Andres Moya - Academia.edu (original) (raw)
Papers by Andres Moya
Molecular Ecology, 2001
The genetic structure of six Iberian populations of the whitefly Bemisia tabaci, two of them biot... more The genetic structure of six Iberian populations of the whitefly Bemisia tabaci, two of them biotype Q, one biotype B, and the other three a mixture of both, has been studied using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). A total of 336 individuals was completely discriminated by means of 234 scored bands. Separate analyses of molecular variance of haploid males and diploid females using the pairwise number of differences between haplotypes showed that biotypes contribute significantly more to the observed variability than populations within biotypes. On average, gene flow between two biotypes of the same population is lower than between populations of identical biotypes. On the basis of these results and the nondetection under natural conditions of a single hybrid, we consider that both biotypes are genetically isolated under the ecological conditions prevailing in the south Iberian Peninsula. All populations of biotype Q presented similar values of intrapopulational diversity, which were higher than the values shown by populations of biotype B.
The genetic diversity of a vesicular stomatitis virus population was analysed by RT-PCR, cloning ... more The genetic diversity of a vesicular stomatitis virus population was analysed by RT-PCR, cloning and sequencing of two " 500 nucleotide regions of the virus genome. PCR amplifications were performed in parallel experiments with both Taq and Pfu DNA polymerases, and important differences were observed. Between 10 and 22 mutations were detected when virus populations were analysed by Taq amplification (20 clones from each region), whereas amplification of the same samples with Pfu revealed between 0 and 5 mutations. PCR fidelity assays, performed under the same PCR conditions as those used in the population analysis, showed that the Taq error-rate estimate of 0n27i10 N 4 misincorporations per bp per cycle was within the range 0001-5630 # 1998 SGM CJCB
Proceedings of The National Academy of Sciences, 1990
When two mitochondrial DNA (mtDNA) haplotypes of Drosophila subobscura compete in experimental po... more When two mitochondrial DNA (mtDNA) haplotypes of Drosophila subobscura compete in experimental populations with discrete generations, one or the other approaches fixation, depending on the nuclear background with which they are associated. The approach to fixation, however, is strongly dependent on the effective number of females in the population, Nf. Whether or not the ultimate fate of a given
Nature Reviews Microbiology, 2004
RNA viruses have become an important area of study for epidemiologists and evolutionary biologist... more RNA viruses have become an important area of study for epidemiologists and evolutionary biologists alike 1-3 . Much of this research is centred on two main themes; understanding the mechanisms of RNA virus evolution, often through experimental analyses, and reconstruction of the epidemiological history of a given virus, namely its origin and spread through populations and the forces that promote its emergence. Here, we review the progress and current state of both these research topics.
Proceedings of The National Academy of Sciences, 2003
Bacterial symbioses are widespread among insects, probably being one of the key factors of their ... more Bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. We present the complete genome sequence of Blochmannia floridanus, the primary endosymbiont of carpenter ants. Although these ants feed on a complex diet, this symbiosis very likely has a nutritional basis: Blochmannia is able to supply nitrogen and sulfur compounds to the host while it takes advantage of the host metabolic machinery. Remarkably, these bacteria lack all known genes involved in replication initiation (dnaA, priA, and recA). The phylogenetic analysis of a set of conserved protein-coding genes shows that Bl. floridanus is phylogenetically related to Buchnera aphidicola and Wigglesworthia glossinidia, the other endosymbiotic bacteria whose complete genomes have been sequenced so far. Comparative analysis of the five known genomes from insect endosymbiotic bacteria reveals they share only 313 genes, a number that may be close to the minimum gene set necessary to sustain endosymbiotic life.
