Biomedical subjects

Carlos A Machado

Publications and source records attributed to Carlos A Machado.

12 recordsLinked to original sources

PubMed2006

Evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific gene flow in Drosophila pseudoobscura and D. persimilis.

There is increasing evidence that chromosomal inversions may facilitate the formation or persistence of new species by allowing genetic factors conferring species-specific adaptations or reproductive isolation to be inherited together and by reducing or eliminating introgression. However, the genomic domain of influence of the inverted regions on introgression has not been carefully studied. Here, we present a detailed study on the consequences that distance from inversion breakpoints has had on the inferred level of gene flow and divergence between Drosophila pseudoobscura and D. persimilis. We identified the locations of the inversion breakpoints distinguishing D. pseudoobscura and D. persimilis in chromosomes 2, XR, and XL. Population genetic data were collected at specific distances from the inversion breakpoints of the second chromosome and at two loci inside the XR and XL inverted regions. For loci outside the inverted regions, we found that distance from the nearest inversion breakpoint had a significant effect on several measures of divergence and gene flow between D. pseudoobscura and D. persimilis. The data fitted a logarithmic relationship, showing that the suppression of crossovers in inversion heterozygotes also extends to loci located outside the inversion but close to it (within 1-2 Mb). Further, we detected a significant reduction in nucleotide variation inside the inverted second chromosome region of D. persimilis and near one breakpoint, consistent with a scenario in which this inversion arose and was fixed in this species by natural selection.

Animals↗

PubMed2006

Functional genomics of cactus host shifts in Drosophila mojavensis.

Understanding the genetic basis of adaptation to novel environments remains one of the major challenges confronting evolutionary biologists. While newly developed genomic approaches hold considerable promise for addressing this overall question, the relevant tools have not often been available in the most ecologically interesting organisms. Our study organism, Drosophila mojavensis, is a cactophilic Sonoran Desert endemic utilizing four different cactus hosts across its geographical range. Its well-known ecology makes it an attractive system in which to study the evolution of gene expression during adaptation. As a cactophile, D. mojavensis oviposits in the necrotic tissues of cacti, therefore exposing larvae and even adults to the varied and toxic compounds of rotting cacti. We have developed a cDNA microarray of D. mojavensis to examine gene expression associated with cactus host use. Using a population from the Baja California population we examined gene expression differences of third instar larvae when reared in two chemically distinct cactus hosts, agria (Stenocereus gummosus, native host) vs. organpipe (Stenocereus thurberi, alternative host). We have observed differential gene expression associated with cactus host use in genes involved in metabolism and detoxification.

Animals↗

PubMed2005

60 million years of co-divergence in the fig-wasp symbiosis.

Figs (Ficus; ca 750 species) and fig wasps (Agaoninae) are obligate mutualists: all figs are pollinated by agaonines that feed exclusively on figs. This extraordinary symbiosis is the most extreme example of specialization in a plant-pollinator interaction and has fuelled much speculation about co-divergence. The hypothesis that pollinator specialization led to the parallel diversification of fig and pollinator lineages (co-divergence) has so far not been tested due to the lack of robust and comprehensive phylogenetic hypotheses for both partners. We produced and combined the most comprehensive molecular phylogenetic trees to date with fossil data to generate independent age estimates for fig and pollinator lineages, using both non-parametric rate smoothing and penalized likelihood dating methods. Molecular dating of ten pairs of interacting lineages provides an unparalleled example of plant-insect co-divergence over a geological time frame spanning at least 60 million years.

Animals↗

PubMed2005

Uncovering evolutionary patterns of gene expression using microarrays.

The advent of microarray technology is providing new insights into fundamental questions in evolutionary biology. Here, we review the recent literature on the use of microarrays to study the evolution of genome-wide patterns of gene expression within and between species. Large levels of variation in gene expression patterns have been observed at the intra and interspecific level, and a substantial fraction of transcriptional variation has a genetic component that is contributed by changes in both cis-acting and trans-acting regulatory elements. We argue that there is solid evidence to show that the temporal dynamics of transcriptional variation is largely determined by natural selection, with the fraction of the transcriptome more closely related to sex and reproduction evolving more rapidly.

Animals↗

PubMed2005

Critical review of host specificity and its coevolutionary implications in the fig/fig-wasp mutualism.

