Additional file 1: Table S1. of Hidden diversity of Nycteribiidae (Diptera) bat flies from the Malagasy region and insights on host-parasite interactions

Nycteribiidae specimens and sequences used in this study, including isolates, GenBank accession numbers, host, and origin. Molecular data produced in the frame of the present work are marked with an asterisk (*). Abbreviations: FMNH, Field Museum of Natural History; KU, University of Kansas Natural History Museum; UADBA, Université d’Antananarivo, Département de Biologie Animale; NA, not available. (DOC 108 kb

Representative genera of nycteribiid bat flies from Madagascar.

<p>A) <i>Penicillidia leptothrinax</i>, adult female, dorsal habitus, from <i>Miniopterus manavi</i>; B) <i>Nycteribia stylidiopsis</i>, adult female, dorsal habitus, from <i>M</i>. <i>gleni</i>; C) <i>Eucampsipoda madagascarensis</i>, adult female, dorsal habitus, from <i>Rousettus madagascariensis</i>.</p

Evolutionary History of Indian Ocean Nycteribiid Bat Flies Mirroring the Ecology of Their Hosts

<div><p>Bats and their parasites are increasingly investigated for their role in maintenance and transmission of potentially emerging pathogens. The islands of the western Indian Ocean hold nearly 50 bat species, mostly endemic and taxonomically well studied. However, investigation of associated viral, bacterial, and external parasites has lagged behind. In the case of their ectoparasites, more detailed information should provide insights into the evolutionary history of their hosts, as well as pathogen cycles in these wild animals. Here we investigate species of Nycteribiidae, a family of obligate hematophagous wingless flies parasitizing bats. Using morphological and molecular approaches, we describe fly species diversity sampled on Madagascar and the Comoros for two cave-roosting bat genera with contrasting ecologies: <i>Miniopterus</i> and <i>Rousettus</i>. Within the sampling area, 11 endemic species of insect-feeding <i>Miniopterus</i> occur, two of which are common to Madagascar and Comoros, while fruit-consuming <i>Rousettus</i> are represented by one species endemic to each of these zones. Morphological and molecular characterization of flies reveals that nycteribiids associated with <i>Miniopterus</i> bats comprise three species largely shared by most host species. Flies of <i>M</i>. <i>griveaudi</i>, one of the two bats found on Madagascar and certain islands in the Comoros, belong to the same taxon, which accords with continued over-water population exchange of this bat species and the lack of inter-island genetic structuring. Flies parasitizing <i>Rousettus</i> belong to two distinct species, each associated with a single host species, again in accordance with the distribution of each endemic bat species.</p></div

Phylogenetic tree based on mitochondrial sequences (COI).

<p>Nycteribiid flies were sampled from bats collected in Madagascar (<i>Miniopterus aelleni</i>, <i>M</i>. <i>gleni</i>, <i>M</i>. <i>griveaudi</i>, <i>M</i>. <i>mahafaliensis</i>, <i>M</i>. <i>majori</i>, <i>M</i>. <i>manavi</i>, <i>M</i>. <i>petersoni</i>, and <i>M</i>. <i>sororculus</i>) and Comoros (<i>Rousettus obliviosus</i> and <i>M</i>. <i>griveaudi</i>). The analysis was carried out using Bayesian Inference under the GTR+I+G substitution model, and nodal support values reflect Bayesian Probabilities. (*) indicates <i>M</i>. <i>griveaudi</i> sampled on Madagascar and Comoros.</p

Nycteribiidae species identified from different bat species of the genera <i>Rousettus</i> and <i>Miniopterus</i> on Madagascar and the *Comoros archipelago and belonging to the genera <i>Eucampsipoda</i>, <i>Nycteribia</i>, and <i>Penicillidia</i>.

<p>+/−: presence/absence of a given parasite on the bat species.</p

Known cave roosting associations of bat species of the genera <i>Rousettus</i> and <i>Miniopterus</i> (this study).

<p>Data from field inventories of species assemblages documented at different sites on Madagascar and the *Comoros archipelago. Names presented in brackets are inferred sympatric occurrences based on capture at a site in close proximity.</p

Gomard_et_al_secY_adk_rrs2_Leptospira_alignments

Sequences (secY, adk and rrs2) of Leptospira from Malagasy bats

Database Malagasy bats

Description of bats collected in Madagasca

Bayesian phylogenetic tree of pathogenic <i>Leptospira</i> species from Mayotte (blue) and Madagascar (green) based on concatenated sequences of five genes (<i>secY</i>, <i>adk</i>, <i>lipL32</i>, <i>lipL41</i> and <i>rrs2</i>, total size: 2215 bp).

<p>The analysis was realized under the GTR+G substitution model. At the nodes, grey and white circles indicate posterior probabilities superior to 0.70 and 0.90, respectively. Strain numbers of cultures produced herein are indicated in parentheses, “K” and “U” designating the sequences obtained from kidney or urine, respectively. Stars indicate lineages common to humans and animals (<i>Rattus rattus</i> or <i>Tenrec ecaudatus</i>). For <i>Homo sapiens</i> str. 200901122, the same sequence type was found in nine cultures from <i>T</i>. <i>ecaudatus</i> (2014TE MDI222, 2014TE MDI224, 2014TE MDI294U, 2014TE MDI295, 2014TE MDI295U, 2014TE MDI306, 2014TE MD308, 2014TE MDI321 and 2014TE MDI321U). For <i>H</i>. <i>sapiens</i> str. 200701204, 200900806, 200901483 and 201003760, the same sequence type found was in seven cultures from <i>R</i>. <i>rattus</i> (2014RR MDI247, 2014RR MDI250, 2014RR MDI251, 2014RR MDI259, 2014RR MDI260, 2014RR MDI284 and 2014RR MDI291). Specimen system: MDI = CRVOI specimen catalogue during field trips to Mayotte; FMNH = Field Museum of Natural History, Chicago; UADBA = Université d’Antananarivo, Département de Biologie Animale, Madagascar; for the other bacterial sequences from <i>H</i>. <i>sapiens</i> and <i>Microgale</i> spp. see Bourhy <i>et al</i>. 2012 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004933#pntd.0004933.ref015" target="_blank">15</a>] and Dietrich <i>et al</i>. 2014 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004933#pntd.0004933.ref004" target="_blank">4</a>]. Museum numbers for <i>Microgale</i> spp.: 575 = UADBA 30869; 588 = UADBA 30289; 590 = UADBA 30291; 1335 = UADBA 32122; 1453 = UADBA 32125; 1467 = UADBA 32101.</p

Animals from the wild and domestic fauna of Mayotte tested for carriage of <i>Leptospira</i> spp. by real-time PCR, culture, and genotyping.

<p>Animals from the wild and domestic fauna of Mayotte tested for carriage of <i>Leptospira</i> spp. by real-time PCR, culture, and genotyping.</p