Proceedings of The Royal Society B: Biological Sciences, 1996
Holocyclic clones of the aphid Rhopalosiphum padi (L.) reproduce by cyclic parthenogenesis, where... more Holocyclic clones of the aphid Rhopalosiphum padi (L.) reproduce by cyclic parthenogenesis, whereas anholocyclic individuals are obligate parthenogens. Mitochondrial DNA and (mtDNA) and random amplified polymorphic DNA markers in R. padi as well as plasmid DNA markers of its bacterial endosymbiont, Buchnera aphidicola, were examined to determine the extent of genetic divergence between clones with these differing breeding systems. These analyses revealed that cyclically parthenogenetic lineages possessed differing mtDNA and plasmid haplotypes than most obligately asexual clones. The extent of sequence divergence between the maternally inherited molecules suggest a relatively ancient origin of asexuality. Our work also identified a random amplified polymorphic DNA marker linked to the life-cycle variation in R. padi. This marker not only permits the rapid diagnosis of breeding system but sets the stage for studies to identify the gene(s) controlling this variation in mode of reproduction.
Molecular Ecology, 2003
To elucidate the co-evolutionary relationships between phloem-feeding insects and their secondary... more To elucidate the co-evolutionary relationships between phloem-feeding insects and their secondary, or facultative, bacterial symbionts, we explore the distributions of three such microbes -provisionally named the R-type (or PASS, or S-sym), T-type (or PABS), and Utype -across a number of aphid and psyllid hosts through the use of diagnostic molecular screening techniques and DNA sequencing. Although typically maternally transmitted, phylogenetic and pairwise divergence analyses reveal that these bacteria have been independently acquired by a variety of unrelated insect hosts, indicating that horizontal transfer has helped to shape their distributions. Based on the high genetic similarity between symbionts in different hosts, we argue that transfer events have occurred recently on an evolutionary timescale. In several instances, however, closely related symbionts associate with related hosts, suggesting that horizontal transfer between distant relatives may be rarer than transmission between close relatives. Our findings on the prevalence of these symbionts within many aphid taxa, along with published observations concerning their effects on host fitness, imply a significant role of facultative symbiosis in aphid ecology and evolution.
Journal of Molecular Evolution, 1995
We have identified and completely sequenced a novel plasmid isolated from the aphid Rhopalosiphum... more We have identified and completely sequenced a novel plasmid isolated from the aphid Rhopalosiphum padi. Evidence which suggests that the plasmid occurs localized within the bacterial endosymbionts is presented. The plasmid contains the four genes that constitute the entire leucine operon. This fact makes it really unique since most plasmids are dispensable and lack genes that encode essential anabolic functions. Four more phloem-feeding aphid species also seem to contain homologous plasmids. Although further work is necessary, we hypothesize that this plasmid has appeared during the evolution of the symbiotic association between the aphid and the bacterial endosymbiont. The fact that this plasmid contains the entire leucine operon can be related to physiological evidence showing that the aphid host's diet of plant phloem is deficient in essential amino acids.
Proceedings of The National Academy of Sciences, 2003
We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Bai... more We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Baizongia pistacea. This strain diverged 80 -150 million years ago from the common ancestor of two previously sequenced Buchnera strains. Here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. As a consequence, the genome assembly unveiled intrapopulational variation, consisting of Ϸ1,200 polymorphic sites. Comparison of the 618-kb (kbp) genome with the two other Buchnera genomes revealed a nearly perfect gene-order conservation, indicating that the onset of genomic stasis coincided closely with establishment of the symbiosis with aphids, Ϸ200 million years ago. Extensive genome reduction also predates the synchronous diversification of Buchnera and its host; but, at a slower rate, gene loss continues among the extant lineages. A computational study of protein folding predicts that proteins in Buchnera, as well as proteins of other intracellular bacteria, are generally characterized by smaller folding efficiency compared with proteins of free living bacteria. These and other degenerative genomic features are discussed in light of compensatory processes and theoretical predictions on the long-term evolutionary fate of symbionts like Buchnera. † Present address: Plant Research International B.V., Business unit Genomics,
Proceedings of The National Academy of Sciences, 1986
The colonization of the New World by the Palearctic species Drosophila subobscura was first detec... more The colonization of the New World by the Palearctic species Drosophila subobscura was first detected in 1978 in South America and around 1982 in western North America. The ensuing dramatic expansion of the species, in territory as well as numbers, provides an opportunity for studying evolution in a scale rarely possible. We have used 10 restriction endonucleases to analyze the mitochondrial DNA (mtDNA) of individuals from 23 widely dispersed localities. Only two mtDNA composite morphs have been detected in the Americas. None of the two morphs has been found in Africa, and only one in the Atlantic islands; but both are widespread in Europe, which provides no clue of the precise geographic origin of the colonizers. The amount of nucleotide-substitution polymorphism detected in D. subobscura is typical for animals, but it is greater in the Old than in the New World, presumably due to the recent colonization by a limited number of colonizers. Assuming standard evolutionary rates of mtDNA base substitution, the mtDNA morphs found in D. subobscura can be traced to a single one that existed no less than one million years ago. We argue against the inference that the D. subobscura flies now living descend from only one or a few females that lived at that time. This type of inference, which we call the "Mother Eve hypothesis," has been made to conclude that the human population went through a severe constriction about 200,000 years ago, so that all living humans descend from only one or a few women who lived at that time. The Mother Eve hypothesis is fallacious.