Figs (Ficus spp., Moraceae) and their pollinating wasps (Agaonidae, Chalcidoidea) constitute perhaps the most tightly integrated pollination mutualism that is known. Figs are characterized by extraordinarily high global and local species diversity. It has been proposed that the diversification of this mutualism has occurred through strict-sense coadaptation and cospeciation between pairs of fig and wasp species that are associated in highly specific one-to-one relationships. However, existing studies cast doubt on the generality of this proposition. Here, we review our current knowledge of the evolutionary history of the fig/fig-wasp mutualism. We critically examine the idea that codivergence between figs and their pollinators has been dominated by strict-sense cospeciation. We present phylogenetic and population genetic data from neotropical fig and fig wasp species that suggest that a more accurate model for diversification in this mutualism is that of groups of genetically well defined wasp species coevolving with genetically less well defined (frequently hybridizing) groups of figs. Last, we use our results to assess previously proposed hypotheses on models of speciation in this mutualism.

Animals↗

PubMed2004

Inbreeding and population structure in two pairs of cryptic fig wasp species.

We used recently developed microsatellites to directly estimate inbreeding levels in two pairs of coexisting cryptic fig wasp species ('Pegoscapus hoffmeyeri sp. A and sp. B', 'P. gemellus sp. A and sp. B'). Previous tests of Hamilton's local mate competition (LMC) theory in fig wasps have used the number of dead foundresses in a fig fruit to indirectly estimate the relative contribution of each to the common brood and thereby the level of local mate competition. Further, the population level of inbreeding has been indirectly estimated using the distribution of foundress numbers across broods. Our direct genetic estimates confirmed previous assumptions that the species characterized by lower foundress numbers showed higher relative levels of inbreeding. However, there were quantitative differences between the observed level of inbreeding and the expectation based on the distribution of foundress numbers in both pollinator species associated with Ficus obtusifolia. Here, genotype compositions of broods revealed that only 23% of fruits with multiple foundresses actually contained brood from more than one foundress, thus explaining at least part of the underestimate of actual sibmating. Within the four wasp species there was no evidence for genetic differentiation among the wasp populations sampled from different trees across 20 km and from different points in time. Further, no genotypic disequilibrium was detected within any of the species. Although F1 hybrids were observed between the two species pollinating F. obtusifolia, there was no evidence of genetic introgression. Finally, we found that 11% of the sons of allospecifically mated mothers were diploid hybrids suggesting a break down of the sex determination system in hybrids.

Animals↗

PubMed2003

The causes of phylogenetic conflict in a classic Drosophila species group.

Bifurcating phylogenies are frequently used to describe the evolutionary history of groups of related species. However, simple bifurcating models may poorly represent the evolutionary history of species that have been exchanging genes. Here, we show that the history of three well-known closely related species, Drosophila pseudoobscura, D. persimilis and D. p. bogotana, is not well represented by a bifurcating phylogenetic tree. The phylogenetic relationships among these species vary widely between different genomic regions. Much of this phylogenetic variation can be explained by the potential of different genomic regions to introgress between species, as measured in laboratory studies. We argue that the utility of multiple markers in species-level phylogenetic studies can be greatly enhanced by knowledge of genomic location and, in the case of hybridizing species, by knowledge of the functional or linkage relationships among the markers and regions of the genome that reduce hybrid fitness.

Animals↗

PubMed2003

Cryptic species of fig-pollinating wasps: implications for the evolution of the fig-wasp mutualism, sex allocation, and precision of adaptation.

Fig-pollinating wasps have provided model systems for developing and testing theories of the evolution of mutualism, sex allocation, and precision of adaptation. With few exceptions, previous studies have assumed one species of pollinator wasp per host fig species. Here we report genetic data demonstrating the coexistence of previously undetected cryptic fig wasp species in at least half of the host fig species surveyed. The substantial mitochondrial sequence differences (4.2-6.1%) imply old divergences ( approximately 1.5-5.1 million years ago) among these species. Furthermore, some cryptic species pairs seem to be sister taxa, whereas others clearly are not, indicating both long-term coexistence on shared hosts and the colonization of novel fig species. These findings undermine the prevalent notion of strict one-to-one specificity between cospeciating figs and their pollinators, thereby challenging existing theory concerning the evolution and stability of mutualisms. Moreover, the incorporation of the genetic information significantly improves the fit of the observed sex ratios to predictions of local mate-competition theory, further strengthening support for sex allocation theory and the precision of adaptation.

Animals↗

PubMed2003

The study of structured populations--new hope for a difficult and divided science.

