheless share many of the same types of parasites Zhang et al., 2016). ...
Many of the outstanding questions in disease ecology and evolution call for combining observation of natural host-parasite populations with experimental dissection of interactions in the field and the laboratory. The "rewilding" of model systems holds great promise for this endeavor. Here, we highlight the potential for development of the nematode Caenorhabditis elegans and its close relatives as a model for the study of disease ecology and evolution. This powerful laboratory model was disassociated from its natural habitat in the 1960s. Today, studies are uncovering that lost natural history, with several natural parasites described since 2008. Studies of these natural Caenorhabditis-parasite interactions can reap the benefits of the vast array of experimental and genetic tools developed for this laboratory model. In this review, we introduce the natural parasites of C. elegans characterized thus far and discuss resources available to study them, including experimental (co)evolution, cryopreservation, behavioral assays, and genomic tools. Throughout, we present avenues of research that are interesting and feasible to address with caenorhabditid nematodes and their natural parasites, ranging from the maintenance of outcrossing to the community dynamics of host-associated microbes. In combining natural relevance with the experimental power of a laboratory supermodel, these fledgling host-parasite systems can take on fundamental questions in evolutionary ecology of disease.
... The situation is much less clear in nonvertebrates. Depending on species, a mtDNA mutation rate much higher (Thomas and Wilson 1991;Blouin et al. 1998;Oliveira et al. 2008;Willett 2012), similar (Powell et al. 1986;Vawter and Brown 1986;Brower and DeSalle 1998), or lower (Shearer et al. 2002;Hellberg 2006;Huang et al. 2008) than the nuDNA mutation rate has been reported. Taking a comparative approach, Lynch et al. (2006) reported contrasted values for the ratio of mtDNA to nuDNA mutation rate (l mit /l nuc ) among animals. ...
It is commonly assumed that mitochondrial DNA (mtDNA) evolves at a faster rate than nuclear DNA (nuDNA) in animals. This has contributed to the popularity of mtDNA as a molecular marker in evolutionary studies. Analyzing 121 multilocus data sets and four phylogenomic data sets encompassing 4,676 species of animals, we demonstrate that the ratio of mitochondrial over nuclear mutation rate is highly variable among animal taxa. In nonvertebrates, such as insects and arachnids, the ratio of mtDNA over nuDNA mutation rate varies between 2 and 6, whereas it is above 20, on average, in vertebrates such as scaled reptiles and birds. Interestingly, this variation is sufficient to explain the previous report of a similar level of mitochondrial polymorphism, on average, between vertebrates and nonvertebrates, which was originally interpreted as reflecting the effect of pervasive positive selection. Our analysis rather indicates that the among-phyla homogeneity in within-species mtDNA diversity is due to a negative correlation between mtDNA per-generation mutation rate and effective population size, irrespective of the action of natural selection. Finally, we explore the variation in the absolute per-year mutation rate of both mtDNA and nuDNA using a reduced data set for which fossil calibration is available, and discuss the potential determinants of mutation rate variation across genomes and taxa. This study has important implications regarding DNA-based identification methods in predicting that mtDNA barcoding should be less reliable in nonvertebrates than in vertebrates.
... Three trials were conducted for each concentration and the worms were incubated at 20°C. The mortality was determined after 24 h and 48 h and 72 h [26]. ...
... However, these markers, often mitochondrial genes, while able to distinguish between members of the same genus or family, are uninformative for higher level taxonomic studies (e.g. Hyman, 1988;Thomas and Wilson, 1991;Powers et al., 1993;Zarlenga et al., 1998;Hoberg et al., 1999;Watts et al., 1999;Nadler et al., 2000). Recently, De Ley and Blaxter ( , 2004 updated the classiWcation of the phylum Nematoda using molecular data available from additional species, with morphological data to assist the placement of taxa for which SSU sequences were not yet available. ...
... However, these markers, often mitochondrial genes, while able to distinguish between members of the same genus or family, are uninformative for higher level taxonomic studies (e.g. Hyman, 1988;Thomas and Wilson, 1991;Powers et al., 1993;Zarlenga et al., 1998;Hoberg et al., 1999;Watts et al., 1999;Nadler et al., 2000). Recently, De Ley and Blaxter ( , 2004 updated the classiWcation of the phylum Nematoda using molecular data available from additional species, with morphological data to assist the placement of taxa for which SSU sequences were not yet available. ...
Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for >200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (f) Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling.
... La distance génétique révélée varie de 0,07x10 -3 pour TR403 à 2,7x10 -3 polymorphismes par paire de bases, soulignant une faible diversité génétique chez C. elegans. Cette information est confortée par des études ultérieures basées sur le polymorphisme de régions codantes pour un nombre d'isolats supérieur (11 à 20 isolats) (Graustein et al., 2002;Jovelin et al., 2003;Thomas et Wilson, 1991) ainsi que sur l'étude du polymorphisme de longueur de fragments amplifiés (AFLP) (Barrière et Félix, 2005) et de microsatellites (Haber et al., 2005;Sivasundar et Hey, 2003). Plus récemment, 97 isolats naturels de C. elegans ont fait l'objet d'une étude de diversité à partir de données obtenues par séquençage de l'ADN autour du site de restriction EcoRI (RAD sequencing) . ...
Caenorhabditis elegans is a commonly studied animal model in laboratories. The discovery ofthe first natural viral infections of Caenorhabditis brings new models to study animal-virusinteractions.The Orsay virus, specifically infecting C. elegans, and the Santeuil virus, specificallyinfecting C. briggsae, are positive single strand RNA viruses (Hepatites, Chikungunya,Coronavirus etc…) disrupting the structure of intestinal cells of their host. However, weobserved a strong variability in the sensitivity to those viruses at the intraspecific level.To identify the genetic basis of the sensitivity, we performed a genome wide association studyon 97 wild isolates of C. elegans. We were able to identify the center of chromosome IV as aregion containing the locus responsible for this sensitivity. A deletion in the drh-1 gene,coding for a RIG-I-Like protein, confers sensitivity to their carrier. RIG-I is known torecognize viral RNA and to trigger an antiviral response through the production of interferonsin vertebrates. However, C. elegans is not able to produce interferons but it appears thatDRH-1 initiates a viral specific siRNA pathway.Immunity genes are under strong selective pressure. Thus, it is surprising that such animportant protein for the antiviral pathway appears to be disrupted in 23% of the wild isolates.This deletion shows high linkage disequilibrium with a broader region of 3Mb, suggestingthat the deletion propagates with this region. However, this region does not seem to provideany advantage to their owner under laboratory conditions.
... However, when time since speciation is relatively short it is unlikely that any one locus will yield shared-derived characters delimiting every species lineage, which argues in favour of the combined analysis of data, provided that different loci do not show major conflicts (Nadler and Pérez-Ponce de León, 2011). In theory, mtDNA genes should be of great value for testing hypotheses of species, due to both a rapid rate of evolution in nematodes (Thomas and Wilson, 1991) and maternal inheritance; the latter results in smaller effective population size than for nuclear genes, so that mtDNA polymorphisms should achieve reciprocal monophyly in descendent species more quickly than autosomal loci (Avise, 1994). For these Uncinaria spp., 12S mtDNA does show evidence of a higher evolutionary rate (compared with nuclear rDNA sequences for the same taxa, e.g., Table 2), but this greater level of sequence divergence does not yield greater phylogenetic resolution. ...
Hookworms of the genus Uncinaria have been widely reported from juvenile pinnipeds, however investigations of their systematics has been limited, with only two species described, Uncinaria lucasi from northern fur seals (Callorhinus ursinus) and Uncinaria hamiltoni from South American sea lions (Otaria flavescens). Hookworms were sampled from these hosts and seven additional species including Steller sea lions (Eumetopias jubatus), California sea lions (Zalophus californianus), South American fur seals (Arctocephalus australis), Australian fur seals (Arctocephalus pusillus), New Zealand sea lions (Phocarctos hookeri), southern elephant seals (Mirounga leonina), and the Mediterranean monk seal (Monachus monachus). One hundred and thirteen individual hookworms, including an outgroup species, were sequenced for four genes representing two loci (nuclear ribosomal DNA and mitochondrial DNA). Phylogenetic analyses of these sequences recovered seven independent evolutionary lineages or species, including the described species and five undescribed species. The molecular evidence shows that U. lucasi parasitizes both C. ursinus and E. jubatus, whereas U. hamiltoni parasitizes O. flavescens and A. australis. The five undescribed hookworm species were each associated with single host species (Z. californianus, A. pusillus, P. hookeri, M. leonina and M. monachus). For parasites of otarids, patterns of Uncinaria host-sharing and phylogenetic relationships had a strong biogeographic component with separate clades of parasites from northern versus southern hemisphere hosts. Comparison of phylogenies for these hookworms and their hosts suggests that the association of U. lucasi with northern fur seals results from a host-switch from Steller sea lions. Morphometric data for U. lucasi shows marked host-associated size differences for both sexes, with U. lucasi individuals from E. jubatus significantly larger. This result suggests that adult growth of U. lucasi is reduced within the host species representing the more recent host-parasite association. Intraspecific host-induced size differences are inconsistent with the exclusive use of morphometrics to delimit and diagnose species of Uncinaria from pinnipeds.
... Plectus minimus Cobb, 1893 was cultured on 1 % agar seeded with E. coli. DNA was prepared as previously described (Thomas and Wilson 1991); RNA was extracted and cDNA was prepared as in Sidow and Thomas (1994). ...
The buccal capsule of Aduncospiculum halicti (Diplogasterina) is compared with that of Zeldia punctata (Cephalobina) and Caenorhabditis elegans (Rhabditina). Characters are mapped on an independent DNA-based phylogenetic tree (inferred from RNA polymerase II and rDNA sequences) to test evolutionary hypotheses. Irrespective of dimorphism, the buccal capsule wall of A. halicti consists of an anterior to posterior series of six cuticular structures classically termed rhabdions. These are defined according to their internal differentiations, discontinuities in profiles, and underlying tissues. Homologies of rhabdions 1 and 2 in A. halicti are proposed on the basis of position and association with adjacent tissues, consistent with those of Cephalobina and Rhabditina. Rhabdion 3 is associated with radial epithelial cells as is the mesorhabdion in C. elegans; this contrasts with Z. punctata, where a rhabdion in a similar position is associated with radial muscle cells. Dorsal and subventral teeth in A. halicti comprise rhabdions 4 and 5; this may be homologous with a corresponding region in Z. punctata but contrasts with C. elegans, where the corresponding region consists of a single metarhabdion. These characters, when mapped on the sequence-based tree, suggest that A. halicti and Diplogasterina share with C. elegans and other Rhabditina derived characters, including a mesorhabdion associated with epithelial cells, but retain some apparently primitive features shared with Cephalobina.