Proceedings of The National Academy of Sciences, 1986
We have studied 15 gene loci coding for enzymes in 121 Trypanosoma cruzi stocks from a wide geogr... more We have studied 15 gene loci coding for enzymes in 121 Trypanosoma cruzi stocks from a wide geographic range-from the United States and Mexico to Chile and southern Brazil. T. cruzi is diploid but reproduction is basically clonal, with very little if any sexuality remaining at present. We
We report a restriction-site study of the mitochondrial DNA (mtDNA) of seven species of the Droso... more We report a restriction-site study of the mitochondrial DNA (mtDNA) of seven species of the Drosophila obscura group. One species (D. azteca) belongs to the afinis subgroup; the other six species are classified in the obscura subgroup, three of them being from the old-world species (D. obscura, D. ambigua, and D. subobscura) and three from the new-world species (D. pseudoobscura, D. persimilis, and D. miranda). The mtDNA patterns suggest that the phylogeny of the group needs to be revised. The Nearctic obscura species appear as more closely related to D. azteca (afinis subgroup) than to the Palearctic species. The three Palearctic species are, in turn, a very heterogeneous group, with D. obscura no more closely related to D. subobscura and D. ambigua than to D. a&is or the Nearctic obscura species. The rates of mtDNA evolution are variable: some lineages have evolved at rates two or three times greater than others. If an average rate of 0.5% nucleotide substitutions/Myr is assumed, the divergence among the four main lineages in the phylogeny would have occurred 12-l 5 Myr ago, during the Miocene, which is consistent with biogeographic information.
Proceedings of The National Academy of Sciences, 2002
Buchnera is a mutualistic intracellular symbiont of aphids. Their association began about 200 mil... more Buchnera is a mutualistic intracellular symbiont of aphids. Their association began about 200 million years ago, with host and symbiont lineages evolving in parallel since that time. During this coevolutionary process, Buchnera has experienced a dramatic decrease of genome size, retaining only essential genes for its specialized lifestyle. Previous studies reported that genome size in Buchnera spp. is very uniform, suggesting that genome shrinkage occurred early in evolution, and that modern lineages retain the genome size of a common ancestor. Our physical mapping of Buchnera genomes obtained from five aphid lineages shows that the genome size is not conserved among them, but has been reduced down to 450 kb in some species. Here we show evidence of six species with a genome size smaller than Mycoplasma genitalium, the smallest bacterial genome reported thus far (580 kb). Our findings strongly suggest that the Buchnera genome is still experiencing a reductive process toward a minimum set of genes necessary for its symbiotic lifestyle.
