Evolution, systematics and historical biogeography of sand flies of the subgenus Paraphlebotomus (Diptera, Psychodidae, Phlebotomus) inferred using restriction-site associated DNA markers.

Jérôme Depaquit,Astrid Cruaud,Guenaëlle Genson,Remi N Charrel,Véronique Lehrter,Jean-Yves Rasplus

doi:10.1371/journal.pntd.0009479

Abstract

Phlebotomine sand flies are the main natural vectors of Leishmania, which cause visceral and tegumentary tropical diseases worldwide. However, their taxonomy and evolutionary history remain poorly studied. Indeed, as for many human disease vectors, their small size is a challenge for morphological and molecular works. Here, we successfully amplified unbiased copies of whole genome to sequence thousands of restriction-site associated DNA (RAD) markers from single specimens of phlebotomines. RAD markers were used to infer a fully resolved phylogeny of the subgenus Paraphlebotomus (11 species + 5 outgroups, 32 specimens). The subgenus was not recovered as monophyletic and we describe a new subgenus Artemievus subg. nov. Depaquit for Phlebotomus alexandri. We also confirm the validity of Ph. riouxi which is reinstated as valid species. Our analyses suggest that Paraphlebotomus sensu nov. originated ca 12.9-8.5 Ma and was possibly largely distributed from peri-Mediterranean to Irano-Turanian regions. Its biogeographical history can be summarized into three phases: i) a first split between Ph. riouxi + Ph. chabaudi and other species that may have resulted from the rise of the Saharan belt ca 8.5 Ma; ii) a Messinian vicariant event (7.3-5.3 Ma) during which the prolonged drought could have resulted in the divergence of main lineages; iii) a recent radiation event (3-2 Ma) that correspond to cycles of wet and dry periods in the Middle East and the East African subregions during the Pleistocene. Interestingly these cycles are also hypothetical drivers of the diversification of rodents, in the burrows of which Paraphlebotomus larvae develop. By meeting the challenge of sequencing pangenomics markers from single, minute phlebotomines, this work opens new avenues for improving our understanding of the epidemiology of leishmaniases and possibly other human diseases transmitted by arthropod vectors.

Highlights

Phlebotomine sand flies (Diptera, Psychodidae) are the main natural vectors of Leishmania, a genus of protozoan parasites which cause visceral and tegumentary neglected tropical diseases worldwide
In the Old World, the subgenus Paraphlebotomus includes the main vectors of Leishmania tropica, the agent of a cutaneous leishmaniasis mostly in North Africa visceral and the Middle West
We fully resolved the phylogeny of the subgenus Paraphlebotomus who was not recovered as monophyletic, meaning it does not include all the ascendants of last common ancestor

Summary

Introduction

Phlebotomine sand flies (Diptera, Psychodidae) are the main natural vectors of Leishmania, a genus of protozoan parasites which cause visceral and tegumentary neglected tropical diseases worldwide. Of the approximately 1,000 species of sand flies, about 70 are vectors of Leishmania [1,2]. Leishmaniases are endemic in nearly 100 countries, mainly in Africa, Asia and Latin America [3]. The estimated annual incidence of cutaneous leishmaniases in humans is 0.7 to 1 million cases and 50,000 to 90,000 cases of visceral leishmaniases were reported in 2017 [4]. Most leishmaniases are zoonotic diseases affecting wild or domestic animals. Canine leishmaniasis is for instance a serious veterinary problem in many countries [14]

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