... The obse:rvations described above suggest that necromenic associations with terrestrial gastropods may be a primitive trait within Caenorhabditis. Because evolutionary lineages in Caenorhabditis are extremely divergent at the molecular level (Emmons et al., 1979;Butler et al., 1981;Thomas & Wilson, 1.991; W. K. Thomas and G. Nunn, pel's. comm.) this scenario implies that necromenic associations in Caenorhabditis have survived for several million years with relatively few modifications. ...
Caenorhabditis vulgaris sp.n. (Nematoda: Rhabditidae), a necromenic associate of pill bugs (Armadillidium vulgare and Armadillidium nasatum) and snails (Oxychilus sp.), is described. C. vulgaris is known from two locations, both in the northeastern United States. It is gonochoristic, with males & females equally abundant. Its associations with pill bugs and snails are as dauer juveniles and appear not to be deleterious to the host animal. These associations are not a requisite part of the C. vulgaris life-cycle; cultures of C. vulgaris can be maintained indefinitely if grown on a bacterial lawn. C. vulgaris can be distinguished from other species of Caenorhabditis based on reproductive, molecular and morphological criteria.
... This species is dedicated to Sydney Brenner, who, 40 years ago, initiated the fundamental work on C. elegans. 2. In papers published before 1995/96 (Binder et al. 1992, Cangiano & La Volpe 1993, Felsenstein & Emmons 1988, Fitch et al. 1995, Hekimi 1990, Hodgkin 1984, Jones & Schedl 1995, Kloek et al. 1996, Lee et al. 1993, Sedensky et al. 1994, Thomas & Wilson 1991, Youngman et al. 1996 ) this nematode was designated as "C. remanei" referring to strain CB5161 isolated in Trinidad and deposited at the CGC in 1988. ...
The new gonochoristic member of the Caenorhabditis Elegans group, C. brenneri sp. n., is described. This species is reproductively isolated at the postmating level from its sibling species, C. remanei. Between these species, only minute morphological differences are found, but there are substantial genetic differences. The stem species pattern of the Ele-gans group is reconstructed. C. brenneri sp. n. deviates from this character pattern only in small diagnostic characters. In mating tests of C. brenneri sp. n. females with C. remanei males, fertilization takes place and juveniles occasionally hatch. In the reverse combination, no offspring were observed. Individuals from widely separated populations of each species can be crossed successfully (e.g. C. brenneri sp. n. populations from Guadeloupe and Sumatra, or C. remanei populations from Japan and Germany). Both species have been isolated only from anthropogenic habitats, rich in decom-posing organic material. C. brenneri sp. n. is distributed circumtropically, C. remanei is only found in northern temperate regions. To date, no overlap of the ranges was found. Hypotheses to explain the allopatric distribution of the two species are discussed. One suggests that the speciation center for the Elegans group was in East Asia, and globally distributed members dispersed from there.
... Transition bias in nucleotide substitution is a ubiquitous phenomenon in animal mitochondrial DNA (mtDNA), having been reported in both vertebrate species (Brown and Simpson 1982; Aquadro and Greenberg 1983; Thomas and Bechkenbach 1989; Bechkenbach et al. 1990; Edwards and Wilson 1990; Irwin et al. 1991) and invertebrate species (DeSalle et al. 1987; Satta et al. 1987; Thomas et al. 1989; Thomas and Wilson 1991). Although the phenomenon of transition bias is poorly understood, two contributing factors have been suggested. ...
The relative contribution of mutation and purifying selection to transition bias has not been quantitatively assessed in mitochondrial
protein genes. The observed transition/transversion (s/v) ratio is (μ
s
P
s)/(μ
v
P
v), where μ
s
and μ
v
denote mutation rate of transitions and transversions, respectively, andP
s andP
v
denote fixation probabilities of transitions and transversions, respectively. Because selection against synonymous transitions
can be assumed to be roughly equal to that against synonymous transversions,P
s/Pv ≈ 1 at fourfold degenerate sites, so that thes/v ratio at fourfold degenerate sites is approximately μ
s
/μ
v
, which is a measure of mutational contribution to transition bias. Similarly, thes/v ratio at nondegenerate sites is also an estimate of μ
s
/μ
v
if we assume that selection against nonsynonymous transitions is roughly equal to that against nonsynonymous transversions.
In two mitochondrial genes, cytochrome oxidase subunit I (COI) and cytochromeb (cyt-b) in pocket gophers, thes/v ratio is about two at nondegenerate and fourfold degenerate sites for both the COI and the cyt-b genes. This implies that mutation contribution to transition bias is relatively small. In contrast, thes/v ratio is much greater at twofold degenerate sites, being 48 for COI and 40 for cyt-b. Given that the μ
s
/μ
v
ratio is about 2, theP
s/Pv ratio at twofold degenerate sites must be on the order of 20 or greater. This suggests a great effect of purifying selection
on transition bias in mitochondrial protein genes because transitions are synonymous and transversions are nonsynonymous at
twofold degenerate sites in mammalian mitochondrial genes. We also found that nonsynonymous mutations at twofold degenerate
sites are more neutral than nonsynonymous mutations at nondegenerate sites, and that the COI gene is subject to stronger purifying
selection than is the cyt-b gene. A model is presented to integrate the effect of purifying selection, codon bias, DNA repair and GC content ons/v ratio of protein-coding genes.
... Another distinctive feature of the trichostrongyloid nematodes is the highly AT-rich mtDNA as is typical of other nematodes . Several authors have suggested this to be a consequence of AT-bias mutation rate in nematodes (Thomas and Wilson, 1991;Hugall et al., 1997). ...
The large stomach worm, Haemonchus contortus, commonly known as "the barber's pole worm", is a blood-sucking nematode found in the abomasa of sheep and goats. This work is the first documentation on the ND4 sequences of H. contortus from sheep and goats in Malaysia and Yemen and the results provide a preliminary insight on the genetic differences of H. contortus found in the two countries. In general, this study showed a high degree of diversity and low population structure of this species within the same country in comparison with higher genetic structuring at a wider geographical scale. The results also showed that the majority of genetic variance was within H. contortus populations. The Malaysian sheep and goat populations investigated appeared to share the same isolate of H. contortus while different isolates may be found in Yemen which must be taken into account in the design of an effective control strategy. Analysis of the internal transcribed spacer-2 (ITS-2) confirmed that all samples investigated in this study belonged to H. contortus. However presence of other Haemonchus species parasitizing these two hosts can only be confirmed by further detailed studies.
... These CaM genes, can be group into three subfamilies of CaM I, CaM II, and CaM III [41,42,43], yet they encode the same CaM protein, which supports the model of ''multiple genes, single protein'' [41,42]. In contrast, there is only a single copy of CaM gene in most invertebrates, such as fruit fly [44] and nematode [45]. In the barnacle B. amphitrite, the single band observed in the digesting genomic DNA with different restriction enzymes indicated that Ba-CaM occurs as a sole gene in the genome, as in many other lower invertebrates (Fig. 3). ...
Barnacles are one of the most common organisms in intertidal areas. Their life cycle includes seven free-swimming larval stages and sessile juvenile and adult stages. The transition from the swimming to the sessile stages, referred to as larval settlement, is crucial for their survivor success and subsequent population distribution. In this study, we focused on the involvement of calmodulin (CaM) and its binding proteins in the larval settlement of the barnacle, Balanus ( = Amphibalanus) amphitrite. The full length of CaM gene was cloned from stage II nauplii of B. amphitrite (referred to as Ba-CaM), encoding 149 amino acid residues that share a high similarity with published CaMs in other organisms. Quantitative real-time PCR showed that Ba-CaM was highly expressed in cyprids, the stage at which swimming larvae are competent to attach and undergo metamorphosis. In situ hybridization revealed that the expressed Ba-CaM gene was localized in compound eyes, posterior ganglion and cement glands, all of which may have essential functions during larval settlement. Larval settlement assays showed that both the CaM inhibitor compound 48/80 and the CaM-dependent myosin light chain kinase (MLCK) inhibitor ML-7 effectively blocked barnacle larval settlement, whereas Ca(2+)/CaM-dependent kinase II (CaMKII) inhibitors did not show any clear effects. The subsequent real-time PCR assay showed a higher expression level of Ba-MLCK gene in larval stages than in adults, suggesting an important role of Ba-MLCK gene in larval development and competency. Overall, the results suggest that CaM and CaM-dependent MLCK function during larval settlement of B. amphitrite.
... Transition bias in nucleotide substitution is a ubiquitous phenomenon in animal mitochondrial DNA (mtDNA), having been reported in both vertebrate species (Aquadro and Greenberg 1983;Bechkenbach et al. 1990;Brown and Simpson 1982;Edwards and Wilson 1990;Irwin et al. 1991;Thomas and Beckenbach 1989) and invertebrate species (DeSalle et al. 1987;Satta et al. 1987;; Thomas and Wilson 1991). Although the phenomenon of transition bias is poorly understood, two contributing factors have been suggested. ...
... Large genetic distances between Caenorhabditis spp. also were estimated from a comparison of the mitochondrial cytochrome oxidase subunit II and calmodulin genes (Thomas and Wilson, 1991). The high levels of 18S divergence were presumed to be due to the ancient origin of nematodes, elevated rates of molecular evolution, or a combination of both factors (Fitch et al., 1995). ...
The ITS region from a wide taxonomic range of nematodes, including secernentean and adenophorean taxa, and free-living, entomopathogenic, and plant-parasitic species, was evaluated as a taxonomic marker. Size of the amplified product aided in the initial determination of group membership, and also suggested groups that may require taxonomic reevaluation. Congeneric species often displayed identically sized ITS regions, but genera such as Pratylenchus and Tylenchorynchus had species with large differences in size. ITS heterogeneity in individuals and populations was identified in several nematode taxa. PCR-RFLP of ITS1 is advocated as a method of taxonomic analysis in genera such as Helicotylenchus that contain numerous species with few diagnostic morphological characteristics.
