INAUGURAL ARTICLE by a Recently Elected Academy Member:Radiation with reticulation marks the origin of a major malaria vector

Advances in genomics have led to an appreciation that introgression is common, but its evolutionary consequences are poorly understood. In recent species radiations the sharing of genetic variation across porous species boundaries can facilitate adaptation to new environments and generate novel phenotypes, which may contribute to further diversification. Most Anopheles mosquito species that are of major importance as human malaria vectors have evolved within recent and rapid radiations of largely nonvector species. Here, we focus on one of the most medically important yet understudied anopheline radiations, the Afrotropical Anopheles funestus complex (AFC), to investigate the role of introgression in its diversification and the possible link between introgression and vector potential. The AFC comprises at least seven morphologically similar species, yet only An. funestus sensu stricto is a highly efficient malaria vector with a pan-African distribution. Based on de novo genome assemblies and additional whole-genome resequencing, we use phylogenomic and population genomic analyses to establish species relationships. We show that extensive interspecific gene flow involving multiple species pairs has shaped the evolutionary history of the AFC since its diversification. The most recent introgression event involved a massive and asymmetrical movement of genes from a distantly related AFC lineage into An. funestus, an event that predated and plausibly facilitated its subsequent dramatic geographic range expansion across most of tropical Africa. We propose that introgression may be a common mechanism facilitating adaptation to new environments and enhancing vectorial capacity in Anopheles mosquitoes.

Once considered a rare anthropogenic aberration in animals, interspecific hybridization is now recognized to be both taxonomically widespread and pervasive, particularly in rapidly diversifying groups (1–3). Moreover, mounting genome-scale evidence suggests that introgression, the genetic exchange between species through hybridization and backcrossing, is also prevalent and may be consequential for evolution. Examples from fish, birds, mammals, and insects—including Anopheles mosquitoes—have shown that introgressed variation favored by natural selection can facilitate adaptation, enhance fitness, and drive evolutionary innovation and diversification (4–7). It has been postulated that introgressive hybridization is most prevalent in species-rich and rapidly diversifying radiations (2, 3, 8). Introgression in these groups may solely be opportunistic, given the multiplicity of young species in geographic proximity, but the process may also favor adaptive radiation through the generation of completely novel phenotypes (6, 9, 10).There are three to four dozen Anopheles mosquito species that are of major importance as human malaria vectors, and all have evolved within recent and rapid radiations of morphologically cryptic species (informally classified as species complexes) (11, 12). Most members of these species complexes play no or very minor roles in disease transmission. The repeated de novo origin of major malaria vectors across these independent species radiations therefore holds clues about the nature of key evolutionary innovations that confer the ability to transmit disease widely and efficiently. However, most Anopheles species complexes are understudied. This is especially true of the secondary or nonvector species for which genomic resources are lacking, and basic knowledge of distribution, ecology, and behavior is scant.Until now, the single best-studied group has been the Anopheles gambiae complex, composed of at least eight morphologically indistinguishable species that diversified rapidly and recently, likely within the last half-million years (7, 13, 14). Phylogenomic analysis revealed widespread genealogical discordance (7). Some discordance was due to incomplete lineage sorting as a result of both rapid radiation and large effective population sizes (7), but the majority was caused by massive introgression between the main vector species, involving both the autosomes and the centromere-proximal region of the X chromosome. So extensive was its impact that the inferred species branching order was evident in only 2% of the genome—mostly on the distal portion of the X chromosome, which is protected from introgression by a succession of fixed chromosomal inversion differences.One of the most medically important of the understudied Anopheles species complexes is the Afrotropical Anopheles funestus complex (AFC). The AFC comprises at least seven morphologically similar species (15–18), yet only An. funestus sensu stricto (hereafter, An. funestus) is a highly efficient malaria vector, rivaled in importance solely by An. gambiae and its sister species Anopheles coluzzii in the An. gambiae complex (19–22). Comparative genomics of these two complexes may therefore be instructive with regard to malaria vectorial capacity. Both groups diversified in sub-Saharan Africa and may have experienced common geographic, ecoclimatic, and anthropogenic forces that shaped their history. In addition, the primary vector An. funestus broadly shares several characteristics with primary vectors in the An. gambiae complex: a geographic range that encompasses most of tropical Africa (Fig. 1A), high levels of chromosomal inversion polymorphism (23–25), large effective population size, and little population genetic structure across the continent (26, 27). Furthermore, the discovery of two very distantly related mitochondrial DNA (mtDNA) haplotypes (clades 1 and 2) segregating in An. funestus (27) raises the prospect of historical introgression analogous to that documented for An. gambiae, prompting an intriguing question: Can introgression be a source of evolutionary novelty leading to augmented vectoral capacity?Open in a separate windowFig. 1.Distribution and genetic variation in the AFC. Color coding of species is consistent across panels. (A) Location and distribution of sampled species, adapted from ref. 21. Approximate sample locations for An. funestus are indicated by a black star. For full sample information, see SI Appendix, Table S1. (B) Phylogeny of complete mtDNA genomes constructed using BEAST2 indicating divergent clades of An. funestus (red shading) and An. funestus-like (green shading) (see SI Appendix, Fig. S12 for phylogeny with outgroup). (C) Neighbor-joining phylogeny averaged over the complete nuclear genome. (D) Summary evolutionary history displaying three introgression events as inferred by the methods described in the main text. Introgression events shown as green horizontal arrows between pairs of species indicate the majority direction of introgression. Median divergence and introgression times are displayed in millions of years ago (Mya). See SI Appendix, Table S11 for details. An. funestus (Fun), An. funestus-like (Lik), An. longipalpis C (Lon), An. parensis (Par), and An. vaneedeni (Van), An. rivulorum (Riv).Here, we examine the role of introgression in the evolution of the AFC, using recent methods of phylogenetic network reconstruction that allow for divergence and reticulation to be inferred jointly. We use a combination of phylogenomic and population genomic analyses, based on de novo genome assemblies and additional whole genome resequencing, to: 1) establish species relationships, 2) determine the direction, extent, and genomic architecture of introgression across the complex, and 3) assess the role of introgression in the evolution of the primary vector An. funestus. We show that extensive interspecific gene flow involving multiple species pairs has shaped the evolutionary history of the AFC since its diversification ∼216 thousand years ago (Kya). The most recent introgression event ∼13 Kya involved a massive and asymmetrical movement of genes from a distantly related AFC lineage into An. funestus, an event that predated and plausibly facilitated its subsequent dramatic geographic range expansion across most of tropical Africa. We propose that introgression may be a common mechanism facilitating adaptation to new environments and enhancing vectorial capacity in Anopheles mosquitoes.