Microbiology and Molecular Biology Reviews, 2004
Proceedings of The National Academy of Sciences, 2000
RNA viruses are excellent experimental models for studying evolution under the theoretical framew... more RNA viruses are excellent experimental models for studying evolution under the theoretical framework of population genetics. For a proper justification of this thesis we have introduced some properties of RNA viruses that are relevant for studying evolution. On the other hand, population genetics is a reductionistic theory of evolution. It does not consider or make simplistic assumptions on the transformation laws within and between genotypic and phenotypic spaces. However, such laws are minimized in the case of RNA viruses because the phenotypic space maps onto the genotypic space in a much more linear way than on higher DNA-based organisms. Under experimental conditions, we have tested the role of deleterious and beneficial mutations in the degree of adaptation of vesicular stomatitis virus (VSV), a nonsegmented virus of negative strand. We also have studied how effective population size, initial genetic variability in populations, and environmental heterogeneity shapes the impact of mutations in the evolution of vesicular stomatitis virus. Finally, in an integrative attempt, we discuss pros and cons of the quasispecies theory compared with classic population genetics models for haploid organisms to explain the evolution of RNA viruses.
New England Journal of Medicine, 1996
In the course of a study conducted in 1992 through 1994 of the efficacy of screening blood donors... more In the course of a study conducted in 1992 through 1994 of the efficacy of screening blood donors for antibodies to hepatitis C virus (HCV), we found that two patients had acquired hepatitis C after cardiac surgery, with the transmission apparently unrelated to blood transfusions. Because their surgeon had chronic hepatitis C, we sought to determine whether he was transmitting the virus to his patients. Of 222 of the surgeon's patients who participated in studies of post-transfusion hepatitis between 1988 and 1994, 6 contracted postoperative hepatitis C, despite the use of only seronegative blood for transfusions. All six patients had undergone valve-replacement surgery. Analyses were performed to compare nucleotide sequences encompassing the hypervariable region at the junction between the coding regions for envelope glycoproteins E1 and E2 in the surgeon, the patients, and 10 controls infected with the same HCV genotype. The surgeon and five of the six patients with hepatitis C unrelated to transfusion were infected with HCV genotype 3; the sixth patient had genotype 1 and was considered to have been infected from another source. Thirteen other patients of the surgeon had transfusion-associated hepatitis C and were also infected with genotype 1. The average net genetic distance between the sequences from the five patients with HCV genotype 3 and those from the surgeon was 2.1 percent (range, 1.1 to 2.5 percent; P < 0.001), as compared with an average distance of 7.6 percent (range, 6.1 to 8.3 percent) between the sequences from the patients and those from the controls. The results of phylogenetic-tree analysis indicated a common epidemiologic origin of the viruses from the surgeon and the five patients. Our findings provide evidence that a cardiac surgeon with chronic hepatitis C may have transmitted HCV to five of his patients during open-heart surgery.
Journal of Molecular Evolution, 2002
Here we present a new sliding window-based method specially designed to detect selective constrai... more Here we present a new sliding window-based method specially designed to detect selective constraints in specific regions of a multiple protein-coding sequence alignment. In contrast to previous window-based procedures, our method is based on a nonarbitrary statistical approach to find the appropriate codon-window size to test deviations of synonymous (dS) and nonsynonymous (dN) nucleotide substitutions from the expectation. The probabilities of dN and dS are obtained from simulated data and used to detect significant deviations of dN and dS in a specific window region of the real sequence alignment. The nonsynonymous-to-synonymous rate ratio (w = dN/dS) was used to highlight selective constraints in any window wherein dS or dN was significantly different from the expectation. In these significant windows, w and its variance [V(w)] were calculated and used to test the neutral hypothesis. Computer simulations showed that the method is accurate even for highly divergent sequences. The main advantages of the new method are that it (i) uses a statistically appropriate window size to detect different selective patterns, (ii) is computationally less intensive than maximum likelihood methods, and (iii) detects saturation of synonymous sites, which can give deviations from neutrality. Hence, it allows the analysis of highly divergent sequences and the test of different alternative hypothesis as well. The application of the method to different human immunodeficiency virus type 1 and to foot-and-mouth disease virus genes confirms the action of positive selection on previously described regions as well as on new regions.