... Although the model organism Caenorhabditis elegans has been well studied in biology, our knowledge of the evolution of natural populations of C. elegans is limited [1]. In the past, molecular variation in C. elegans has been studied using assays involving single mitochondrial and nuclear genes [2], transposons [3,4], amplified fragment length polymorphisms (aflps), and microsatellites5678. In this study, we investigate genetic variation in three strains of C. elegans: N2, CB4856, and CB4858 using large-scale DNA sequence datasets91011. ...
Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode Caenorhabditis elegans (CB4856 and CB4858) and the reference genome (N2).
The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison.In both CB4856 and CB4858, based on a measure of the strength of selection (ka/ks), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, ka/ks values are smaller in the autosomes than in the X chromosome. In addition, in CB4858, ka/ks values differ between chromosomes.
The clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the ka/ks ratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome.
... This finding is in contrast with a recently published study of partial sequences of the second internal transcribed spacer of nuclear rDNA, wherein B. ailuri and B. schroederi are more closely related to each other than to B. transfuga . This discordance in the nuclear and mt phylogenies is surprising and may be due to a greater rate of nucleotide change in the mt genomes of nematodes than that seen in nuclear-encoded sequences, as reported in many other organisms (Thomas and Wilson, 1991). Studies of the mt genomes of other Baylisascaris species may be useful in testing this hypothesis further. ...
... Further investigation of the genomic region surrounding Csp5-spc-1 in a more extensive collection of population samples from different localities would help determine the causes of the unusual patterns of polymorphism at this locus. Despite the streamlined morphology that is largely devoid of obvious differences among Caenorhabditis species , it is becoming clear that individual species harbour enormous genetic variation at the molecular level—in addition to the well-known high molecular divergence between species (Thomas & Wilson 1991; Stein et al. 2003; Cutter 2008a). This molecular population genetic biodiversity provides unprecedented opportunity to combine the laboratory experimental tractability of these organisms to characterize organismal function and evolution at the genetic level. ...
Most relatives of the self-fertilizing hermaphroditic nematode model organism Caenorhabditis elegans reproduce via obligate outbreeding between males and females, which also represents the ancestral mode of reproduction within the genus. However, little is known about the scope of genetic diversity and differentiation within such gonochoristic species, especially those found outside of temperate Europe and North America. It is critical to understand the evolutionary processes operating in these species to provide a framework for deciphering the evolution of hermaphroditism and a baseline for the application of outcrossing Caenorhabditis to problems in evolutionary genetics. Here, we investigate for the first time molecular sequence variation for Caenorhabditis sp. 5, a species found commonly in eastern Asia. We identify enormous levels of standing genetic variation that approach the levels observed in the marine broadcast-spawning sea squirt, Ciona savignyi. Although we document significant isolation by distance, we demonstrate that the high polymorphism within C. sp. 5 is not because of strong differentiation among populations or to the presence of cryptic species. These findings illustrate that molecular population genetic approaches to studying obligately outbreeding species of Caenorhabditis will prove powerful in identifying and characterizing functionally and evolutionarily important features of the genome.
Background
Coccidiosis caused by Eimeria zuernii (Eimeriidae: Coccidia) represents a significant economic threat to the bovine industry. Understanding the evolutionary and genetic biology of E. zuernii can assist in new interaction developments for the prevention and control of this protozoosis.
Methods
We defined the evolutionary and genetic characteristics of E. zuernii by sequencing the complete mitogenome and analyzing the genetic diversity and population structure of 51 isolates collected from eight yak breeding parks in China.
Results
The 6176-bp mitogenome of E. zuernii was linear and encoded typical mitochondrial contents of apicomplexan parasites, including three protein-coding genes [PCGs; cytochrome c oxidase subunits I and III (cox1 and cox3), and cytochrome b (cytb)], seven fragmented small subunit (SSU) and 12 fragmented large subunit (LSU) rRNAs. Genome-wide comparative and evolutionary analyses showed cytb and cox3 to be the most and least conserved Eimeria PCGs, respectively, and placed E. zuernii more closely related to Eimeria mephitidis than other Eimeria species. Furthermore, cox1-based genetic structure defined 24 haplotypes of E. zuernii with high haplotype diversities and low nucleotide diversities across eight geographic populations, supporting a low genetic structure and rapid evolutionary rate as well as a previous expansion event among E. zuernii populations.
Conclusions
To our knowledge, this is the first study presenting the phylogeny, genetic diversity, and population structure of the yak E. zuernii, and such information, together with its mitogenomic data, should contribute to a better understanding of the genetic and evolutionary biological studies of apicomplexan parasites in bovines.
Graphical Abstract
Human mitochondria contain a high copy number, maternally transmitted genome (mtDNA) that encodes 13 proteins required for oxidative phosphorylation. Heteroplasmy arises when multiple mtDNA variants co-exist in an individual and can exhibit complex dynamics in disease and in aging. As all proteins involved in mtDNA replication and maintenance are nuclear-encoded, heteroplasmy levels can, in principle, be under nuclear genetic control, however this has never been shown in humans. Here, we develop algorithms to quantify mtDNA copy number (mtCN) and heteroplasmy levels using blood-derived whole genome sequences from 274,832 individuals of diverse ancestry and perform GWAS to identify nuclear loci controlling these traits. After careful correction for blood cell composition, we observe that mtCN declines linearly with age and is associated with 92 independent nuclear genetic loci. We find that nearly every individual carries heteroplasmic variants that obey two key patterns: (1) heteroplasmic single nucleotide variants are somatic mutations that accumulate sharply after age 70, while (2) heteroplasmic indels are maternally transmitted as mtDNA mixtures with resulting levels influenced by 42 independent nuclear loci involved in mtDNA replication, maintenance, and novel pathways. These nuclear loci do not appear to act by mtDNA mutagenesis, but rather, likely act by conferring a replicative advantage to specific mtDNA molecules. As an illustrative example, the most common heteroplasmy we identify is a length variant carried by >50% of humans at position m.302 within a G-quadruplex known to serve as a replication switch. We find that this heteroplasmic variant exerts cis-acting genetic control over mtDNA abundance and is itself under trans-acting genetic control of nuclear loci encoding protein components of this regulatory switch. Our study showcases how nuclear haplotype can privilege the replication of specific mtDNA molecules to shape mtCN and heteroplasmy dynamics in the human population.
The Caenorhabditis elegans hermaphrodite is essentially a female that produces sperm. In C. elegans, tra-2 promotes female fates and must be repressed to achieve hermaphrodite spermatogenesis. In an effort to learn how mating systems evolve, we have cloned tra-2 from C. remanei, the closest gonochoristic relative of C. elegans. We found its structure to be similar to that of Ce-tra-2 but its sequence to be divergent. RNA interference demonstrates that Cr-tra-2 promotes female fates. Two sites of tra-2 regulation are required for the onset of hermaphrodite spermatogenesis in C. elegans. One, the MX region of TRA-2, is as well conserved in C. remanei as it is in C. briggsae (another male/hermaphrodite species), suggesting that this control is not unique to hermaphrodites. Another, the DRE/TGE element of the tra-2 3′ UTR, was not detected by sequence analysis. However, gel-shift assays demonstrate that a factor in C. remanei can bind specifically to the Cr-tra-2 3′ UTR, suggesting that this translational control is also conserved. We propose that both controls are general and do not constitute a novel “switch” that enables sexual mosaicism in hermaphrodites. However, subtle quantitative or qualitative differences in their employment may underlie differences in mating system seen in Caenorhabditis.
We have attempted interspecific hybridizations among six species of rhabditid nematodes: Caenorhabditis elegans, Caenorhabditis briggsae, Caenorhabditis remanei, Caenorhabditis sp. v, Rhabditis sp., and Pelodera teres. Copulation was observed in all crosses between Caenorhabditis species; however, none resulted in the generation of stable hybrid populations. No copulation was observed in crosses between Caenorhabditis males and Rhabditis or Pelodera females, even when congeneric females were present, suggesting that Caenorhabditis males are able to selectively recognize congeneric females by a short-range stimulus. All pairwise combinations of Caenorhabditis species were isolated to some degree by gametic mechanisms; 7 of 12 combinations were cross infertile and 5 of 12 were cross-fertile but had low brood sizes. In cross-fertile combinations, most hybrid embryos were inviable and arrested prior to gastrulation. Only in crosses of C. briggsae males to C. sp. v females did any hybrids survive embryogenesis. Most of these C. briggsae/C. sp. v hybrids arrested during larval development, and the few that reached adulthood invariably were female. These results are consistent with the presence of at least two lethal factors in the C. briggsae-C. sp. v combination: a maternal lethal factor in the cytoplasm of C. briggsae and a recessive lethal factor on the X chromosome of C. sp. v.
Very little is known about the distribution of genetic variance within and among populations of parasitic helminths. In this study we used mitochondrial DNA (mtDNA) restriction fragment analysis to describe the population genetic structure of Ostertagia ostertagi, a nematode parasite of cattle, in the United States. Estimates of within-population mtDNA diversity are 5 to 10 times greater than typical estimates reported for species in other taxa. Although populations are genetically differentiated for a key life-history trait, greater than 98% of the total genetic diversity is partitioned within populations, and the geographic distribution of individual mtDNA haplotypes suggests high gene flow among populations.
Mitochondria from all organisms studied to date have their own mitochondrial DNA (mtDNA), distinct from that of the nucleus. Animal mtDNA carries the genetic information for two rRNAs, a complete set of tRNAs and only a few essential components of the respiratory complexes: three subunits of the cytochrome oxidase (COI, COII and COIII), the cytochrome b (Cyt b), the subunits 6 and 8 of the Fo ATPase complex and several subunits of the NADH dehydrogenase (ND1-ND6 and ND4L). In addition, each molecule contains a control region in which signals of DNA duplication and transcription are included (for a review see Wolstenholme, 1993).
