Plasmodium falciparum, the most virulent agent of human malaria, shares a recent 25 common ancestor with the gorilla parasite P. praefalciparum. Little is known about the other gorilla 26 and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum but none of 27 them are capable of establishing repeated infection and transmission in humans. To elucidate 28 underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple 29 genomes from all known Laverania species. The completeness of our dataset allows us to conclude 30 that interspecific gene transfers as well as convergent evolution were important in the evolution of 31 these species. Striking copy number and structural variations were observed within gene families 32 and one, stevor shows a host specific sequence pattern. The complete genome sequence of the 33 closest ancestor of P. falciparum enables us to estimate confidently for the first time the timing of 34 the beginning of speciation to be 40,000-60,000 years ago followed by a population bottleneck 35 around 4,000-6,000 years ago. Our data allow us also to search in detail for the features of P. 36 falciparum that made it the only member of the Laverania able to infect and spread in humans. 37 39Main Text: 40The evolutionary history of Plasmodium falciparum, the most common and deadliest human 41 malaria parasite, has been the subject of uncertainty and debate 1,2 . Recently it has become clear that 42 P. falciparum is derived from a group of parasites infecting African Great Apes and known as the 43Laverania subgenus 2 . Until 2009, the only other species known in this subgenus was a parasite of 44 chimpanzees known as P. reichenowi, for which only one isolate was available 3 . It is now clear that 45 there are a total of at least seven species in Great Apes that naturally infect chimpanzees (P. gaboni, 46 P. billcollinsi and P. reichenowi), gorillas (P. praefalciparum, P. blacklocki and P. adleri) 4,5 , or 47 humans (P. falciparum) ( Fig. 1a). Within this group, P. falciparum is the only parasite that has 48 successfully adapted to humans after a transfer from gorillas and subsequently spread all over the 49 world 2 . 50Over time there have been various estimates concerning the evolutionary history of P. 51 falciparum with the speciation event having been estimated to be anywhere between 10,000 to 5.5 52 million years ago, the latter falsely based on the date of the chimpanzee-human split 6,7 . Others 53 report a bottleneck less than 10,000 years ago 8 , but suggest a drop to a single progenitor parasite. 54The latter seems unlikely due to the presence of allelic dimorphisms that predate speciation events 55 and therefore could not have both been transmitted if a new species were founded by a single 56 individual infection. Also, the dating of the speciation cannot be accurately estimated without the 57 genome sequence of P. praefalciparum, the closest living sister species to P. falciparum. 58The absence of in vitro culture or a usable animal mode...

Plasmodium vivax is responsible of the majority of malaria infections outside Africa. Its closer genetic relative, Plasmodium vivax--like, was discovered in African great apes and suggested to have given rise to P. vivax in humans. We generated two newly P.vivax--like reference genomes and 9 additional P. vivax--like genotypes, to unravel the evolutionary history of P. vivax. We showed a clear separation between the two clades, a higher genetic diversity of P. vivax--like parasites in comparison to the P. vivax ones, and the potential existence of two sub--clades of P. vivax--like. We dated the relative split between P. vivax and P. vivax--like as three times shorter than the split between P. ovale wallikeri and P. ovale curtesi and 1.5 times longer than the split between Plasmodium malariae. The sequencing of the P. vivax--like genomes is an undeniable advance in the understanding of P. vivax biology, evolution and emergence in human populations. not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. Significance statementsThe copyright holder for this preprint (which was . http://dx.doi.org/10.1101/205302 doi: bioRxiv preprint first posted online 3 Main text.Plasmodium vivax, the most prevalent human malaria parasite outside Africa, is responsible for severe and incapacitating clinical symptoms in humans 1 . Traditionally, P. vivax has been neglected because of its lower mortality in comparison to Plasmodium falciparum 2,3 . Its ability to produce a dormant liver--stage form (hypnozoite), responsible of relapsing infections, makes it a challenging public health issue for malaria elimination.The recent emergence of antimalarial drug resistance 4 as well as the discovery of severe and even fatal human cases 2,5,6 has renewed the interest for this enigmatic species, including its evolutionary history and its origin in humans.Earlier studies placed the origin of P. vivax in humans in Southeast Asia ("Out of Asia" hypothesis) based on its phylogenetic position in a clade of parasites infecting Asian monkeys 7 . At that time, the closest known relative of P. vivax was considered to be Plasmodium cynomolgi, an Asian monkey parasite 8 . However, this hypothesis was recently challenged with the discovery of another Plasmodium species, genetically closer to P. vivax than P. cynomolgi, circulating in African great apes (chimpanzees and gorillas) 9,10 . This new lineage (hereafter named Plasmodium vivax--like) was considered by certain authors to have given rise to P. vivax in humans following a transfer of parasites from African apes 10 , but this "Out of Africa" hypothesis still remains debated.Moreover, a transfer of P. vivax--like parasites has been documented, thus making possible the release of new strains in new hosts species, specifically in human populations 9 . In such a context, it now seems fundamental to characterize the genome of the closest ape--relative to the human P. vivax parasite in order to get a better understanding of the evolution of this para...

Plasmodium falciparum, the most virulent agent of human malaria, spread from Africa to all continents following the out-of-Africa human migrations. During the transatlantic slave trade between the 16th and 19th centuries, it was introduced twice independently to the Americas where it adapted to new environmental conditions (new human populations and mosquito species). Here, we analyzed the genome-wide polymorphisms of 2,635 isolates across the current P. falciparum distribution range in Africa, Asia, Oceania, and the Americas to investigate its genetic structure, invasion history, and selective pressures associated with its adaptation to the American environment. We confirmed that American populations originated from Africa with at least two independent introductions that led to two genetically distinct clusters, one in the North (Haiti and Colombia) and one in the South (French Guiana and Brazil), and the admixed Peruvian group. Genome scans revealed recent and more ancient signals of positive selection in the American populations. Particularly, we detected positive selection signals in genes involved in interactions with hosts (human and mosquito) cells and in genes involved in resistance to malaria drugs in both clusters. We found that some genes were under selection in both clusters. Analyses suggested that for five genes, adaptive introgression between clusters or selection on standing variation was at the origin of this repeated evolution. This study provides new genetic evidence on P. falciparum colonization history and on its local adaptation in the Americas.

Many emerging infectious diseases originate from wild animals, so there is a profound need for surveillance and monitoring of their pathogens. However, the practical difficulty of sample acquisition from wild animals tends to limit the feasibility and effectiveness of such surveys. Xenosurveillance, using blood‐feeding invertebrates to obtain tissue samples from wild animals and then detect their pathogens, is a promising method to do so. Here, we describe the use of tsetse fly blood meals to determine (directly through molecular diagnostic and indirectly through serology), the diversity of circulating blood‐borne pathogens (including bacteria, viruses and protozoa) in a natural mammalian community of Tanzania. Molecular analyses of captured tsetse flies (182 pools of flies totalizing 1728 flies) revealed that the blood meals obtained came from 18 different vertebrate species including 16 non‐human mammals, representing approximately 25% of the large mammal species present in the study area. Molecular diagnostic demonstrated the presence of different protozoa parasites and bacteria of medical and/or veterinary interest. None of the six virus species searched for by molecular methods were detected but an ELISA test detected antibodies against African swine fever virus among warthogs, indicating that the virus had been circulating in the area. Sampling of blood‐feeding insects represents an efficient and practical approach to tracking a diversity of pathogens from multiple mammalian species, directly through molecular diagnostic or indirectly through serology, which could readily expand and enhance our understanding of the ecology and evolution of infectious agents and their interactions with their hosts in wild animal communities.