Journal of Molecular Biology, 1996
Molecular Ecology, 2001
The genetic structure of six Iberian populations of the whitefly Bemisia tabaci, two of them biot... more The genetic structure of six Iberian populations of the whitefly Bemisia tabaci, two of them biotype Q, one biotype B, and the other three a mixture of both, has been studied using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). A total of 336 individuals was completely discriminated by means of 234 scored bands. Separate analyses of molecular variance of haploid males and diploid females using the pairwise number of differences between haplotypes showed that biotypes contribute significantly more to the observed variability than populations within biotypes. On average, gene flow between two biotypes of the same population is lower than between populations of identical biotypes. On the basis of these results and the nondetection under natural conditions of a single hybrid, we consider that both biotypes are genetically isolated under the ecological conditions prevailing in the south Iberian Peninsula. All populations of biotype Q presented similar values of intrapopulational diversity, which were higher than the values shown by populations of biotype B.
The genetic diversity of a vesicular stomatitis virus population was analysed by RT-PCR, cloning ... more The genetic diversity of a vesicular stomatitis virus population was analysed by RT-PCR, cloning and sequencing of two " 500 nucleotide regions of the virus genome. PCR amplifications were performed in parallel experiments with both Taq and Pfu DNA polymerases, and important differences were observed. Between 10 and 22 mutations were detected when virus populations were analysed by Taq amplification (20 clones from each region), whereas amplification of the same samples with Pfu revealed between 0 and 5 mutations. PCR fidelity assays, performed under the same PCR conditions as those used in the population analysis, showed that the Taq error-rate estimate of 0n27i10 N 4 misincorporations per bp per cycle was within the range 0001-5630 # 1998 SGM CJCB
Proceedings of The National Academy of Sciences, 1990
When two mitochondrial DNA (mtDNA) haplotypes of Drosophila subobscura compete in experimental po... more When two mitochondrial DNA (mtDNA) haplotypes of Drosophila subobscura compete in experimental populations with discrete generations, one or the other approaches fixation, depending on the nuclear background with which they are associated. The approach to fixation, however, is strongly dependent on the effective number of females in the population, Nf. Whether or not the ultimate fate of a given
Nature Reviews Microbiology, 2004
RNA viruses have become an important area of study for epidemiologists and evolutionary biologist... more RNA viruses have become an important area of study for epidemiologists and evolutionary biologists alike 1-3 . Much of this research is centred on two main themes; understanding the mechanisms of RNA virus evolution, often through experimental analyses, and reconstruction of the epidemiological history of a given virus, namely its origin and spread through populations and the forces that promote its emergence. Here, we review the progress and current state of both these research topics.
Proceedings of The National Academy of Sciences, 2003
Bacterial symbioses are widespread among insects, probably being one of the key factors of their ... more Bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. We present the complete genome sequence of Blochmannia floridanus, the primary endosymbiont of carpenter ants. Although these ants feed on a complex diet, this symbiosis very likely has a nutritional basis: Blochmannia is able to supply nitrogen and sulfur compounds to the host while it takes advantage of the host metabolic machinery. Remarkably, these bacteria lack all known genes involved in replication initiation (dnaA, priA, and recA). The phylogenetic analysis of a set of conserved protein-coding genes shows that Bl. floridanus is phylogenetically related to Buchnera aphidicola and Wigglesworthia glossinidia, the other endosymbiotic bacteria whose complete genomes have been sequenced so far. Comparative analysis of the five known genomes from insect endosymbiotic bacteria reveals they share only 313 genes, a number that may be close to the minimum gene set necessary to sustain endosymbiotic life.