The addition of nucleotide sequence data to systematics has dramatically altered the study of relationships among organisms. In some respects, it has merely intensified the debate involving congruence between morphological and nonmorphological data sets (Patterson et al., 1993; Swofford, 1991; Hillis, 1987). In other regards, it has shifted the focus of the debate to methods of handling large data sets comprised of nonmorphological characters (Felsenstein, 1988; Hillis and Huelsenbeck, 1992; Simon, 1991; Swofford and Olsen, 1990). Nucleotide sequence alignment, assessments of homology, tree building protocols, and tree optimization and evaluation procedures are all recognized as critical components in contemporary systematic analysis. It is indisputable that molecular methods will have an impact in nematode systematics. Already there is a rapidly accumulating literature in molecular systematics, albeit some of it rather obtuse and difficult to interpret. Some fields, such as mammalian systematics, have vigorously embraced the new technologies. Nematode molecular systematics is in its infancy, with less than a dozen technical papers using nucleotide sequence data to assess relationships among nematodes. Yet it could be argued that molecular systematics will have its greatest impact among the lesser understood taxa, those that have received scant attention due to small size of the organisms and conservation of morphological characters. Molecular systematics can put nematodes on the same footing as better understood organisms.
A conceptual model is proposed that defines the soil and environmental conditions determining suitable and unsuitable habitats for soil biota in the McMurdo Dry Valley ecosystem of Antarctica. We hypothesized that if dispersal of soil fauna among the dry valleys was equal, then diverse and abundant communities of soil organisms would develop in all suitable habitats. The majority of soils sampled across the valleys (65%) support up to three soil invertebrate taxa (tardigrades, rotifers, nematodes). The rest of the soils are presumed to be unsuitable habitats as none of the target organisms were found, but there appears to be no single soil property that defines a suitable or unsuitable habitat. Most soils contain only one invertebrate taxa (nematodes); two and three taxa communities are rare. There are no other soil systems known where nematodes represent the top of the food chain and where food webs appear so simple in structure. Nematodes are more abundant and more widely distributed than either tardigrades or rotifers. The species diversity of nematodes is very low (n = 3), with only Scottnema lindsayae, a microbial feeder, occurring throughout the dry valleys. In many locations, soil conditions may be outside the tolerances of dispersing organisms preventing community establishment, thus creating the patchy distribution of soil biota that uniquely defines the dry valley landscape. The unusually low diversity and low functional redundancy of the dry valley soils suggest that these systems will be highly disrupted by the loss or decline of even a single species that is sensitive to environmental change. We suggest that nematodes may be a useful indicator organism for detecting environmental change in the dry valley system. As more people enter the dry valleys, human-induced impacts will directly affect soil habitats and the associated biota and the ecosystem functions they perform.
Mutations in the mitochondrial genome have been implicated in numerous human genetic disorders and offer important data for
phylogenetic, forensic, and population genetic studies. Using a long-term series of Caenorhabditis elegans mutation accumulation lines, we performed a wide-scale screen for mutations in the mitochondrial genome that revealed a mutation
rate that is two orders of magnitude higher than previous indirect estimates, a highly biased mutational spectrum, multiple
mutations affecting coding function, as well as mutational hotspots at homopolymeric nucleotide stretches.
In this work I used the internal transcribed spacer 1 of ribosomal DNA (ITS1) and the mitochondrial genes cytochrome oxidase subunit I (cox1) and NADH dehydrogenase subunit 4 (nd4) genes to investigate genetic diversity and phylogeny of six species of the entomopathogenic nematode Heterorhabditis. The ITS1-rDNA phylogenetic trees suggested the division of the unknown isolates into two major phylogenetic groups: the HP88 group and the Oswego group. All cox1 based phylogenetic trees agreed for the division of unknown isolates into three phylogenetic groups: KMD10 and GPS5 and the HP88 group containing the remaining 11 isolates. KMD10, GPS5 represent potentially new taxa. The cox1 analysis also suggested that HP88 is divided into two subgroups: the GPS11 group and the Oswego subgroup. Our results suggest that the HP88 group is most closely related to H. downesi K122 followed by H. marelatus Oregon, H. zealandica X1, H. megidis (UK and Jun) and H. indica EG2, respectively. Neither nd4 gene sequence- nor ND4 amino acid- based phenetic and phylogenetic trees were able to completely resolve the phylogenetic relationships among species of Heterorhabditis. We concluded that cox1 gene has a potential for molecular differentiation and diagnosis between closely related species within Heterorhabditis while nd4 is not an ideal target for reconstruction of phylogeny or molecular differentiation. We also used the major sperm protein gene (msp) to investigate genetic diversity among 13 strains of Heterorhabditis bacteriophora. Phenetic and phylogenetic analysis showed the presence of high genetic structuring within H. bacteriophora. Results suggest that all the strains currently recognized as H. bacteriophora may not belong to the same species. Finally, we investigated the phylogeny and population structure of the nematode Bursaphelenchus conicaudatus and its insect vector Psacothea hilaris from the Japanese islands. Phylogenetic and phenetic analyses indicated the existence of subspecies structure in B. conicaudatus and support the current subspecies groupings of P. hilaris subspecies with few exceptions. All fixation indices indicated the presence of high genetic differentiation among the local populations of both the nematode and its insect vector. The effective numbers of migrants showed definite but limited gene flow among insect and nematode local populations.
Amyloid fibrils of systemic amyloidosis are low molecular weight subunit proteins with poor immunogenicity and a tendency to polymerize. Antibodies to these proteins are useful for the detection of amyloid deposits in-situ. The extracellular location of amyloid deposits and proximity to congophilic angiopathy suggest the potential of labeled monocional antibodies (MAb) for in vivo radioimmunodetection. The authors tested feasibility of this approach using two rat MAbs to mouse AA protein in casein-induced amyloidosis, a model system for human secondary amyloidosis. The antibodies were labeled with I-125, I-123, and In-111 with good specificity retention. Amyloidotic mice were pretreated with 50 ..mu..g colchicine ip 3 hr before receiving radioiodinated MAb via the tall vein. Controls included injection of MAb to normal mice and of labeled polyclonal normal rat IgG (pIg) into amyloidotic and control mice. Blood clearance of MAb was faster in amyloidotic than control groups. Fractionation studies showed that both MAb and pIg were uncomplexed. Studies up to 96 hr showed specific and high uptake at sites of amyloid deposition (saline perfused liver, spleen, kidney. Specific localization was confirmed by whole body autoradiography (I-125, 20 ..mu..Ci/animal; 50 ..mu..g MAb) and by external imaging (I-123, 200 ..mu..Ci/animal, 10-15 ..mu..g MAb) of amyloidotic mice studied at 4-72 hr. Amyloidotic animals showed perifollicular localization in spleen, periportal in liver, and glomerular in kidney; scans of controls showed diffuse early washout. These results document the feasibility of using MAbs to fibril subunit proteins for the in vivo detection and therapy of amyloidosis.
Caenorhabditis briggsae is a member of the 'elegans group', a monophyletic clade of seven species within Caenorhabditis (Sudhaus & Kiontke, 1996). Species iden-ti cations within this group are dif cult. C. briggsae and C. elegans can be distinguished in that they are her-maphroditic whereas other members of the elegans group are gonochoristic (Maupas, 1900; Nigon & Dougherty, 1949; Sudhaus & Kiontke, 1996). C. briggsae and C. clavopapillata can be distinguished from other elegans group members based on their patterns of caudal papillae (Kreis & Faust, 1933; Nigon & Dougherty, 1949; Fried-man et al., 1977). Despite the general utility of caudal papillae patterns as diagnostic characters, their use to discriminate between C. briggsae and C. elegans came into question when a strain of C. briggsae, PB800, was obtained that displayed an elegans pattern at a high frequency. The canonical C. briggsae arrangement of caudal papillae is a 2/4+3 pattern with the third and fourth pair frequently being fused together (Nigon & Dougherty, 1949; Fig. 1A). This pattern also was reported for a second C. briggsae strain, AF16 (Fodor et al., 1983). The C. briggsae arrangement differs from those of C. elegans and C. remanei which have a 2+(1)+3+3 pattern (Maupas, 1900; Sudhaus, 1974; Baird et al., 1994; Fig. 1B, C). Immediately after its establishment, 70% of PB800 males displayed an elegans pattern on both sides. With subsequent inbreeding, this frequency decreased but still remained relatively high (see below). To address their use as diagnostic characters, caudal papillae patterns of AF16, PB800 and three additional C. briggsae strains, HK104, HK105, and VT847, were determined by microscopic observations using differential interference contrast optics (magni cation 400£). These strains were established from collections at disparate lo- cations and should each represent a genetically distinct population (Table 1). Identi cations of PB800, HK104, HK105, and VT847 as C. briggsae were con rmed by mating tests with AF16 (data not shown). These tests were scored as positive if the frequency of males approached 50% in the F1 generation. In the absence of mating, male frequencies resulting from self-fertilisation are less than 1% (Nigon & Dougherty, 1949). For PB800, additional mating tests with AF16 were conducted with sperm-depleted hermaphrodites (Baird et al., 1992). These mat-ing tests were scored as positive if any F1 progeny were obtained. Among and within the C. briggsae strains AF16, PB800, HK104, HK105 and VT847, considerable varia-tion in caudal papillae pattern was observed (Figs 1, 2). In AF16 and VT847, 2/4+3 patterns predominated with more than 85% of males exhibiting this briggsae pattern on both sides. (Expression of caudal papillae patterns on left and right sides was independent, hence the frequency of males exhibiting a single pattern on both sides was equal to the square of the overall frequency of that pattern.) In PB800, HK104, and HK105, frequencies of 2/4+3 and 2+(1)+3+3 patterns were approximately equal. In these strains, ap-proximately 25% of males exhibited a briggsae pattern on both sides and approximately 25% an elegans pattern on both sides. Among the observed 2/4+3 patterns, the frequency with which caudal papillae 3 and 4 were fused also varied from strain to strain. This variation was corre-lated with the overall frequency of 2/4+3 patterns; fusions of caudal papillae 3 and 4 were most frequent in AF16 and VT847 and least frequent in PB800, HK104, and HK105. Other patterns also were observed at lower frequencies in PB800 and HK105. These included a 2+(2)+2+3 pat-tern, a 'sixless' pattern in which caudal papillae assumed a cylindrical morphology and was displaced anteriorly (see c ° Koninklijke Brill NV, Leiden, 2001 373
A phylogenetic analysis was conducted using morphological characters. Eleven of the 18 Caenorhabditis-species described were investigated. The polarity for character transformations was established and a cladogram and the character set of the stem species reconstructed. There are two possible positions for R. plicata. It was not possible to resolve the phylogenetic relationship of the Elegans-group, which consists of seven species, including the four best-known Caenorhabditis-species. Transformation series of characters, e.g. the structure of the precloacal lip, are presented. The evolution of a pharyngeal sleeve is discussed. For the terms caudal papilla, bursal papilla and ray are given precise definitions. Two individual rays are specified as ‘anterior dorsal’ and ‘posterior dorsal’. We present here a new case of a Rhabditis with 10 pairs of bursal papillae where one pair (no. 10) is the phasmids. Information on the geographical distribution and the ecology of the Caenorhabditis-species is given. The markedly different ecological niches of these species must be derived from a way of life in the stem species in patchily distributed decomposing organic material which necessitated a phoretic phase with waving behaviour of the dauer juveniles.
