Whole‐genome sequencing reveals absence of recent gene flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea

Abstract

Anopheles mosquitoes are the vectors of several human diseases including malaria. In many malaria endemic areas, several species of Anopheles coexist, sometimes in the form of related sibling species that are morphologically indistinguishable. Determining the size and organization of Anopheles populations, and possible ongoing gene flow among them is important for malaria control and, in particular, for monitoring the spread of insecticide resistance alleles. However, these parameters have been difficult to evaluate in most Anopheles species due to the paucity of genetic data available. Here, we assess the extent of contemporary gene flow and historical variations in population size by sequencing and de novo assembling the genomes of wild-caught mosquitoes from four species of the Anopheles punctulatus group of Papua New Guinea. Our analysis of more than 50 Mb of orthologous DNA sequences revealed no evidence of contemporary gene flow among these mosquitoes. In addition, investigation of the demography of two of the An. punctulatus species revealed distinct population histories. Overall, our analyses suggest that, despite their similarities in morphology, behaviour and ecology, contemporary sympatric populations of An. punctulatus are evolving independently.

Discovery of flavivirus-derived endogenous viral elements inAnophelesmosquito genomes supports the existence ofAnopheles-associated insect-specific flaviviruses

“…sinensis mosquitoes. We screened 24 publicly available Anopheles genomes (Holt et al 2002; Zhou et al 2014; Logue et al 2015; Neafsey et al 2015) for flaviviral sequences, and validated in silico hits both at the DNA and RNA levels in vivo . The two newly described flavivirus-derived EVEs are phylogenetically related to ISFs, and support the existence of a previously unsuspected Anopheles -associated clade of ISFs.…”

Population genomics of the filarial nematode parasite Wuchereria bancrofti from mosquitoes

“…from Logue et al . (). (B) Multiple sequential Markovian coalescent ( MSMC ) of 6 haplotypes from three unrelated Wb L3 worms: L3‐17E, L3‐4873 and L3‐4853.…”

“…Following the peak size, A. farauti no.4 experienced a dramatic bottleneck in contrast to A. punctulatus which has been increasing (Logue et al . ). Future studies on Wb should include data on vector species composition that could be tested for a correlation with genetic diversity of Wb infections, specifically the COI.…”

“…If A. punctulatus were to replace A. farauti, then transmission of Wb may be reduced. Logue et al (2015) used PSMC to reconstruct the demographic history of mosquito species from the Anopheles punctulatus group in PNG. They observed a divergent history for A. punctulatus and A. farauti no.4 approximate to the timing of human arrival in PNG.…”

“…Interestingly, a secondary peak population size in A. farauti no.4 corresponds with the observed peak population size in Wb, approximately 8000 years ago. Following the peak size, A. farauti no.4 experienced a dramatic bottleneck in contrast to A. punctulatus which has been increasing (Logue et al 2015). Future studies on Wb should include data on vector species composition that could be tested for a correlation with genetic diversity of Wb infections, specifically the COI.…”