The Drosophila quinaria species group is a speciose lineage of mushroom-feeding flies studied for their specialist ecology, their parasites, population genetics, and the evolution of immune systems. Quinaria species are part of the Drosophila subgenus.
Mushroom-feeding ecology
Quinaria group species are commonly found on wild mushrooms, and can metabolize toxic compounds in Amanita mushrooms, such as ibotenic acid and alpha-amanitin. Mushroom sites also host a number of natural enemies. For instance, as a consequence of their mushroom-feeding ecology, Quinaria species are frequently infected by nematodes of the genus Howardula. Some Quinaria species are more or less susceptible to nematode parasitization, though the immunological reasons remain unclear. One possibility to explain this variance is differences in defensive bacterial symbionts. However another could be natural resource use, as most eukaryotes are unable to withstand the toxins in Amanita mushrooms, and thus development in these toxic mushrooms protects the flies from parasitism.
The ancestor of Quinaria species and related flies likely switched from a generalist ecology to become exclusively mushroom-feeders. From there, different mushroom-feeding lineages emerged, some of which reverted to feeding on decaying vegetation, such as Drosophila quinaria. Understanding the evolutionary forces that promoted a mushroom-feeding lifestyle, or reversion back to a more generalist ecology, can help understand concepts such as speciation and genetics of adaptation.
Quinaria group species such as Drosophila falleni are attracted to mushroom sites by cuing in on specific odourants that are common in rotting mushrooms, such as 1-pentanol, 1-octen-3-ol, and 3-methyl-1-butanol. Compared to Drosophila melanogaster, D. falleni are attracted to far more specific cues from rotting mushrooms. When D. falleni are infected by Howardula nematodes, infected flies become more averse to acetate-containing compounds such as ethyl acetate or propyl acetate. Conversely, infected flies become more attracted to 1-nonanol. This observation ties behavioural change to infection status, specifically identifying compounds that the fly becomes more or less averse to. Comparisons between mushroom-feeding Drosophila and D. melanogaster, and also between mushroom-specific Howardula parasitic nematodes and generalist nematodes could yield insight into how host-pathogen interactions alter olfactory preferences.
Systematics Evidence from phylogenetic studies suggests that the Quinaria group may be paraphyletic, comprising two clades. However, different phylogenetic analysis methods yield different results, so the exact systematics of the Quinaria group are still not fully confirmed.
Phylogeny ASTRAL phylogenetic cladogram topology from Scott Chialvo and colleagues (2019).
Related species Quinaria species are related to the Drosophila cardini, Drosophila bizonata, and Drosophila testacea species groups. Evolutionary studies in these various mushroom-feeding Drosophila have contributed to understanding how symbiotic bacteria can drastically affect host evolution, the impact of various genetic elements in natural populations, and speciation.
Genetics and genomics Various Quinaria group species have contributed to genetic studies in different fashions. So far the genomes of four Quinaria species, D. guttifera, D. innubila, D. quinaria, and D. palustris have been sequenced. Additional sequence data has been generated for Drosophila falleni and Drosophila phalerata. The genome of D. innubila was sequenced for a study in 2019, and boasts a very complete assembly rivalling that of the classic genetic model Drosophila melanogaster. In September 2020, a study of Drosophila sex pheromone communication sequenced the genomes of D. quinaria, and D. palustris, as well as many outgroup lineages of the Quinaria species group.
Gene regulation on the fly
The patterning of Drosophila wings has long been of interest to evolutionary biologists as understanding the genetic changes underlying wing patterning helps understand how evolution can act to promote novel designs. Drosophila guttifera (the "Polka-dotted fruit fly") has conspicuous dot patterns on its wings made of black melanin. Different variations of these dot patterns occur in different Quinaria group species, ranging from only one melanin spot on the wing band at the anterior costal vein in D. innubila, to two wing band spots in D. phalerata, to conspicuous polka-dots in D. guttifera. One method to study these patterns has been to compare gene regulation amongst different Drosophila species. The Drosophila Wnt signalling pathway regulates wing development. In the Wnt pathway, the Wingless gene encodes a ligand involved in the local development of melanin synthesis in the wing. Other genes in the Wnt signalling pathway such as yellow and ebony are also involved in melanin regulation. Studies in the major genetic model organism Drosophila melanogaster are how the Wnt signalling pathway was first suspected. These studies implicated genes such as Wingless in wing development through mutations in Wnt signalling and the Wingless gene. Following this, studies in different species such as Drosophila biarmipes and Drosophila guttifera revealed different patterns of yellow gene expression. As a result of these comparative studies, and owing to its attractive wing patterning, D. guttifera is now used as a comparative model to understand gene network interactions amongst Wingless, yellow, and other Wnt signalling genes. Understanding how these networks cooperate to regulate wing patterning also helps scientists understand how gene regulatory networks work in other systems such as health or development. Using conspicuous patterns like polka dot distribution on wings makes understanding general principles of gene regulation more approachable.