Pristionchus pacificus (Diplogastridae, Nematoda) has recently been described as a ‘satelite’ organism for a functinal comparative approach, becuase genetic, molecular and cell-biological tools can be used in way similar to the genetic model organism Caenorhabditis elegans. This tudy describes the analysis of two previously isolated strains of P. pacificus for the occurrence of restriction fragment length polymorphisms (RFLPs). In all, 14 of 17 randomly chosen cDNA clones give polymorphisms after hybridization to EcoRI digested genomic DNA of the populations from California and Washington. This polymorphism is much higher than polymorphism found among different strains in C. elegans. Therefore this study compares most of the nucleotide sequence of the Ppa-let-60/ras gene between the two strains. No base-pair substitutions were found between these two sequences within the coding regions. However, within the untranslated region, four base-pair substitutions in introns and the deletion of three base-pairs in the 5′ sequence and in intron 4 have been observed. Since the two strains interbreed, RFLPs can be used as molecular markers for future chromosomal walking and gene cloning.
Molecular hyperdiversity has been documented in viruses, prokaryotes and eukaryotes. Such organisms undermine the assumptions of the infinite-sites mutational model, because multiple mutational events at a site comprise a non-negligible portion of polymorphisms. Moreover, different sampling schemes of individuals from species with subdivided populations can profoundly influence resulting patterns and interpretations of molecular variation. Inspired by molecular hyperdiversity in the nematode Caenorhabditis sp. 5, which exhibits average pairwise differences among synonymous sites of >5% as well as modest population structure, we investigated via coalescent simulation the joint effects of a finite-sites mutation (FSM) process and population subdivision on the variant frequency spectrum. From many demes interconnected through a stepping-stone migration model, we constructed local samples from a single deme, pooled samples from several demes and scattered samples of a single individual from numerous demes. Compared with a single panmictic population at equilibrium, we find that high population mutation rates induce a deficit of rare variants (positive Tajima's D) under a FSM model. Population structure also induces such a skew for local samples when migration is high and for pooled samples when migration is low. Contrasts of sampling schemes for C. sp. 5 imply high mutational input coupled with high migration. We propose that joint analysis of local, pooled and scattered samples for species with subdivided populations provides a means of improving inference of demographic history, by virtue of the partially distinct patterns of polymorphism that manifest when sequences are analyzed according to differing sampling schemes.
Hermaphroditism has evolved several times independently in nematodes. The model organism Caenorhabditis elegans and Pristionchus pacificus are self-fertile hermaphrodites with rare facultative males. Both species are members of different families: C. elegans belongs to the Rhabditidae and P. pacificus to the Diplogastridae. Also, both species differ in their ecology: C. elegans is a soil-dwelling nematode that is often found in compost heaps. In contrast, field studies in Europe and North America indicate that Pristionchus nematodes are closely associated with scarab beetles. In C. elegans, several recent studies have found low genetic diversity and rare out-crossing events. Little is known about diversity levels and population structure in free-living hermaphroditic nematodes outside the genus Caenorhabditis. Taking a comparative approach, we analyse patterns of molecular diversity and linkage disequilibrium in 18 strains of P. pacificus from eight countries and four continents. Mitochondrial sequence data of P. pacificus isolates reveal a substantially higher genetic diversity on a global scale when compared to C. elegans. A mitochondrial-derived hermaphrodite phylogeny shows little geographic structuring, indicating several worldwide dispersal events. Amplified fragment length polymorphism and single strand conformation polymorphism analyses demonstrate a high degree of genome-wide linkage disequilibrium, which also extends to the mitochondrial genome. Together, these findings indicate distinct patterns of genetic variation of the two species. The low level of genetic diversity observed in C. elegans might reflect a recent human-associated dispersal, whereas the P. pacificus diversity might reflect a long-lasting and ongoing insect association. Thus, despite similar lifestyle characteristics in the laboratory, the reproductive mode of hermaphroditism with rare facultative males can result in distinct genetic variability patterns in different ecological settings.
Quatre-vingt-treize souches du nématode libre du sol #Caenorhabditis elegans$ ont été isolées à partir d'échantillons de sol et de matières organiques en décomposition provenant de différents sites du Québec. L'examen morphologique et des croisements avec la souche anglaise "standard" Bristol (N2) ont servi à l'identification des souches. Quelques caractéristiques biologiques (durée du développement oeuf-adulte, viabilité, longueur, fécondité à quatre différentes températures) de six souches de #C. elegans$ isolées de quatre régions du Québec ont été étudiées. Une étude préliminaire de la sensibilité de ces souches à quatre substances toxiques (la diphénylamine, le pentachlorophénol, le 4-chlorobiphényle et le 2,2'-dichlorobiphényle) a démontré l'existence de différences entre ces souches. (Résumé d'auteur)
Recombination rate and linkage disequilibrium, the latter a function of population genomic processes, are the critical parameters for mapping by linkage and association, and their patterns in Caenorhabditis elegans are poorly understood. We performed high-density SNP genotyping on a large panel of recombinant inbred advanced intercross lines (RIAILs) of C. elegans to characterize the landscape of recombination and, on a panel of wild strains, to characterize population genomic patterns. We confirmed that C. elegans autosomes exhibit discrete domains of nearly constant recombination rate, and we show, for the first time, that the pattern holds for the X chromosome as well. The terminal domains of each chromosome, spanning about 7% of the genome, exhibit effectively no recombination. The RIAILs exhibit a 5.3-fold expansion of the genetic map. With median marker spacing of 61 kb, they are a powerful resource for mapping quantitative trait loci in C. elegans. Among 125 wild isolates, we identified only 41 distinct haplotypes. The patterns of genotypic similarity suggest that some presumed wild strains are laboratory contaminants. The Hawaiian strain, CB4856, exhibits genetic isolation from the remainder of the global population, whose members exhibit ample evidence of intercrossing and recombining. The population effective recombination rate, estimated from the pattern of linkage disequilibrium, is correlated with the estimated meiotic recombination rate, but its magnitude implies that the effective rate of outcrossing is extremely low, corroborating reports of selection against recombinant genotypes. Despite the low population, effective recombination rate and extensive linkage disequilibrium among chromosomes, which are techniques that account for background levels of genomic similarity, permit association mapping in wild C. elegans strains.
With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.
The complete sequence of the 16,569-base pair human mitochondrial genome is presented. The genes for the 12S and 16S rRNAs, 22 tRNAs, cytochrome c oxidase subunits I, II and III, ATPase subunit 6, cytochrome b and eight other predicted protein coding genes have been located. The sequence shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.
Electrophoretic comparisons have been made for 24 enzymes in theBergerac andBristol strains ofCaenorhabditis elegans and the related species,Caenorhabditis briggsae. No variation was detected between the two strains ofC. elegans. In contrast, the two species,C. elegans andC. briggsae exhibited electrophoretic differences in 22 of 24 enzymes. A consensus 5S rRNA sequence was determined forC. elegans and found to be identical to that fromC. briggsae. By analogy with other species with relatively well established fossil records it can be inferred that the time of divergence between the two nematode species is probably in the tens of millions of years.
The limited anatomical evolution during a time period in which proteins undergo extensive changes supports the hypothesis that anatomical evolution is not dependent on overall protein changes.
We cloned and sequenced a segment of mitochondrial DNA from human, chimpanzee, gorilla, orangutan, and gibbon. This segment is 896 bp in length, contains the genes for three transfer RNAs and parts of two proteins, and is homologous in all 5 primates. The 5 sequences differ from one another by base substitutions at 283 positions and by a deletion of one base pair. The sequence differences range from 9 to 19% among species, in agreement with estimates from cleavage map comparisons, thus confirming that the rate of mtDNA evolution in primates is 5 to 10 times higher than in nuclear DNA. The most striking new finding to emerge from these comparisons is that transitions greatly outnumber transversions. Ninety-two percent of the differences among the most closely related species (human, chimpanzee, and gorilla) are transitions. For pairs of species with longer divergence times, the observed percentage of transitions falls until, in the case of comparisons between primates and non-primates, it reaches a value of 45. The time dependence is probably due to obliteration of the record of transitions by multiple substitutions at the same nucleotide site. This finding illustrates the importance of choosing closely related species for analysis of the evolutionary process. The remarkable bias toward transitions in mtDNA evolution necessitates the revision of equations that correct for multiple substitutions at the same site. With revised equations, we calculated the incidence of silent and replacement substitutions in the two protein-coding genes. The silent substitution rate is 4 to 6 times higher than the replacement rate, indicating strong functional constraints at replacement sites. Moreover, the silent rate for these two genes is about 10% per million years, a value 10 times higher than the silent rate for the nuclear genes studied so far. In addition, the mean substitution rate in the three mitochondrial tRNA genes is at least 100 times higher than in nuclear tRNA genes. Finally, genealogical analysis of the sequence differences supports the view that the human lineage branched off only slightly before the gorilla and chimpanzee lineages diverged and strengthens the hypothesis that humans are more related to gorillas and chimpanzees than is the orangutan. Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/48036/1/239_2005_Article_BF01734101.pdf
With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.
