Catálogo de publicaciones - libros

Statistical analysis of aligned DNA sequences, both among and within species, has proven to be a valuable tool for inferring the evolutionary history of genetic loci. Of particular interest are cases where the observed data depart from the neutral expectation and suggest adaptive evolution due to positive natural selection. In this chapter, we use the and genes to demonstrate methods of evolutionary inference from both inter- and intraspecific DNA sequence data. Interspecific comparisons suggest that these three paralogous, testes-expressed genes have diverged in function following duplication and have evolved under different selective constraints. The three genes show the increased rate of between-species amino acid replacement common to genes with reproductive function, which may be the result of recurrent positive selection. Intraspecific comparison of alleles provides evidence for more recent positive selection in this region of the genome. There are two divergent haplotype groups segregating in the worldwide population, one of which has risen to high frequency within the past 5000 years. The observed pattern of within-species variation may best be explained by a selective sweep that has not gone to completion.

Anumber of recent studies have suggested that the rapid evolution of genes involved in sexual reproduction is driven by conflict between the sexes. Such genes include the ones that have a role in mating behavior, postmating gamete interactions, and fertilization (i.e., sex-related genes). However, in many cases an alternative scenario with males coadapting to female-driven changes appears as an equally likely one. Studies on the molecular evolution of sex-related genes have mainly focused on males, with few exceptions. We suggest that the combined analysis of intraspecific polymorphism and interspecies divergence will allow to make predictions on whether sex-related genes evolution is driven by conflict or coadaptation between the sexes. Such approach, made possible by rapid accumulation of DNA sequence information, will benefit from studies designed to identify male and female gene products that interact with each other during mate signaling, fertilization, and postzygotic development.

The gene cluster at the base of the X-chromosome is unique to the lineage of . The repeating unit in the cluster was formed from a duplication and fusion of the genes, , which juxtaposed the 3′ untranslated region of the third intron of encodes Annexin 10 and Cdic encodes a cytoplasmic dynein intermediate chain. The 3′ untranslated region of contains two promoter elements, including a testis-specific element, and intron 3 contains a third promoter element; together these elements result in testis-specific transcription of . The Sdic protein features a novel amino terminus derived in part from intron 3 which contains motifs similar to those in axonemal dyneins. It has been demonstrated that the Sdic protein becomes incorporated into the tails of mature sperm. The evolution of the cluster required several deletions, at least one insertion, at least eleven nudeotide substitutions, and an estimated tenfold tandem duplication, all of which took place in the 1–3 million years since the divergence of from . Evidence for the ongoing evolution of including a recent selective sweep is found in the low levels of polymorphism across neighboring genes in the region, a large number of fixed amino acid replacements relative to fixed synonymous nucleotide substitutions, and a frequency spectrum of polymorphic nucleotides skewed toward rare variants. The analysis of polymorphism and divergence in the region, however, is complicated by the possible effects of background selection caused by deleterious new mutations, owing to the reduced amount of recombination in the region associated with its proximity to centromeric heterochromatin. We present the rapid evolution of this novel gene as a fascinating example of male-driven evolution incurred by recurrent selective sweeps.

In this chapter, neutrality tests based on haplotype distribution are evaluated as a way of detecting selective sweeps. Several kinds of haplotype tests are reviewed, including haplotype number, haplotype diversity and haplotype partition tests. We focus on incomplete sweeps, where recombination between the selected locus and a given marker allows for several preexisting neutral lineages to survive the sweep and for some preexisting genetic variation to remain in a sample. Several problems are addressed, including the distinction between possible alternative hypotheses, the effect of sampling strategy, of conditioning the statistics on the population mutational parameter θ and/or the observed number of polymorphic sites and, finally, the effect of intragenic recombination together with the choice of one- vs. two-tailed tests. Corresponding guidelines are proposed. To compare the power of haplotype tests and of other classical tests to detect selective sweeps, we use a simple selective sweep model with a deterministic approximation, allowing for genetic exchange between the selected locus and a given neutral marker. We conclude that there are ways of overcoming the difficulties in applying the tests, which are powerful means for revealing incomplete selective sweep effects.

