Ancient origin of an urban underground mosquito

Abstract

Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. Here we investigate a widely cited example of urban adaptation, Culex pipiens form molestus, also known as the London Underground Mosquito. Population genomic analysis of ~350 contemporary and historical samples counter the popular hypothesis that molestus originated belowground in London less than 200 years ago. Instead, we show that molestus first adapted to human environments aboveground in the Middle East over the course of >1000 years, likely in concert with the rise of agricultural civilizations. Our results highlight the role of early human society in priming taxa for contemporary urban evolution and have important implications for understanding arbovirus transmission.

Figure 1.. Culex pipiens form molestus behavior, ecology, and hypothetical origin.

(A) Female Cx. pipiens complex mosquito. (B) Behavioral and physiological characteristics of Cx. pipiens forms in northern Eurasia. At warmer latitudes molestus can breed aboveground. (C) Example microhabitats: a city park (pipiens) and the flooded basement of an apartment complex (molestus). (D) Two hypotheses describing molestus’ origin. Hypothesis 1 (left) posits that belowground molestus evolved from local aboveground pipiens in situ within the past 100–200 years. Hypothesis 2 (right) posits that molestus first evolved in an aboveground context thousands of years ago, possibly in association with early agricultural societies of the Mediterranean basin, with colonization of belowground habitats (dotted arrow) occurring much later (22, 23). [Image credits: Lawrence Reeves (mosquito); Yuki Haba (city park); Colin Malcolm (flooded basement)]

Fig. 2.. Form molestus is genetically isolated from pipiens across the Western Palearctic.

(A) Sampled populations, colored by average PC1 value. Circles and triangles represent aboveground and belowground locations, respectively. Half-circles indicate that both pipiens and molestus were collected in the same or nearby aboveground sites. (B) PCA of genetic variation across all samples in (A) (n = 357). (C) PC1 values plotted against latitude, with marginal frequency histogram at top. The gray dashed line indicates a natural break in the histogram, inferred to separate pipiens and molestus (PC1 = 0.04). Thick outlines mark individuals from North Africa and the Middle East. Asterisk marks a putative F1 hybrid from southwest Russia (Stavropol). Inset shows position of historical London samples in a combined PCA with contemporary mosquitoes (n=22, collected 1940–1985; see also fig. S1). (D) PC1 values for pipiens and molestus individuals collected in the exact same day and trap (green lines) or in the same general location (within 5–45 km; grey lines).

Fig. 3.. Ancestral latitudinal gradient within pipiens suggests molestus arose at the southern edge of the Western Palearctic

(A) Hybridization gradient hypothesis: the genetic gradient within pipiens may result from increasing levels of gene flow with molestus as one moves from north to south. (B) Z scores of genome-wide f3 values for each pipiens population when modeled as a mixture of northern pipiens (Sweden) and northern molestus (Belgium). Significantly negative f3 values (Z < −3, green outlines) are consistent with the presence of admixture. (C) f3 statistics of pipiens populations with significant signs of admixture, plotted against latitude. (D) Ancestral gradient hypothesis: the genetic gradient within pipiens may be ancestral, with molestus evolving from southern pipiens populations. (E) Fraction of derived alleles shared by each pipiens population with northern pipiens versus northern molestus. Culex torrentium was used as the outgroup. Light brown in the map shows the Mediterranean climate zone. (F) Fraction of derived alleles shared with northern pipiens vs. molestus, plotted against latitude. Both (C) and (F) include linear regression line with 95% confidence interval and Pearson’s correlation test statistics. Across all analyses, only populations with four or more individuals were included.

Fig. 4.. Form molestus evolved thousands of years ago in the Middle East.

(A) molestus clade excerpted from neighbor-joining tree based on pairwise genetic distance (Dxy) among putatively unadmixed pipiens and molestus individuals from the global sample (32). Terminal branches are collapsed at the root of each population, with a symbol and number indicating microhabitat and sample size, respectively (32). Map inset shows distribution of two subgroups of molestus from the tree (orange/red) and pipiens (dark grey). Only molestus is present in Egypt, marked by an asterisk. Black circles mark nodes with >95% bootstrap support. See fig. S5 for the full tree. (B) Genome-wide nucleotide diversity (π) of populations shown in (A). (C) Relative cross-coalescence (rCC) rate between Moroccan pipiens (MAK) and Egyptian molestus (ADR) inferred from phased, whole genome sequences (32). rCC rate is expected to plateau at 1, going backwards in time, when populations have merged into a single ancestral population. Rapid divergence is observed between ~10K and 1K years ago, with a split time (T; rCC rate=50%) of 2,141 years (black dashed arrow) based on estimates of generation time and mutation rate (32). Biologically reasonable upper and lower bounds for these parameters give minimum and maximum split times of 1,298 and 12,468 years (grey arrowheads). Thick black line shows genome-wide result, and light grey lines show 100 bootstrap replicates. Illustration credits: Wheat, Freepik.com. Pharaoh and Glacier, Vecteezy.com.

Fig. 5.. Introgression from molestus into pipiens is associated with human density.

(A) Schematic of West Nile virus transmission dynamics. Form pipiens-molestus hybrids, which have intermediate biting preference (42), are implicated in the spillover of WNV from birds to humans (40, 41). (B) Base tree used to simultaneously estimate three potential sources of introgression into focal pipiens populations (X pip): northern pipiens (Sweden, SWE), Middle Eastern molestus (Egypt, ADR), and northern molestus (Belgium, BVR). (C–D) Population-specific estimates of ‘gene flow’ from northern pipiens (C), which accounts for the ancestral latitudinal gradient, and northern molestus (D). We did not detect gene flow into any population from Middle Eastern molestus (fig. S8). (E) Correlation between gene flow from northern molestus (D) and human population density within circles of varying radius around each collection site. (F) Gene flow from northern molestus as a function of human density within a 3-km radius of each collection site. Three outliers in grey (Cook’s distance > 4) were excluded, but regression remains significant if included (P = 0.005, R² = 0.18). [Image credit: Phylopic.com (bird and human)]

Fig. 6.. Inferred evolutionary history of molestus.

Three sequential panels show the inferred history of molestus. Left: The latitudinal genetic gradient characterizing extant pipiens populations in the Western Palearctic predates molestus. Middle: The rise of dense, settled, agricultural communities in the Middle East 2000–10,000 years ago, including along the Nile River in Egypt, would have provided new ecological opportunities for mosquitoes that could adapt to human hosts and habitats—driving the evolution of molestus. Right: Eventually molestus must have spread north, where it became established alongside pipiens in the warm Mediterranean region by the 1800s (but possibly earlier) and in belowground microhabitats of cold, northern cities by the early 1900s. Our distance tree (Fig. 4A) suggests that molestus was further spread (most likely by humans) overland all the way to East Asia and from the Mediterranean region overseas to America and Australia.