In 2015, the genome of Drosophila guttifera was sequenced by the laboratory of Sean B. Carroll providing an answer on how different wing patterns emerge in this species. The authors found that additional copies of genetic switches called "enhancers" drives the polka-dot pattern on the wings of D. guttifera. These enhancers were a subset of cis-regulatory elements. As such, new evolutionary patterns can arise without modifying the active gene, by instead modifying existing enhancer regions. This leads to different patterns of gene expression, in the case of D. guttifera, resulting in different patterning on its wings.
Population genetics and speciation
Speciation describes when two populations diverge sufficiently such that they are considered different species, often because they can no longer successfully reproduce with one another. This process is intuitive for conspicuous examples such as ring species, wherein a population splits due to a geographical barrier such as a mountain range, leading to allopatric populations. However why species diverge when their geographic ranges overlap (sympatric speciation) is less understood.
The sister species Drosophila subquinaria and Drosophila recens overlap in geographic range and are capable of hybridization, meaning they can successfully reproduce with each other; however the offspring are very sickly. Thus, these two species are almost fully reproductively isolated, despite overlapping in geographic range. One reason for this is behavioural, driven by pheromones. D. subquinaria females readily avoid mating with males from other species, but surprisingly D. subquinaria females also avoid mating with males from the same species in allopatric populations. However D. recens females do not distinguish between males from different populations. Pheromones in the cuticle of the males differ between geographic ranges of D. subquinaria, possibly explaining how females distinguish males from different populations. The bacterial symbiont Wolbachia is common in populations of D. recens, and causes cytoplasmic incompatibility in crosses between D. recens males and D. subquinaria females. This has led to D. subquinaria females in sympatry with Wolbachia-infected D. recens to be more choosy when making a mate choice, while D. subquinaria females that are not sympatric with D. recens do not make this distinction.
The D. subquinaria species complex is made all the more challenging to interpret by continued gene flow between D. recens and D. subquinaria. Beyond these two species, Drosophila transversa is also capable of hybridization with both D. subquinaria and D. recens. Ginsberg and colleagues showed that the direction of gene flow is biased from D. recens into sympatric populations of D. subquinaria. This is likely due to increased one-directional mating success between D. recens females and D. subquinaria males in sympatry, but may also depend on the efficiency with which the D. recens X chromosome acts in a D. subquinaria genetic background.
There is also a sex ratio-distorting X chromosome in D. recens that may factor in to both speciation between D. recens and D. subquinaria, and selection on D. recens populations more generally. This selfish X chromosome is one of a number of selfish genetic elements in the Quinaria and Testacea Drosophila species groups. In D. recens, females with two copies of the selfish X are sterile, while males have reduced fertility. These deleterious effects are offset by the transmission advantage that the X chromosome has in males, where it kills off all Y-bearing sperm, leaving that male to sire only selfish X-bearing daughters, which in turn produce more sons that will again sire only daughters.
Much of the work characterizing subquinaria-recens speciation is built on a body of work initiated in the 1970s by John Jaenike and fellow researchers.
Microbial symbiosis Symbiosis refers to the interactions amongst living organisms. These interactions can range from parasitism to mutual benefit. Often whether something should be considered a parasite or a beneficial symbiont is context-dependent. For instance, reproductive manipulators like Spiroplasma bacteria can kill their hosts sperm to benefit the symbiont at the cost of the host. But these same bacteria can defend the host against immune challenge by parasites.
Endosymbionts Bacterial endosymbionts are bacteria that live inside host compartments like inside host cells or in the blood. Endosymbionts are widespread in insects. The bacterial symbiont Wolbachia infects anywhere from 20 to 70% of all insects, while Spiroplasma is found in ~10% of Drosophila. These endosymbionts can have a number of different consequences from cytoplasmic incompatibility, male-killing, feminization, or defensive symbiosis.
Wolbachia Wolbachia is the most widespread of bacterial endosymbionts in insects and arthropods. Wolbachia bacteria are distant relatives of mitochondria, and like mitochondria, live inside host cells. Also like mitochondria, Wolbachia are inherited through females, so sons and daughters inherit Wolbachia almost exclusively from their mothers. Wolbachia are also commonly referred to as reproductive parasites. In different insects and arthropods, Wolbachia manipulate host reproduction to increase the number of females in the population. This benefits the Wolbachia as they are passed on from mothers to their offspring.