1. Evolutionary biology of bacteria

Evolutionary genomics of bacteria

    The increasing availability of bacterial genomes has opened the possibility for addressing fundamental questions of the evolutionary biology of bacteria:  what does the genome wide variation can tell us about the demographic history of bacterial species? how has the gene composition of the genomes changed over time? how the acquisition of genes (outside of the common drug resistance genes) via lateral gene transfer has contributed to the adaptation of bacterial species to new niches?

I have been working on applying some of the recent advances in population genomic techniques to understand the evolutionary history of Streptococcus mutans, a bacteria involved in the development of the dental cavities. A manuscript, presenting the results of a very comprehensive set of analyses, performed on 57 newly s
equenced genomes of S. mutans is under review. These analyses reveal that S. mutans populations have been expanding, most likely after the origin of agriculture. More importantly, we have found that there is a subset of genes, unique to this species, which are functionally involved in the metabolism of sugars and resistance to low pH environments; selective pressures that the bacteria had to face after the change of diet that accompanied the development of agriculture.

  I have also performed demographic analyses with a more limited scope, aimed to understand the demographic history of Helicobacter pylori using a set of published genomes. How good are methods based on the site frequency spectrum at inferring the demographic history of bacteria that recombines frequently? I am in the process of writing a manuscript to present the results of this work.

  I also maintain an active collaboration with my colleague Caitlin Pepperell at the University of Wisconsin-Madisson. Caitlin is interested in the evolution of pathogenic bacteria, specifically in Mycobacterium tuberculosis, and I have collaborated with her on the analysis of TB genomes using novel approaches, while our mutual overlap at Stanford. We plan on continuing our collaboration beyond TB and try to understand the impact of horizontal gene transfer in bacterial populations.

  1. 1.Evolutionary biology of bacteria

  2. 2.Population genetics and phylogenetics of Plasmodium

  3. 3.Evolutionary Genomics of Theobroma cacao

Biology of recombination in bacteria

  In bacteria, recombination is a rare event and not part of its reproductive process. Nevertheless, it has been increasingly recognized the importance that Horizontal gene transfer (in broad sense) plays in the adaptive evolution of bacteria species. Because of its ability to acquire genes and genetic elements from other organisms, the pace of adaptive evolution in bacteria (i.e. invasion of new niches, competition against
other bacteria or acquisition of resistance to antibiotics and other environmental stresses) needs not be limited by the amount of standing variation in the population. But, then we can ask ourselves, why bacteria maintain an intricate machinery for homologous gene recombination? What is the the impact of homologous gene recombination on the maintenance and accessibility of standing genetic variation in populations where sex is not frequent and not linked to reproduction? These are questions that are not well understood.  Our work suggest that, once established in the population, the ability to recombine can be maintained in the population at the expense of its costs. Nevertheless, because of the frequency and density dependent nature of horizontal gene transfer in bacteria, the benefits of recombination are not that clear when this ability is rare.  This study has produced testable hypothesis about the evolution of recombination in bacterial populations that I plan on pursuing in the future using Streptococcus pneumoniae as a model system. An alternative model system that I plan on evaluating this hypothesis is Acinetobacter ssp., in collaboration with Pål Johnsen.
Another important aspect of recombination in bacteria is to understand the factors that limit or promote the acquisition of foreign DNA into the cell. My previous work, done in collaboration with Daniel Rozen (now at the University of Leiden, the Netherlands) has shown that, contrary to some hypothesis proposed in the microbial molecular genetics literature, the polymorphism in the competence system responsible for inducing the uptake of DNA does not maintain genetically differentiated populations. This research has also open the door to interesting findings on the evolution of the polymorphism of two component systems (receptor - signal peptides) and we plan on pursuing additional experimental work to understand how polymorphism can be maintained by purifying selection via compensatory mutations.  The interesting bit is that although sequence wise the competence system presents strong similarities with self-compatibility systems in plants, the mechanisms maintaining polymorphism in the population are radically different.

  Additional work performed by Benjamin Evans, a former student of Danny Rozen has shown results that are consistent with our original assessment of the impact of the polymorphism on the population substructure of S. pneumoniae. We are preparing a manuscript presenting the results of this research.

