Research
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, until now (Matzkin 2013).
One of our core study organisms, Drosophila mojavensis, is a cactophilic Sonoran Desert endemic member of the Repleta group and its well studied ecology makes it an excellent system to study the genetic basis of adaptation. As a cactophile, D. mojavensis oviposits in the necrotic tissues of cacti, therefore exposing larvae and even adults to the varied and sometimes toxic compounds of rotting cacti. Drosophila mojavensis is composed of four host races (Mainland Sonoran, Baja California , Mojave and Catalina Is.), each with its own specific cactus host (Organpipe, Agria, Barrel, and Prickly Pear, respectively).  We use and developed several genomic tools, such as next-gen sequencing (DNA and RNAseq) and complete genome expression microarrays, to investigate the genetics of adaptation in D. mojavensis

Ecological genomics of host adaptation in D. mojavensis

We were involved in the sequencing and assembly of the first D. mojavensis genome (from Catalina Island) (D12GC 2007). Currently we have set out to sequence, assemble ascaffold_tablend annotate the genomes of the other three host populations (Baja California, Mojave Desert and mainland Sonora Desert). We have generated both short and long insert (180 bp and 3 kb, respectively) libraries and have sequenced them in a HiSeq 2500 at HudsonAlpha. For each genome we have obtain approximately 16 billion base pairs of sequence. Using the previously assembled Catalina Island genome we have been able to construct the great majority of the genome scaffold (93-97%, see table). We are currently generating de novo assemblies using the mate pair sequences. From our initial draft assemblies we have been able to obtain the sequences of 14,238 genes from each of the three host populations, which is the majority (~98%) of the genes annotated in the published genome (14,581). We have performed a series of analyses on the pattern of molecular evolution across the four host population's genomes (Allan and Matzkin, in prep). omegadistThe figure on the left illustrates the distribution of log2 of dN/dS values calculated using PAML (ω).  Values for 10,788 loci out of the 13,821 loci assembled are shown.  Loci with five or fewer substitutions (2,974 loci), sequence alignment uncertainties (417) and with undeterminable dN/dS or ka/ks values (59 loci) were filtered from the primary dataset (Allan and Matzkin, in prep). PAML analysis have shown 422 loci (after FDR correction, there were 1,151 loci prior to correction) that show evidence of positive selection. Further investigations on these genes have illustrated the changes associated with local ecological adaptation across the host populations. Furthermore, in collaboration with Teri Markow (UCSD) we have sequenced and begun to assemble the genomes of the sister species D. arizonae (cactus generalist) and the sibling species D. navojoa (Opuntia breeder).

Ecological transcriptomics of host adaptation in D. mojavensis

Our initial transcriptional analysis involved the examination of differential gene expression associated with necrotic cactus host use and shifts in several populations of D. mojavensis (Matzkin et. al 2006; Matzkin 2012).

In the presence of environmental change, natural selection can shape the transcriptome. Those genotypes that are better able to modulate gene expression to maximize fitness will be favored. Therefore, it is important to examine gene expression at the population level in order to distinguish random or neutral gene expression variation from the pattern produced by natural selection. We examined the level of standing genetic variation both within and between the D. mojavensis populations (Matzkin and Markow 2013). This population level approach allowed us to identify genes involved in past cactus host shifts. Among the set of genes identified were a set of genes previously known to be involved in xenobiotic metabolism.


Evolutionary genomics of speciation

Following mating D. mojavensis produces a reaction mass in the lower reproductive tract that last hours upon conspecific mating, but could last days if not longer upon heterospecific mating (much investigated by Teri Markow). Previously we have investigated the transcriptional consequences within the lower reproductive tracts of females following heterospecific mating (Bono et al. 2011). In that study we additionally observed the transfer of RNA transcripts from the male to the female via the ejaculate. In collaboration with Jeremy Bono (UCCS) and as a follow up from our previous study we are analysis the pattern of evolution in several of the candidate genes from Bono et al. (2011).

Role of Glutathione S-transferase D1 in cactus host adaptation

Members of the Glutathione S-transferase gene family have been known to play a role in detoxification in many taxa, including insects. A gene with high homology to the D. melanogaster Glutathione S-transferase-D1 (GstD1) locus was differentially expressed in a Baja California D. mojavensis isofemale line as a response to utilizing an alternative host (S. thurberi) (Matzkin et. al 2006). In both D. melanogaster and in Anopheles gambiae, GstD1 has been implicated in the resistance of these species to the insecticide DDT. I have examined the pattern of sequence variation of the GstD1 locus from all four D. mojavensis opulations, D. arizonae (its sister species) and D. navojoa (outgroup) (Matzkin 2008). The data suggest that in the Baja California and Sonora population of D. mojavensis GstD1 has gone through a period of adaptive amino acid evolution as reflected by the ratio of silent to replacement fixations and polymorphisms. Polarizing these data using D. navojoa indicates that the positive selection occurred in the lineage leading to these D. mojavensis populations. Further analyses indicate that of the seven amino acid fixations that occurred in the D. mojavensis lineage two of them occur in the active site pocket, potentially having a significant affect on substrate specificity and possibly in the adaptation to alternative cactus hosts (Matzkin 2008). Currently we have heterlogously expressed GSTD1 and have begun to access the functional and kinetic differences associated with the amino acid substitutions observed between the different host populations.


Transcriptional and functional genomics of stress adaptation in D. mojavensis

The necrosis of each cactus species provides each of the resident D. mojavensis populations with a distinct chemical environment. In addition, the abiotic environment experienced by D. mojavensis can be equally as harsh. In the summer internal cactus necrosis can reach upwards of 51° C (Matzkin unpub.) and the humidity can range between 10 to 90% (Gibbs et al. 2003). As it might be expected D. mojavensis has one of the greatest resistances to desiccation and heat shock of all Drosophila (Gibbs and Matzkin 2001; Matzkin et al. 2007). We have examined the differential gene expression in D. mojavensis females and males associated with the ability to resist desiccating condition (Matzkin and Markow 2009). There are significant quantitative and qualitative gene expression differences in how males and females react to the desiccating desert environement. Additionally, we have begun to examine the transcriptional effects of starvation and thermal stress adaptation in D. mojavensis.

Evolution of sensory pathways in cactophilic Drosophila

In addition to genes associated with performance, genes involved in host preference likely played a major role in cactus host adaptation. We have began to examine the pattern of transcriptional and sequence variation at several gene families associated with preference such as odorant receptors, gustatory receptors and odorant binding proteins. Furthermore, we are examining the effect of the local ecological adaptation of the four host populations on the sensory behavior of adults. We are testing and array of compounds to assess variation in preference and repulsion between the population and linking it to the known chemical composition of the cactus hosts.

Genetic mechanisms of detoxification in D. mojavensis

The focus of our recently award NSF grant is to quantify the fitness consequences of different host race-specific alleles of two candidate detoxification genes.  For each gene, the allele of each host race will be introgressed into the genetic background of the other.  The known ecology of D. mojavensis will be utilized to better assess the fitness consequence of each introgressed allele.  To determine fitness effects, the replicate introgression lines will be reared in necrotic cactus tissues of two host races.  Viability, stress resistance and metabolic pools content assays will be performed to determine the fitness effects. 

 

Department of Biological Sciences