With the polymerase chain reaction (PCR) and versatile primers that amplify the whole cytochrome b gene (approximately 1140 bp), we obtained 17 complete gene sequences representing three orders of hoofed mammals (ungulates) and dolphins (cetaceans). The fossil record of some ungulate lineages allowed estimation of the evolutionary rates for various components of the cytochrome b DNA and amino acid sequences. The relative rates of substitution at first, second, and third positions within codons are in the ratio 10 to 1 to at least 33. For deep divergences (greater than 5 million years) it appears that both replacements and silent transversions in this mitochondrial gene can be used for phylogenetic inference. Phylogenetic findings include the association of (1) cetaceans, artiodactyls, and perissodactyls to the exclusion of elephants and humans, (2) pronghorn and fallow deer to the exclusion of bovids (i.e., cow, sheep, and goat), (3) sheep and goat to the exclusion of other pecorans (i.e., cow, giraffe, deer, and pronghorn), and (4) advanced ruminants to the exclusion of the chevrotain and other artiodactyls. Comparisons of these cytochrome b sequences support current structure-function models for this membrane-spanning protein. That part of the outer surface which includes the Qo redox center is more constrained than the remainder of the molecule, namely, the transmembrane segments and the surface that protrudes into the mitochondrial matrix. Many of the amino acid replacements within the transmembrane segments are exchanges between hydrophobic residues (especially leucine, isoleucine, and valine). Replacement changes at first and second positions of codons approximate a negative binomial distribution, similar to other protein-coding sequences. At four-fold degenerate positions of codons, the nucleotide substitutions approximate a Poisson distribution, implying that the underlying mutational spectrum is random with respect to position.
The 15,697-nucleotide sequence of Paracentrotus lividus mitochondrial DNA is reported. This genome codes for 2 rRNAs, 22 tRNAs, and 12 mRNAs which specify 13 subunits of the mitochondrial inner membrane respiratory complexes. The gene arrangement differs from that of other animal species. The two ribosomal genes 16 S and 12 S are separated by a stretch of about 3.3 kilobase pairs which contains the ND1 and ND2 genes and a cluster of 15 tRNA genes. The ND4L coding sequence is not contained in the ND4 mRNA but has its own mRNA which maps between the tRNA(Arg) and the Co II genes. The main noncoding region, located in the tRNA gene cluster, is only 132 nucleotides long, but contains sequences homologous to the mammalian displacement loop. Other short noncoding sequences are interspersed in the genome: they contain a conserved AT consensus which probably has a role in transcription or RNA processing. As regards the mitochondrial genetic code, the codons AGA and AGG specify serine and are recognized by a tRNA with a GCU anticodon, whereas AUA and AAA code for isoleucine and asparagine rather than for methionine and lysine. Except for ND4L which starts with AUC and ATPase 8 which starts with GUG, AUG is used as the initiation codon. In 11 out of 13 cases the genes terminate with the canonical stop codons UAA or UAG. These observations suggest that during invertebrate evolution each lineage developed its own mechanism of mitochondrial DNA replication and transcription and of RNA processing and translation.
The nucleotide sequence of a segment of the mitochondrial DNA (mtDNA) molecule of the liver fluke Fasciola hepatica (phylum Platyhelminthes, class Trematoda) has been determined, within which have been identified the genes for tRNA(ala), tRNA(asp), respiratory chain NADH dehydrogenase subunit I (ND1), tRNA(asn), tRNA(pro), tRNA(ile), tRNA(lys), ND3, tRNA(serAGN), tRNA(trp), and cytochrome c oxidase subunit I (COI). The 11 genes are arranged in the order given and are all transcribed from the same strand of the molecule. The overall order of the F. hepatica mitochondrial genes differs from what is found in other metazoan mtDNAs. All of the sequenced tRNA genes except the one for tRNA(serAGN) can be folded into a secondary structure with four arms resembling most other metazoan mitochondrial tRNAs, rather than the tRNAs that contain a T psi C arm replacement loop, found in nematode mtDNAs. The F. hepatica mitochondrial tRNA(serAGN) gene contains a dihydrouridine arm replacement loop, as is the case in all other metazoan mtDNAs examined to date. AGA and AGG are found in the F. hepatica mitochondrial protein genes and both codons appear to specify serine. These findings concerning F. hepatica mtDNA indicate that both a dihydrouridine arm replacement loop-containing tRNA(serAGN) gene and the use of AGA and AGG codons to specify serine must first have occurred very early in, or before, the evolution of metazoa.
Evolutionary conservation, predicted membrane topography of the subunits, and known chemical and physical properties of the catalytic metals in cytochrome oxidase provided the basis for plausible structural models of the enzyme's redox centres. Subunit II probably binds one of the copper ions (CuA) whilst subunit I is likely to bind the two haems (a and a3) and the other redox-active copper (CuB). Two cysteine and two histidine residues of subunit II are the likely ligands of CuA, forming a centre that may be structurally similar to that in azurin. The two haems may be sandwiched between two transmembranous segments of subunit I, one of which also provides a histidine ligand to CuB. A third segment may provide two more histidine ligands to the latter. The model was constructed with a 4 A Fe-Cu distance in the binuclear haem a3-CuB centre, and a 14 A distance between the haem irons. The subunit I model involves only three transmembranous helices which bind three catalytic metal groups. The fit of this model to several known physicochemical properties of the redox centres is analysed.
While the majority of DNA in eukaryotes is in the nucleus, a small but functionally significant amount is found in organelles such as chloroplasts and mitochondria. A recent, rather remarkable, finding has been that in vertebrates the DNA in the mitochondria (mtDNA) is evolving 5-10 times faster than the DNA in the nucleus. No similar studies have been done with invertebrates. Using the technique of DNA X DNA hybridization, we have measured the degree of nucleotide substitution between Drosophila melanogaster and Drosophila yakuba for both single-copy nuclear DNA (scnDNA) and mtDNA. The change in melting temperature is the same in both types of DNA hybrids. Thus we conclude that mtDNA and scnDNA are evolving at similar rates in these Drosophila. Considerable DNA sequence data are available for the mtDNAs studied, allowing us to estimate that a 1 degree C change in melting temperature corresponds to a 1.5-2% base-pair mismatch.
Genes sequences from Escherichia coli, Salmonella typhimurium, and other members of the Enterobacteriaceae show a negative correlation between the degree of synonymous-codon usage bias and the rate of nucleotide substitution at synonymous sites. In particular, very highly expressed genes have very biased codon usage and accumulate synonymous substitutions very slowly. In contrast, there is little correlation between the degree of codon bias and the rate of protein evolution. It is concluded that both the rate of synonymous substitution and the degree of codon usage bias largely reflect the intensity of selection at the translational level. Because of the high variability among genes in rates of synonymous substitution, separate molecular clocks of synonymous substitution might be required for different genes.
The complete nucleotide sequence of the mitochondrial DNA (mtDNA) molecule of the parasitic nematode worm Ascaris suum has been determined. This molecule lacks genes for tRNAs of the standard form. Instead, 21 sequences are found that can be folded into structures that resemble tRNAs in which the T psi C arm and variable loop are missing and replaced with a single loop of between 4 and 12 nucleotides. Considerations of various properties of these sequences, including the number, predicted anticodons, conserved nucleotides, direction of transcription, base composition, and relative gene arrangements are consistent with the interpretation that they are genes for a different sort of tRNA. Transfer RNA genes with a similar potential secondary structure are found in mtDNA of the free-living nematode Caenorhabditis elegans, suggesting that this unusual form of tRNA is used by all nematode mitochondria.
We have compared nucleotide sequences of corresponding segments of the mitochondrial DNA (mtDNA) molecules of Drosophila yakuba and Drosophila melanogaster, which contain the genes for six proteins and seven tRNAs. The overall frequency of substitution between the nucleotide sequences of these protein genes is 7.2%. As was found for mtDNAs from closely related mammals, most substitutions (86%) in Drosophila mitochondrial protein genes do not result in an amino acid replacement. However, the frequencies of transitions and transversions are approximately equal in Drosophila mtDNAs, which is in contrast to the vast excess of transitions over transversions in mammalian mtDNAs. In Drosophila mtDNAs the frequency of C----T substitutions per codon in the third position is 2.5 times greater among codons of two-codon families than among codons of four-codon families; this is contrary to the hypothesis that third position silent substitutions are neutral in regard to selection. In the third position of codons of four-codon families transversions are 4.6 times more frequent than transitions and A----T substitutions account for 86% of all transversions. Ninety-four percent of all codons in the Drosophila mtDNA segments analyzed end in A or T. However, as this alone cannot account for the observed high frequency of A----T substitutions there must be either a disproportionately high rate of A----T mutation in Drosophila mtDNA or selection bias for the products of A----T mutation. --Consideration of the frequencies of interchange of AGA and AGT codons in the corresponding D. yakuba and D. melanogaster mitochondrial protein genes provides strong support for the view that AGA specifies serine in the Drosophila mitochondrial genetic code.
The complete sequence of the 17,553-nucleotide Xenopus laevis mitochondrial genome has been determined. A comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a similar gene order and compact genomic organization. The encoded genes for 22 tRNAs, two ribosomal RNAs, and 13 proteins (COI, COII, COIII, ATPase 6, cytochrome b, and eight additional unidentified reading frames) in the amphibian mitochondria are highly homologous to their mammalian counterparts. Although the amphibian mitochondrial genome contains a significantly larger displacement loop region than the mammalian mitochondrial genomes, there are several regions of sequence homology near the putative sites for heavy and light strand transcription initiation and heavy strand replication. The unique mitochondrial genetic code observed in the mammalian mitochondrial systems is similar to that of the X. laevis mitochondrial genome because of the presence of only 22 encoded tRNAs and the high degree of homology between the predicted protein sequences. However, the amphibian system exclusively utilizes AUG as the start codon in all 13 open reading frames and shows a preference for codons ending in U rather than ending in C. In addition, the X. laevis mitochondrial genome employs the encoded AGA stop codon once and the UAA stop codon three times and requires polyadenylation to provide the nine other UAA stop codons. These observations suggest that the mechanisms of replication, transcription, processing, and translation in mitochondria are highly conserved throughout higher vertebrates.
Photoactivatable arylazido phospholipids (Bisson, R., and Montecucco, C. (1981) Biochem. J. 193, 757-763) have been used to study the arrangement in the membrane of beef heart cytochrome c oxidase subunit II. Fragmentation of the photocross-linked polypeptide showed that sequence 20-98, which contains two long stretches of uncharged amino acid residues (Steffens, G. J., and Buse, G. (1979) Hoppe-Seyler's Z. Physiol. Chem. 360, 613-619), is in contact with lipids. Edman degradation of the labeled peptide indicated that His 26, Thr 27 and Met 29 are involved in the interaction with the polar head region of the bilayer. These data have been used to propose a scheme for the folding of subunit II in the mitochondrial membrane.