Proceedings of The Royal Society B: Biological Sciences, 1996
Holocyclic clones of the aphid Rhopalosiphum padi (L.) reproduce by cyclic parthenogenesis, where... more Holocyclic clones of the aphid Rhopalosiphum padi (L.) reproduce by cyclic parthenogenesis, whereas anholocyclic individuals are obligate parthenogens. Mitochondrial DNA and (mtDNA) and random amplified polymorphic DNA markers in R. padi as well as plasmid DNA markers of its bacterial endosymbiont, Buchnera aphidicola, were examined to determine the extent of genetic divergence between clones with these differing breeding systems. These analyses revealed that cyclically parthenogenetic lineages possessed differing mtDNA and plasmid haplotypes than most obligately asexual clones. The extent of sequence divergence between the maternally inherited molecules suggest a relatively ancient origin of asexuality. Our work also identified a random amplified polymorphic DNA marker linked to the life-cycle variation in R. padi. This marker not only permits the rapid diagnosis of breeding system but sets the stage for studies to identify the gene(s) controlling this variation in mode of reproduction.
Molecular Ecology, 2003
To elucidate the co-evolutionary relationships between phloem-feeding insects and their secondary... more To elucidate the co-evolutionary relationships between phloem-feeding insects and their secondary, or facultative, bacterial symbionts, we explore the distributions of three such microbes -provisionally named the R-type (or PASS, or S-sym), T-type (or PABS), and Utype -across a number of aphid and psyllid hosts through the use of diagnostic molecular screening techniques and DNA sequencing. Although typically maternally transmitted, phylogenetic and pairwise divergence analyses reveal that these bacteria have been independently acquired by a variety of unrelated insect hosts, indicating that horizontal transfer has helped to shape their distributions. Based on the high genetic similarity between symbionts in different hosts, we argue that transfer events have occurred recently on an evolutionary timescale. In several instances, however, closely related symbionts associate with related hosts, suggesting that horizontal transfer between distant relatives may be rarer than transmission between close relatives. Our findings on the prevalence of these symbionts within many aphid taxa, along with published observations concerning their effects on host fitness, imply a significant role of facultative symbiosis in aphid ecology and evolution.
Journal of Molecular Evolution, 1995
We have identified and completely sequenced a novel plasmid isolated from the aphid Rhopalosiphum... more We have identified and completely sequenced a novel plasmid isolated from the aphid Rhopalosiphum padi. Evidence which suggests that the plasmid occurs localized within the bacterial endosymbionts is presented. The plasmid contains the four genes that constitute the entire leucine operon. This fact makes it really unique since most plasmids are dispensable and lack genes that encode essential anabolic functions. Four more phloem-feeding aphid species also seem to contain homologous plasmids. Although further work is necessary, we hypothesize that this plasmid has appeared during the evolution of the symbiotic association between the aphid and the bacterial endosymbiont. The fact that this plasmid contains the entire leucine operon can be related to physiological evidence showing that the aphid host's diet of plant phloem is deficient in essential amino acids.
Proceedings of The National Academy of Sciences, 2003
We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Bai... more We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Baizongia pistacea. This strain diverged 80 -150 million years ago from the common ancestor of two previously sequenced Buchnera strains. Here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. As a consequence, the genome assembly unveiled intrapopulational variation, consisting of Ϸ1,200 polymorphic sites. Comparison of the 618-kb (kbp) genome with the two other Buchnera genomes revealed a nearly perfect gene-order conservation, indicating that the onset of genomic stasis coincided closely with establishment of the symbiosis with aphids, Ϸ200 million years ago. Extensive genome reduction also predates the synchronous diversification of Buchnera and its host; but, at a slower rate, gene loss continues among the extant lineages. A computational study of protein folding predicts that proteins in Buchnera, as well as proteins of other intracellular bacteria, are generally characterized by smaller folding efficiency compared with proteins of free living bacteria. These and other degenerative genomic features are discussed in light of compensatory processes and theoretical predictions on the long-term evolutionary fate of symbionts like Buchnera. † Present address: Plant Research International B.V., Business unit Genomics,
Proceedings of The National Academy of Sciences, 1986
The colonization of the New World by the Palearctic species Drosophila subobscura was first detec... more The colonization of the New World by the Palearctic species Drosophila subobscura was first detected in 1978 in South America and around 1982 in western North America. The ensuing dramatic expansion of the species, in territory as well as numbers, provides an opportunity for studying evolution in a scale rarely possible. We have used 10 restriction endonucleases to analyze the mitochondrial DNA (mtDNA) of individuals from 23 widely dispersed localities. Only two mtDNA composite morphs have been detected in the Americas. None of the two morphs has been found in Africa, and only one in the Atlantic islands; but both are widespread in Europe, which provides no clue of the precise geographic origin of the colonizers. The amount of nucleotide-substitution polymorphism detected in D. subobscura is typical for animals, but it is greater in the Old than in the New World, presumably due to the recent colonization by a limited number of colonizers. Assuming standard evolutionary rates of mtDNA base substitution, the mtDNA morphs found in D. subobscura can be traced to a single one that existed no less than one million years ago. We argue against the inference that the D. subobscura flies now living descend from only one or a few females that lived at that time. This type of inference, which we call the "Mother Eve hypothesis," has been made to conclude that the human population went through a severe constriction about 200,000 years ago, so that all living humans descend from only one or a few women who lived at that time. The Mother Eve hypothesis is fallacious.