Natural populations, including those of humans, have complex geographies and histories. Studying how they evolve is difficult, but it is possible with population-based DNA sequence data. However, the study of structured populations is divided by two distinct schools of thought and analysis. The phylogeographic approach is fundamentally graphical and begins with a gene-tree estimate. By contrast, the more traditional approach of using summary statistics is fundamentally mathematical. Both approaches have limitations, but there is promise in newer probabilistic methods that offer the flexibility and data exploitation of the phylogeographic approach in an explicitly model-based mathematical framework.

Animals↗

PubMed2002

The distribution of Wolbachia in fig wasps: correlations with host phylogeny, ecology and population structure.

We surveyed for the presence and identity of Wolbachia in 44 species of chalcid wasps associated with 18 species of Panamanian figs. We used existing detailed knowledge of the population structures of the host wasps, as well as the ecological and evolutionary relationships among them, to explore the relevance of each of these factors to Wolbachia prevalence and mode of transmission. Fifty-nine per cent of these wasp species have Wolbachia infections, the highest proportion reported for any group of insects. Further, neither the presence nor the frequency of Wolbachia within hosts was correlated with the population structure of pollinator hosts. Phylogenetic analyses of wsp sequence data from 70 individuals representing 22 wasp species show that neither the close phylogenetic relationship nor close ecological association among host species is consistently linked to close phylogenetic affinities of the Wolbachia associated with them. Moreover, no genetic variation was detected within any Wolbachia strain from a given host species. Thus, the spread of Wolbachia within host species exceeds the rate of horizontal transmission among species and both exceed the rate of mutation of the wsp gene in Wolbachia. The presence and, in some cases, high frequency of Wolbachia infections within highly inbred species indicate that the Wolbachia either directly increase host fitness or are frequently horizontally transferred within these wasp species. However, the paucity of cospeciation of Wolbachia and their wasp hosts indicates that Wolbachia do not persist within a given host lineage for long time-periods relative to speciation times.

Animals↗

PubMed2002

Sequence variation in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) and trypanothione reductase (TR) genes of Trypanosoma cruzi.

Dihydrofolate reductase-thymidylate synthase (DHFR-TS) and trypanothione reductase (TR) are important enzymes for the metabolism of protozoan parasites from the family Trypanosomatidae (e.g. Trypanosoma spp., Leishmania spp.) that are targets of current drug-design studies. Very limited information exists on the levels of genetic polymorphism of these enzymes in natural populations of any trypanosomatid parasite. We present results of a survey of nucleotide variation in the genes coding for those enzymes in a large sample of strains from Trypanosoma cruzi, the agent of Chagas' disease. We discuss the results from an evolutionary perspective. A sample of 31 strains show 39 silent and five amino acid polymorphisms in DHFR-TS, and 35 silent and 11 amino acid polymorphisms in TR. No amino acid replacements occur in regions that are important for the enzymatic activity of these proteins, but some polymorphisms occur in sites previously assumed to be invariant. The sequences from both genes cluster in four major groups, a result that is not fully consistent with the current classification of T. cruzi in two major groups of strains. Most polymorphisms correspond to fixed differences among the four sequence groups. Two tests of neutrality show that there is no evidence of adaptive divergence or of selective events having shaped the distribution of polymorphisms and fixed differences in these genes in T. cruzi. However, one nearly significant reduction of variation in the TR sequences from one sequence group suggests a recent selective event at, or close to, that locus.

Amino Acid Sequence↗

PubMed2002

Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives.

The divergence of Drosophila pseudoobscura from its close relatives, D. persimilis and D. pseudoobscura bogotana, was examined using the pattern of DNA sequence variation in a common set of 50 inbred lines at 11 loci from diverse locations in the genome. Drosophila pseudoobscura and D. persimilis show a marked excess of low-frequency variation across loci, consistent with a model of recent population expansion in both species. The different loci vary considerably, both in polymorphism levels and in the levels of polymorphisms that are shared by different species pairs. A major question we address is whether these patterns of shared variation are best explained by gene flow or by persistence since common ancestry. A new test of gene flow, based on patterns of linkage disequilibrium, is developed. The results from these, and other tests, support a model in which D. pseudoobscura and D. persimilis have exchanged genes at some loci. However, the pattern of variation suggests that most gene flow, although occurring after speciation began, was not recent. There is less evidence of gene flow between D. pseudoobscura and D. p. bogotana. The results are compared with recent work on the genomic locations of genes that contribute to reproductive isolation between D. pseudoobscura and D. persimilis. We show that there is a good correspondence between the genomic regions associated with reproductive isolation and the regions that show little or no evidence of gene flow.

Animals↗