Genome evolution in three species of cactophilic drosophila

We report genomes of two species of cactophilic Drosophila: Drosophila arizonae and D. navojoa. These two are the closest relatives of D. mojavensis, forming the D. mojavensis cluster. D. mojavensis and D. arizonae diverged from D. navojoa ∼5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species are also separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a past role of the inversions in preventing gene flow, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions

Transcriptional responses of ecologically diverse drosophila species to larval diets differing in relative sugar and protein ratios

We utilized three ecologically diverse Drosophila species to explore the influence of ecological adaptation on transcriptomic responses to isocaloric diets differing in their relative proportions of protein to sugar. Drosophila melanogaster, a cosmopolitan species that breeds in decaying fruit, exemplifies individuals long exposed to a Western diet higher in sugar, while the natural diet of the cactophilic D. mojavensis, is much lower in carbohydrates. Drosophila arizonae, the sister species of D. mojavensis, is largely cactophilic, but also utilizes rotting fruits that are higher in sugars than cacti. We exposed third instar larvae for 24 hours to diets either (1) high in protein relative to sugar, (2) diets with equal amounts of protein and sugar, and (3) diets low in protein but high in sugar. As we predicted, based upon earlier interspecific studies of development and metabolism, the most extreme differences in gene expression under different dietary conditions were found in D. mojavensis followed by D. arizonae. No differential expression among diets was observed for D. melanogaster, a species that survives well under all three conditions, with little impact on its metabolism. We suggest that these three species together provide a model to examine individual and population differences in vulnerability to lifestyle-associated health problems such as metabolic syndrome and diabetes

The genomics of species divergence in drosophila

How do new species arise and diverge? Has been a fundamental question in evolutionary biology. The process of species divergence can be studied at many different levels of biological organization. However, it is until the recent advancements of genome sequencing technologies that genome-wide signatures of species divergence have started to unveil the complex genomic landscape of speciation. In this dissertation we investigate the landscape of genomic divergence using a classic pair of Drosophila species. We generated four new high quality genome assemblies for Drosophila pseudoobscura and D. persimilis to explore the genomic differences at three different levels. We first characterized the structural variation landscape between D. pseudoobscura and D. persimilis and stablished its association with transposable elements and tested how intrinsic genomic factors, such as recombination, influence the accumulation ofstructural variation associated with transposable elements in both species. With a combination of high-quality genome assemblies and a comprehensive population genomics data set, we also explored how the contribution of recombination rate and introgression promote sequence divergence with the potential of forming species barriers. Moreover, we investigated how gene co-expression networks potentially rewiring between species contribute to the divergence landscape between D. pseudoobscura and D. persimilis. Our work highlights the complex landscape of species divergence occurring at multiple levels of organization. Moreover, the integration of potential species drivers identified at different scales shed lights on the molecular mechanisms involved in speciation

Expression changes of shared genes that were differentially expressed in <i>D</i>. <i>arizonae</i> and <i>D</i>. <i>mojavensis</i> in LPHS-HPLS.

<p>Expression changes of shared genes that were differentially expressed in <i>D</i>. <i>arizonae</i> and <i>D</i>. <i>mojavensis</i> in LPHS-HPLS.</p

Heat map of all differentially expressed genes of <i>D</i>. <i>arizonae</i> and their associated GO terms.

<p>A) Heat map of the 64 differentially expressed genes analyzed by TopHat-Cufflinks. Color intensity represents the mean of gene expression of the Cufflinks-determined FPKM values for two replicates in each treatment (FDR<0.05). B) Pie charts of functional annotation of affected genes through diets. Analysis was done using the web tool of Gene Ontology Consortium (<a href="http://geneontology.org/" target="_blank">http://geneontology.org</a>). BP = biological process, MF = molecular function, CC = cellular components. Numbers inside the pie charts are the number of genes associated to each term, and genes that belong to more than one term were counted also in those respective categories.</p

Heat map of all differentially expressed genes of <i>D</i>. <i>mojavensis</i> and their associated GO terms.

<p>A) Heat map of the 141 differentially expressed genes analyzed by TopHat-Cufflinks. Color intensity represents the mean of gene expression of the Cufflinks-determined FPKM values for two replicates in each treatment (FDR<0.05). B) Pie charts of functional annotation of affected genes through diets. Analysis was done using the web tool of Gene Ontology Consortium (<a href="http://geneontology.org/" target="_blank">http://geneontology.org</a>). BP = biological process, MF = molecular function, CC = cellular components. Color codes are the same as Fig 3 for each chart. Numbers inside the pie charts are the number of genes associated to each term, and genes that belong to more than one term were counted also in those respective categories.</p

Differentially expressed genes between diets in <i>D</i>. <i>arizonae</i> and <i>D</i>. <i>mojavensis</i>.

<p>Third instar larvae were exposed to different diets during 24hrs and RNA-Seq analysis was performed with TopHat-Cufflinks (FDR<0.05). (A, C and E) Analysis of differentially expressed genes in <i>D</i>. <i>arizonae</i>. (B, D and F) Analysis of differentially expressed genes in <i>D</i>. <i>mojavensis</i>. (A-B) Matrix analysis showing the number of genes that changed between diets. (C-D) Venn diagrams showing the number of genes that were significantly different in more than one paired comparisons. (E-F) Number of genes that were up-regulated (black bars) and down-regulated (white bars) in each paired comparison between diets.</p

Genes validated by RT-qPCR.

<p>Nine genes were differentially expressed by RNASeq and <i>Adh1</i> was used for comparison with <i>Adh2</i>.</p

Validation of differentially expressed genes by RT-qPCR.

<p>A) Differentially expressed genes between more extreme diets (LPHS-HPLS) of <i>Drosophila arizonae</i>, using 18S transcript as internal control. Genes are: a = XLOC_001916 (<i>Adh1</i>), b = XLOC_001917 (<i>Adh2</i>), c = XLOC_007196 (<i>G6pd</i>), d = XLOC_012803, e = XLOC_008841, f = XLOC_000655, g = XLOC_011578, h = XLOC_000511, i = XLOC_008657, j = XLOC_005117. B) Differentially expressed genes between more extreme diets (HPLS-LPHS) of <i>Drosophila mojavensis</i>, using 18S transcript as internal control. Genes are: a = <i>Adh1</i>, b = <i>Adh2</i>, c = <i>G6pd</i>, d = <i>Xdh</i>, e = GI11539, f = GI15562, g = GI20954, h = GI21508, i = GI23443, j = GI23906, k = GI14996, l = GI15007, m = GI19975, n = GI20777, o = GI23074.</p

Habitabilidad y política de vivienda

En esta obra, en la que participan destacados investigadores y profesores, dedicados al estudio de la problemática habitacional se presentan diferentes análisis que permiten conocer cuales son las condiciones de habitabilidad y las características de la actual política de vivienda de México. En sus capítulos se abordan los principales desafíos que enfrentan las familias mexicanas para acceder a una vivienda digna y decorosa y cuales son los retos económicos, políticos, territoriales, arquitectónicos, ambientales, financieros y culturales de las formas de producción habitacional en México y en otros países, en el marco de una sociedad global