Proceedings of The National Academy of Sciences, 1986
We have studied 15 gene loci coding for enzymes in 121 Trypanosoma cruzi stocks from a wide geogr... more We have studied 15 gene loci coding for enzymes in 121 Trypanosoma cruzi stocks from a wide geographic range-from the United States and Mexico to Chile and southern Brazil. T. cruzi is diploid but reproduction is basically clonal, with very little if any sexuality remaining at present. We
We report a restriction-site study of the mitochondrial DNA (mtDNA) of seven species of the Droso... more We report a restriction-site study of the mitochondrial DNA (mtDNA) of seven species of the Drosophila obscura group. One species (D. azteca) belongs to the afinis subgroup; the other six species are classified in the obscura subgroup, three of them being from the old-world species (D. obscura, D. ambigua, and D. subobscura) and three from the new-world species (D. pseudoobscura, D. persimilis, and D. miranda). The mtDNA patterns suggest that the phylogeny of the group needs to be revised. The Nearctic obscura species appear as more closely related to D. azteca (afinis subgroup) than to the Palearctic species. The three Palearctic species are, in turn, a very heterogeneous group, with D. obscura no more closely related to D. subobscura and D. ambigua than to D. a&is or the Nearctic obscura species. The rates of mtDNA evolution are variable: some lineages have evolved at rates two or three times greater than others. If an average rate of 0.5% nucleotide substitutions/Myr is assumed, the divergence among the four main lineages in the phylogeny would have occurred 12-l 5 Myr ago, during the Miocene, which is consistent with biogeographic information.
Proceedings of The National Academy of Sciences, 2002
Buchnera is a mutualistic intracellular symbiont of aphids. Their association began about 200 mil... more Buchnera is a mutualistic intracellular symbiont of aphids. Their association began about 200 million years ago, with host and symbiont lineages evolving in parallel since that time. During this coevolutionary process, Buchnera has experienced a dramatic decrease of genome size, retaining only essential genes for its specialized lifestyle. Previous studies reported that genome size in Buchnera spp. is very uniform, suggesting that genome shrinkage occurred early in evolution, and that modern lineages retain the genome size of a common ancestor. Our physical mapping of Buchnera genomes obtained from five aphid lineages shows that the genome size is not conserved among them, but has been reduced down to 450 kb in some species. Here we show evidence of six species with a genome size smaller than Mycoplasma genitalium, the smallest bacterial genome reported thus far (580 kb). Our findings strongly suggest that the Buchnera genome is still experiencing a reductive process toward a minimum set of genes necessary for its symbiotic lifestyle.