Studies of genomic polymorphism among populations have revealed that this parasite is surprisingly homogenous for most genetic loci. Past events in the evolution of the species have lead to vast reductions in genetic variation due to either demographic or selective sweeps, starting with the origin of Malarias Eve perhaps as recently as 3,000 year ago. Subsequently, selective pressures such as those imposed by use of anti-malarial drugs, including chloroquine, may have further diminished variation over large regions of the genome. Nonetheless, it is clear that P. falciparum retains extraordinary ability to persist due in part to genomic novelties, such as repetitive antigen genes, which allow for rapid proliferation of genetic diversity despite demographic constraints. Understanding the precise mechanisms by which this adaptive potential is maintained and generated will be vital step in developing sustainable strategies to reduce malaria transmission and lessen the burden on human health.

We have presented equivalence scales derived from a survey where subjects have been asked to assess the income needs of different hypothetical households given five levels of reference income of a reference household. We find that equivalence scales obtained negatively depend on the level of reference income. This finding strongly questions the results of previous studies where equivalence scales have been assumed to be constant. Obviously, this constancy assumption either means an overestimation of the needs of “rich” or the underestimation of the needs of “poor” multi-person households or the mis-specification of the needs of both. Second, the number of adults in the household turns out to be an important criterion for the evaluation of children needs. According to our respondents, the income needs of children are an increasing function of the number of adult household members. It is, therefore, necessary to broaden economic models with respect to this interaction.

Biodiversity in the bacterial world is strongly influenced by “periodic selection,” in which natural selection recurrently purges diversity within a bacterial population. Owing to the extreme rarity of recombination in bacteria, selection favoring an adaptive mutation eliminates nearly all the diversity within an ecotype (defined as the set of strains using about the same ecological niche, so that an adaptive mutant or recombinant out-competes to extinction strains from the same ecotype). Diversity within an ecotype is only transient, awaiting its demise with the next periodic selection event. Ecological diversity in bacteria is governed by three kinds of mutations (or recombination events). Niche-invasion mutations found a new ecotype, such that the new genotype and its descendants escape the diversity-purging effect of periodic selection from their former ecotype. Periodic selection mutations then make the different ecotypes more distinct by purging the diversity within but not between ecotypes. Lastly, speciation-quashing mutations may occur, which can extinguish another ecotype even after it has had several private, periodic selection events. For example, an ecotype that shares all its resources with another ecotype, albeit in different proportions, may be extinguished by an extraordinarily fit adaptive mutation from the other ecotype.

Sequence clusters, as determined by a variety of criteria, are expected to correspond to ecotypes. Sequence-based approaches suggest that a typical named species contains many ecotypes.

That periodic selection occurs in nature is evidenced by the modest levels of sequence diversity observed within bacterial species, levels that are too low to be explained by genetic drift. Also, a special kind of periodic selection event, driven by “adapt globally, act locally” mutations, is inferred when strains fall into discrete sequence clusters over most of their genomes, but are aberrantly homogeneous in a small chromosomal region. Beyond establishing a history of periodic selection, this pattern can help corroborate that a set of sequence clusters correspond to ecotypes.

Studies of genomic polymorphism among populations have revealed that this parasite is surprisingly homogenous for most genetic loci. Past events in the evolution of the species have lead to vast reductions in genetic variation due to either demographic or selective sweeps, starting with the origin of Malarias Eve perhaps as recently as 3,000 year ago. Subsequently, selective pressures such as those imposed by use of anti-malarial drugs, including chloroquine, may have further diminished variation over large regions of the genome. Nonetheless, it is clear that P. falciparum retains extraordinary ability to persist due in part to genomic novelties, such as repetitive antigen genes, which allow for rapid proliferation of genetic diversity despite demographic constraints. Understanding the precise mechanisms by which this adaptive potential is maintained and generated will be vital step in developing sustainable strategies to reduce malaria transmission and lessen the burden on human health.

In this chapter, neutrality tests based on haplotype distribution are evaluated as a way of detecting selective sweeps. Several kinds of haplotype tests are reviewed, including haplotype number, haplotype diversity and haplotype partition tests. We focus on incomplete sweeps, where recombination between the selected locus and a given marker allows for several preexisting neutral lineages to survive the sweep and for some preexisting genetic variation to remain in a sample. Several problems are addressed, including the distinction between possible alternative hypotheses, the effect of sampling strategy, of conditioning the statistics on the population mutational parameter θ and/or the observed number of polymorphic sites and, finally, the effect of intragenic recombination together with the choice of one- vs. two-tailed tests. Corresponding guidelines are proposed. To compare the power of haplotype tests and of other classical tests to detect selective sweeps, we use a simple selective sweep model with a deterministic approximation, allowing for genetic exchange between the selected locus and a given neutral marker. We conclude that there are ways of overcoming the difficulties in applying the tests, which are powerful means for revealing incomplete selective sweep effects.