Ecology and evolution of bacteriocins

      Agents that kill the organisms that produce them or other, genetically identical members of their populations are intriguing puzzles for ecologists and evolutionary biologists. How can such “self-killing” agents, which, on a first consideration appear to be a considerable disadvantage to the organisms that
produce them evolve and be maintained by natural selection?  One possibility we have suggested is that this agents can be maintained if during the interaction of different bacterial populations or species, the producing species kill their competitors more than they kill themselves.

This work, at the intersection of experiments and mathematical modeling has also opened the door for an interesting hypothesis about the maintenance of self-killing agents with a set of testable hypotheses: if the toxin producing bacteria kills others more than it kill itself, then such a system could potentially be maintained. Nevertheless, as with the advantage of recombination, this mechanism engenders a cost to the organism and its action is frequency or density-dependent, making the question about its origin and maintenance very controversial. It seems that this mechanism could easily be maintained while common, but it would have problems at invading when rare. The question is not rhetorical, as for any strategy of biotic control of infections by symbiotic or carrier organisms, or intervention and control of contaminated cultures (i.e in dairy industry or cocoa fermentation), it would be ideal to count on bacteriocins that kill the organisms that produce them as well: once the contaminants have been accounted for, there is no need for the organism that produces the toxin.

  1. 2.Population genetics and Phylogenetics of Plasmodium

Plasmodium, the causing agent of malaria, is one of the most interesting parasites that impact human
health worldwide.  It is a parasite with a complex life cycle, that involves the sexual reproduction in the mosquito vector (or intermediary host), and asexual stages in different tissues of the vertebrate host. It infects many different vertebrate hosts, including several species of non-human primates, and most of the evidence suggests that the four Plasmodium species infecting humans, might have resulted from a host shift from a non-human parasite. Since my MSc. studies I have maintained a continuous collaboration with Ananias Escalante at ASU, studying phylogenetic relationships among Plasmodium species, trying to understand the demographic history of Plasmodium vivax, and studying the patterns of variation in well known antigen proteins like the apical me
mbrane antigen (AMA-1).  Our work suggests that Plasmodium vivax is more closely related to parasites infecting macaques than parasite species infecting african primates. This work was followed by a more thorough analysis where we estimated the time to most recent common ancestor (TMRCA) of Plasmodium vivax populations, using full mitochondrial genomes, under the coalescent that revealed Asian populations being the oldest populations of Plasmodium.

Our interest in understanding the demographic history of Plasmodium vivax is not only an academic exercise, but also a necessary step towards understanding the ecological scenario in which selection has acted and how adaptation to the human host has historically occurred, and how drug resistance rises and spread in the population.  Also, because recombination is tight to transmission, understanding the dynamics of seasonal epidemics and the overall historical changes will eventually help us make predictions on the speed at which adaptive evolution can occur in this species.

most of the analysis we have done so far have used a single locus (mitochondrial genomes) and I am planning on moving to full genomes analysis of Plasmodium vivax to better understand the demography and signatures of selection in this organism.

3. Evolutionary Genomics of Theobroma cacao

  Theobroma cacao L (cacao: Malvaceae) is a small tree endemic to the amazonian rain forest, where it
most likely evolved, and it persists in natural populations of naturally interbreeding plants (and inbreeding plants, as it is a species with a complex system of self-incompatibility, where a fraction of the population is able to self-fertilize). 

Previous work of our collaborator Juan Carlos Motamayor has shown that there are at least 10 main groups of genetically differentiated populations of cacao.  This work has been based on the analysis of microsatellite markers.  We are generating full genome sequence of accessions from the different groups to investigate in more detail the evolutionary history of cacao and identify the genetic basis of phenotypic traits. Only a small group of cacao plants have been used for breeding programs worldwide, thus identifying genomic resources among natural genotypes of cacao that could be of use in breeding programs is uttermost importance. Also, we would like to develop cacao as a model system for how to map complex traits in long-lived tropical trees where generating multi generational mapping populations is not feasible.

Cacao crops have an enormous economic impact, not only on the economy of chocolate producing countries, but also and most importantly on the economy of cocoa producing countries. Having a positive impact in society out of my research is as important to me as satisfying my intellectual curiosity and this project has a great potential of benefiting people in the long term.