The sequence of the region of the mitochondrial genome that encodes cytochrome oxidase subunit II (COII) has been determined for each of two closely related rat species, Rattus norvegicus and R. rattus. Comparison of the two sequences shows that 94.4% of the nucleotide substitutions are silent. The occurrence of this high proportion of silent substitutions leads us to propose that the rapid evolution of mtDNA relative to nuclear DNA is due only to silent changes and that amino acid-altering substitutions accumulate in nuclear and mtDNA at comparable rates. Other novel features of the nucleotide substitution pattern in the rat COII gene are a high transition/transversion ratio (8.0:1) and a strong bias toward C in equilibrium T transitions in the light strand. Comparison of the R. norvegicus COII sequence with the bovine and human sequences show that there may be selective constraints on some silent positions within the gene and that its rate of evolution may be different in different mammalian lineages.
Examines the form and frequency of 3 types of change in mtDNA: base substitution, length variation and sequence rearrangement. Knowledge of molecular processes allows informed use of mtDNA variation in evolutionary studies.-P.J.Jarvis
The advent of direct sequencing via the polymerase chain reaction (PCR) has opened up the possibility of molecular studies on museum specimens. Here we analyze genetic variation in populations over time by applying PCR to DNA extracted from museum specimens sampled from populations of one species over the last 78 years. Included in this study were 43 museum specimens of the Panamint kangaroo ratDipodomys panamintinus from localities representing each of three geographically distinct subspecies. These specimens were originally collected and prepared as dried skins in 1911, 1917, or 1937. For each specimen, a 225-bp segment of the mitochondrial genome was sequenced. These mitochondrial DNA sequences were compared to those of 63 specimens collected at the same localities in 1988. The three subspecies were nearly completely distinct. Only 2 of the 106 individuals shared mitochondrial types between subspecies. For all three localities, the diversity levels were maintained between the two temporal samples. The concordance observed between the two temporally separate phylogenies supports the use of museum specimens for phylogenetic inference. This study demonstrates the accuracy and routine nature of the use of museum specimens in the analysis of mitochondrial sequence variation in natural populations and, importantly, that a temporal aspect can now be added to such studies.
A combination of restriction analysis and direct sequencing via the polymerase chain reaction (PCR) was used to build trees relating mitochondrial DNAs (mtDNAs) from 50 individuals belonging to five species of Australian babblers (Pomatostomus). The trees served as a quantitative framework for analyzing the direction and tempo of evolution of an intraspecific length polymorphism from a third mitochondrial ancestor. The length polymorphism lies between the cytochrome b and 12S rRNA (srRNA) genes. Screening of mtDNAs within and between the five species with restriction enzymes showed that Pomatosomus temporalis was polymorphic for two smaller size classes (M and S) that are completely segregated geographically, whereas mtDNAs from the other four species were exclusively of a third, larger size (L). Inter- and intraspecific phylogenetic trees relating mtDNAs based on restriction maps, cytochrome b sequences obtained via PCR, and the two data sets combined were compared to one another statistically and were broadly similar except for the phylogenetic position of Pomatosomus halli. Both sets of phylogenies imply that only two deletion events can account for the observed intraspecific distribution of the three length types. High levels of base-substitutional divergence were detected within and between northern and southern lineages of P. temporalis, which implies a low level of gene flow between northern and southern regions as well as a low rate of length mutation. These conclusions were confirmed by applying coalescent theory to the statistical framework provided by the phylogenetic analyses.
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.
During the evolution of echinoderm mitochondrial (mt) DNA, a transfer RNA gene lost its tRNA function and became part of a protein-coding gene. To examine the evolutionary consequences of this event, we sequenced 961 bp of mtDNA in five sea urchin species. This enabled us to build a tree relating the mtDNAs and use it for analyzing the pattern and process of evolutionary substitutions in the former leucine tRNA gene, which now is a 5' extension of the gene for NADH dehydrogenase subunit 5 (ND5). This 5' extension is now evolving at the same rate and under the same protein-coding constraints as the rest of ND5. The adjacent (upstream) serine tRNA gene, however, has been evolving at a reduced rate, consistent with the possibility that it has assumed a punctuation role in processing of the primary transcript that was once fulfilled by the former leucine tRNA gene.
Sequence comparisons were made from 2214 bp of mitochondrial DNA cloned from six Pacific salmonid species. These sequences include the genes for ATPase subunit 6, cytochrome oxidase subunit 3, NADH dehydrogenase subunit 3, NADH dehydrogenase subunit 4L, tRNA(GLY), and tRNA(ARG). Variation is found at 338 silent and 12 nonsilent positions of protein coding genes and 10 positions in the two tRNA sequences. A single 3-bp length difference was also detected. In all pairwise comparisons the sequence divergence observed in the fragment was higher than that previously predicted by restriction enzyme analysis of the entire molecule. The inferred evolutionary relationship of these species is consistent between methods. The distribution of silent variation shows a complex pattern with greatly reduced variation at the junctions of genes. The variation in the tRNA sequences is concentrated in the DHU loop. The close relationship of these species and extensive sequence analyzed allows for an analysis of the spectrum of substitutions that includes the frequencies of all 12 possible substitutions. The observed spectrum of substitutions is related to potential pathways of spontaneous substitution. The salmonid sequences show an extremely high ratio of silent to replacement substitutions. In addition the amino acid sequences of the four proteins coded in this fragment show a consistently high level of identity with the Xenopus sequences. Taken together these data are consistent with a slower rate of amino acid substitution among the cold-blooded vertebrates when compared to mammals.
The sequence of a region of honeybee (Apis mellifera ligustica) mitochondrial DNA, which contains the genes for cytochrome c oxidase subunits I and II (CO-I and CO-II) and inferred genes for tRNA(Asp), tRNA(Leu)UUR, tRNA(Lys), and tRNA(Trp), is presented. The region includes the segment previously identified as incurring a length increase in some other bee strains, including Africanized bees. The sequence information of this study and of that by Vlasak et al. shows that several shifts of tRNA genes have occurred between Apis and Drosophila, but shifts of other kinds of genes have yet to be demonstrated. The CO-I and CO-II gene sequences are both more A+T rich than are the corresponding Drosophila genes. Parsimony analyses using the mouse and Xenopus sequences as outgroups show significantly more amino acid substitutions on the branch to Apis (120) than on that to Drosophila (44), indicating a difference in the long-term evolutionary rates of hymenopteran and dipteran mtDNA.
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Sequences are reported for portions of two mitochondrial genes from a domestic horse and a plains zebra and compared to those published for a quagga and a mountain zebra. The extinct quagga and plains zebra sequences are identical at all silent sites, whereas the horse sequence differs from both of them by 11 silent substitutions. Postmortem changes in quagga DNA may account for the two coding substitutions between the quagga and plains zebra sequences. The hypothesis that the closest relative of the quagga is the domestic horse receives no support from these data. From the extent of sequence divergence between horse and zebra mitochondrial DNAs (mtDNAs), as well as from information about the fossil record, we estimate that the mean rate of mtDNA divergence in Equus is similar to that in other mammals, i.e., roughly 2% per million years.
The sequence of the 16,019 nucleotide-pair mitochondrial DNA (mtDNA) molecule of Drosophila yakuba is presented. This molecule contains the genes for two rRNAs, 22 tRNAs, six identified proteins [cytochrome b, cytochrome c oxidase subunits I, II, and III (COI-III), and ATPase subunits 6 and 8] and seven presumptive proteins (URF1-6 and URF4L). Replication originates within a region of 1077 nucleotides that is 92.8% A + T and lacks any open reading frame larger than 123 nucleotides. An equivalent to the sequence found in all mammalian mtCDNAs that is associated with initiation of second-strand DNA synthesis is not present in D. yakuba mtDNA. Introns are absent from D. yakuba mitochondrial genes and there are few (0-31) intergenic nucleotides. The genes found in D. yakuba and mammalian mtDNAs are the same, but there are differences in their arrangement and in the relative proportions of the complementary strands of the molecule that serve as templates for transcription. Although the D. yakuba small and large mitochondrial rRNA genes are exceptionally low in G and C and are shorter than any other metazoan rRNA genes reported, they can be folded into secondary structures remarkably similar to the secondary structures proposed for mammalian mitochondrial rRNAs. D. yakuba mitochondrial tRNA genes, like their mammalian counterparts, are more variable in sequence than nonorganelle tRNAs. In mitochondrial protein genes ATG, ATT, ATA, and in one case (COI) ATAA appear to be used as translation initiation codons. The only termination codon found in these genes is TAA. In the D. yakuba mitochondrial genetic code, AGA, ATA, and TGA specify serine, isoleucine, and tryptophan, respectively. Fifty-nine types of sense condon are used in the D. yakuba mitochondrial protein genes, but 93.8% of all codons end in A or T. Codon-anticodon interactions may include both G-A and C-A pairing in the wobble position. Evidence is summarized that supports the hypothesis that A and T nucleotides are favored at all locations in the D. yakuba mtDNA molecule where these nucleotides are compatible with function.
The discovery that the rate of evolution of vertebrate mitochondrial DNA is rapid, compared to the rate for vertebrate nuclear DNA, has resulted in its widespread use in evolutionary studies. Comparison of mitochondrial and nuclear DNA divergences among echinoid and vertebrate taxa of similar ages indicates that the rapid rate of vertebrate mitochondrial DNA evolution is, in part, an artifact of a widely divergent rate of nuclear DNA evolution. This disparity in relative rates of mitochondrial and nuclear DNA divergence suggests that the controls and constraints under which the mitochondrial and nuclear genomes operate are evolving independently, and provides evidence that is independent of fossil dating for a robust rejection of a generalized molecular clock hypothesis of DNA evolution.
This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time and bacterial RNA divergence which can be used to estimate times of divergence between other branches in the bacterial tree. According to this approach,Salmonella typhimurium andEscherichia coli diverged between 120 and 160 million years (Myr) ago, a date which fits with evidence that the chief habitats occupied now by these two enteric species became available that long ago.