Microbiology and Molecular Biology Reviews, 2004
Proceedings of The National Academy of Sciences, 2000
RNA viruses are excellent experimental models for studying evolution under the theoretical framew... more RNA viruses are excellent experimental models for studying evolution under the theoretical framework of population genetics. For a proper justification of this thesis we have introduced some properties of RNA viruses that are relevant for studying evolution. On the other hand, population genetics is a reductionistic theory of evolution. It does not consider or make simplistic assumptions on the transformation laws within and between genotypic and phenotypic spaces. However, such laws are minimized in the case of RNA viruses because the phenotypic space maps onto the genotypic space in a much more linear way than on higher DNA-based organisms. Under experimental conditions, we have tested the role of deleterious and beneficial mutations in the degree of adaptation of vesicular stomatitis virus (VSV), a nonsegmented virus of negative strand. We also have studied how effective population size, initial genetic variability in populations, and environmental heterogeneity shapes the impact of mutations in the evolution of vesicular stomatitis virus. Finally, in an integrative attempt, we discuss pros and cons of the quasispecies theory compared with classic population genetics models for haploid organisms to explain the evolution of RNA viruses.
New England Journal of Medicine, 1996
In the course of a study conducted in 1992 through 1994 of the efficacy of screening blood donors... more In the course of a study conducted in 1992 through 1994 of the efficacy of screening blood donors for antibodies to hepatitis C virus (HCV), we found that two patients had acquired hepatitis C after cardiac surgery, with the transmission apparently unrelated to blood transfusions. Because their surgeon had chronic hepatitis C, we sought to determine whether he was transmitting the virus to his patients. Of 222 of the surgeon's patients who participated in studies of post-transfusion hepatitis between 1988 and 1994, 6 contracted postoperative hepatitis C, despite the use of only seronegative blood for transfusions. All six patients had undergone valve-replacement surgery. Analyses were performed to compare nucleotide sequences encompassing the hypervariable region at the junction between the coding regions for envelope glycoproteins E1 and E2 in the surgeon, the patients, and 10 controls infected with the same HCV genotype. The surgeon and five of the six patients with hepatitis C unrelated to transfusion were infected with HCV genotype 3; the sixth patient had genotype 1 and was considered to have been infected from another source. Thirteen other patients of the surgeon had transfusion-associated hepatitis C and were also infected with genotype 1. The average net genetic distance between the sequences from the five patients with HCV genotype 3 and those from the surgeon was 2.1 percent (range, 1.1 to 2.5 percent; P < 0.001), as compared with an average distance of 7.6 percent (range, 6.1 to 8.3 percent) between the sequences from the patients and those from the controls. The results of phylogenetic-tree analysis indicated a common epidemiologic origin of the viruses from the surgeon and the five patients. Our findings provide evidence that a cardiac surgeon with chronic hepatitis C may have transmitted HCV to five of his patients during open-heart surgery.
Journal of Molecular Evolution, 2002
Here we present a new sliding window-based method specially designed to detect selective constrai... more Here we present a new sliding window-based method specially designed to detect selective constraints in specific regions of a multiple protein-coding sequence alignment. In contrast to previous window-based procedures, our method is based on a nonarbitrary statistical approach to find the appropriate codon-window size to test deviations of synonymous (dS) and nonsynonymous (dN) nucleotide substitutions from the expectation. The probabilities of dN and dS are obtained from simulated data and used to detect significant deviations of dN and dS in a specific window region of the real sequence alignment. The nonsynonymous-to-synonymous rate ratio (w = dN/dS) was used to highlight selective constraints in any window wherein dS or dN was significantly different from the expectation. In these significant windows, w and its variance [V(w)] were calculated and used to test the neutral hypothesis. Computer simulations showed that the method is accurate even for highly divergent sequences. The main advantages of the new method are that it (i) uses a statistically appropriate window size to detect different selective patterns, (ii) is computationally less intensive than maximum likelihood methods, and (iii) detects saturation of synonymous sites, which can give deviations from neutrality. Hence, it allows the analysis of highly divergent sequences and the test of different alternative hypothesis as well. The application of the method to different human immunodeficiency virus type 1 and to foot-and-mouth disease virus genes confirms the action of positive selection on previously described regions as well as on new regions.
Journal of Molecular Biology, 1996