The median extent of divergence betweenS. typhimurium andE. coli at synonymous sites for 21 kilobases of protein-coding DNA is 100%. This implies a silent substitution rate of 0.7–0.8%/Myr—a rate remarkably similar to that observed in the nuclear genes of mammals, invertebrates, and flowering plants. Similarities in the substitution rates of eucaryotes and procaryotes are not limited to silent substitutions in protein-coding regions. The average substitution rate for 16S rRNA in eubacteria is about 1%/50 Myr, similar to the average rate for 18S rRNA in vertebrates and flowering plants. Likewise, we estimate a mean rate of roughly 1%/25 Myr for 5S rRNA in both eubacteria and eucaryotes.
For a few protein-coding genes of these enteric bacteria, the extent of silent substitution since the divergence ofS. typhimurium andE. coli is much lower than 100%, owing to extreme bias in the usage of synonymous codons. Furthermore, in these bacteria, rates of amino acid replacement were about 20 times lower, on average, than the silent rate. By contranst, for the mammalian genes studied to date, the average replacement rate is only four to five times lower than the rate of silent substitution.
Sequence comparisons were made for up to 667 bp of DNA cloned from 14 kinds of Hawaiian Drosophila and five other dipteran species. These sequences include parts of the genes for NADH dehydrogenase (subunits 1, 2, and 5) and rRNA (from the large ribosomal subunit). Because the times of divergence among these species are known approximately, the sequence comparisons give insight into the evolutionary dynamics of this molecule. Transitions account for nearly all of the differences between sequences that have diverged by less than 2%: for these sequences the mean rate of divergence appears to be about 2%/Myr. In comparisons involving greater divergence times and greater sequence divergence, relatively more of the sequence differences are due to transversions. Specifically, the fraction of these differences that are counted as transversions rises from an initial value of less than 0.1 to a plateau value of nearly 0.6. The time required to reach half of the plateau value, about 10 Myr, is similar to that for mammalian mtDNA. The mtDNAs of flies and mammals are also alike in the shape of the curve relating the percentage of positions at which there are differences in protein-coding regions to the time of divergence. For both groups of animals, the curve has a steep initial slope ascribable to fast accumulation of synonymous substitutions and a shallow final slope resulting from the slow accumulation of substitutions causing amino acid replacements. However, the percentage of all sites that can experience a high rate of substitution appears to be only about 8% for fly mtDNA compared to about 20% for mammalian mtDNA.(ABSTRACT TRUNCATED AT 250 WORDS)
Single-copy sequences can be enzymatically amplified from genomic DNA by the polymerase chain reaction. By using unequal molar amounts of the two amplification primers, it is possible in a single step to amplify a single-copy gene and produce an excess of single-stranded DNA of a chosen strand for direct sequencing or for use as a hybridization probe. Further, individual alleles in a heterozygote can be sequenced directly by using allele-specific oligonucleotides either in the amplification reaction or as sequencing primers. By using these methods, we have studied the allelic diversity at the HLA-DQA locus and its association with the serologically defined HLA-DR and -DQ types. This analysis has revealed a total of eight alleles and three additional haplotypes. This procedure has wide applications in screening for mutations in human genes and facilitates the linking of enzymatic amplification of genes to automated sequencing.
We have determined the DNA sequence changes in 487 spontaneous mutations in the N-terminal part of the lacI gene in mutH, mutL, and mutS strains of Escherichia coli. These strains display elevated spontaneous mutation rates because of a deficiency in the process of postreplicative mismatch correction. As a consequence the mutational spectra reveal the nature of spontaneous DNA replication errors. The spectra consist of base substitutions (75%) and single-base deletions (25%). Among the base substitutions, transitions (both A.T----G.C and G.C----A.T) are strongly favored over transversions (96% versus 4%). Large site-to-site differences are observed among identical base substitutions, presumably reflecting the modulating effects of neighboring bases. The single-base-deletion spectrum is dominated by a large hotspot at a run of adjacent identical base pairs, implying a Streisinger-slippage mechanism. The data, when compared to a previously determined wild-type spectrum, also provide information on the specificity of the mismatch repair system.
This chapter presents an up-to-date account of the organization, structure, and evolution of mammalian mitochondrial genes, with the belief that the knowledge of these features should supply valuable information to understand the interrelationships between the mitochondrion and the rest of the cell. The concerted effort of several laboratories has produced a great deal of information on the structure of mitochondrial genomes of several mammalian species. Mitochondria1 DNA ( MtDNA) sequence of man, cow, and mouse as well as a large part of rat sequence have been determined and the transcription products of these DNAs have been identified and mapped. Mammalian MtDNA is a circular closed double-stranded molecule, containing about 16,500 base pairs. This gene organization is it extremely compact with the exception of the region containing the origin of replication of the mtDNA heavy strand (D-loop region), the heavy (H)-strand is completely filled with discrete products. The mammalian transcripts are colinear with the DNA, showing a relevant difference in the gene organization as compared to lower eukaryote mtDNA such as yeast and N. crassa —that is,the lack of introns.
A novel gene from the nematode Caenorhabditis elegans was isolated by hybridization with a human calmodulin complementary DNA probe. This gene, cal-1, is present at one copy per haploid genome. In-situ hybridization of the cloned gene to metaphase chromosomes allowed us to assign it to the nematode linkage group IV. The polypeptide predicted from the sequence of this gene displays structural features of both calmodulin and troponin C.
Methods are described for the isolation, complementation and mapping of mutants of Caenorhabditis elegans, a small free-living nematode worm. About 300 EMS-induced mutants affecting behavior and morphology have been characterized and about one hundred genes have been defined. Mutations in 77 of these alter the movement of the animal. Estimates of the induced mutation frequency of both the visible mutants and X chromosome lethals suggests that, just as in Drosophila, the genetic units in C. elegans are large.
Modification of beef heart cytochrome c oxidase with 1-ethyl-3-[3-[ 14C](trimethylamino)propyl]carbodiimide ([ 14C]ETC) was found to dramatically inhibit the high-affinity phase of the reaction with cytochrome c. Reaction conditions leading to a 50% inhibition of V max resulted in a 12-fold increase in the K m for cytochrome c. This inhibition was accompanied by the incorporation of 1.2 ± 0.3 mol of [ 14C]ETC into subunit II and much smaller levels of incorporation into the other subunits. The sites labeled by [ 14C]ETC were determined by hydrolyzing subunit II with trypsin in the presence of 1% octyl β-D-glucopyranoside and separating the resulting peptides by reverse-phase high-pressure liquid chromatography. The tryptic peptides were then further hydrolyzed with Staphylococcus aureus protease to determine that Glu-18, Asp-112, Glu-114, and Glu-198 were the major residues labeled. Binding one molecule of cytochrome c to cytochrome c oxidase dramatically protected Asp-112, Glu-114, and Glu-198 from labeling by [ 14C]ETC and prevented the loss in electron-transfer activity. We propose that the negatively charged carboxylates on Asp-112, Glu-114, and Glu-198 are involved in cytochrome c binding and that their conversion to bulky, positively charged ETC-carboxyl groups inhibits the reaction with cytochrome c. Asp-112 and Glu-114 are located in a highly conserved sequence (104-115) containing alternating acidic and aromatic residues. These aromatic residues could serve as an electron-transfer pathway from cytochrome c to cytochrome a or the EPR-visible copper. Glu-198 is located between the conserved cysteines-196 and -200 which have been proposed to serve as ligands for the EPR-visible copper.
To determine whether DNA survives and can be recovered from the remains of extinct creatures, we have examined dried muscle from a museum specimen of the quagga, a zebra-like species (Equus quagga) that became extinct in 1883 (ref. 1). We report that DNA was extracted from this tissue in amounts approaching 1% of that expected from fresh muscle, and that the DNA was of relatively low molecular weight. Among the many clones obtained from the quagga DNA, two containing pieces of mitochondrial DNA (mtDNA) were sequenced. These sequences, comprising 229 nucleotide pairs, differ by 12 base substitutions from the corresponding sequences of mtDNA from a mountain zebra, an extant member of the genus Equus. The number, nature and locations of the substitutions imply that there has been little or no postmortem modification of the quagga DNA sequences, and that the two species had a common ancestor 3-4 Myr ago, consistent with fossil evidence concerning the age of the genus Equus.
Simultaneous editing of multiple nucleic acid sequences with ESEE
- A T Beckenbach
CABOT, E. L., and A. T. BECKENBACH, 1989 Simultaneous editing
of multiple nucleic acid sequences with ESEE. Comput. Appl.
Biosci. 5: 233-234.
Directional mutation pressure and neutral mo
SUEOKA, N., 1988 Directional mutation pressure and neutral mo-
J. Mol. EvoI. 28: 497-516.
- E M Prager
- R D Sage
- M Stoneking
PALUMBI, E. M. PRAGER, R. D. SAGE and M. STONEKING,
1985 Mitochondrial DNA and two perspectives on evolutionary genetics. Biol. J. Linn. SOC. 2 6 375-400.
Rates of nucleotide substitution in Drosophila mitochondrial DNA and nuclear DNA are similar
- A Caccone
- G D Amato
- C Yoon
POWELL, J. R., A. CACCONE, G. D. AMATO and C. YOON,
1986 Rates of nucleotide substitution in Drosophila mitochondrial DNA and nuclear DNA are similar. Proc. Natl. Acad. Sci.
USA 83: 9090-9093.
We are grateful for the strains and information provided by D
- A Rose
- R Comments
- D Okimoto
- Wolstenholme For
- Unpublished Comments
- Results
- M Baillie
- G Edgely
- A Poinar
- R Rose
- Russell
- The Caenorhabditis Genetics
- Center
PRASAD and A. ROSE for comments and discussions as well as R.
OKIMOTO and D. WOLSTENHOLME for comments and unpublished
results. We are grateful for the strains and information provided
by D. BAILLIE, M. EDGELY, G. POINAR, A. ROSE, R. RUSSELL and
the Caenorhabditis Genetics Center. This work received support
from a National Institutes of Health postdoctoral fellowship to
W.K.T. and from National Science Foundation and National Institutes of Health grants to A.C.W.
LITERATURE CITED
Wilson the Steinernema-Caenorhabditis set to more distantly related nematodes
- W K Thomas
W. K. Thomas and A. C. Wilson
the Steinernema-Caenorhabditis set to more distantly
related nematodes.
PAUP: phylogenetic analysis using parsimony , version 3.0b
SWOFFORD, D. L., 1989 PAUP: phylogenetic analysis using parsimony, version 3.0b. Illinois Natural History Survey, Cham-
paign.