News from the other side (of Africa) Evolution of rodent hosts and their parasites in Eastern Africa Josef Bryja and many others Institute of Vertebrate Biology, Czech Academy of Sciences, Brno Institute of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic How it started ... (Czech „rodentologue“ activities in Africa) 2004 2004 Dakar Niokolo Koba National Park – biodiversity survey Sudanian savanna Guinean forest „Black rat survey“ 2006 Dakar „first phylogeography papers“ 2008 65 Niger river Senegal river 70 18 Clade D 66 62 58 Clade C1 37 12 28 64 SENEGAL 7 25 22 13 63 9 52 17 32 15 NIGER 51 41 20 48 10 59 60 MALI 27 23 40 46 34 38 19 50 47 835 44 43 29 30 26 31 21 54 81 39 45 33 14 57 BURKINA 149 16 82 42 11 24 36 69 56 FASO 55 83 6 GUINEA 61 NIGERIA 91 2 5 68 86 3 67 53 76 Clade B 71 GHANA 87 4 72 75 IVORY 77 88 73 COAST Volta river 84 85 78 79 Clade A 80 CAMEROON 89 74 90 BENIN TOGO Jump to the „other side“ ... 2010 2015 September 2015 – 8336 rodents and shrews ... ... comparative phylogeography, evolution of viruses, taxonomic implications, etc. ... again influenced by „Montpellier“ people Evolution of rodents and their parasites in open habitats of East Africa Czech Science Foundation 2015‐2017 Project no. 15‐20229S Mastomys natalensis sharp contact zone of two genetic lineages, no obvious geographical barrier Acomys spinossisimus group Heliophobius mole‐rats Aethomys chrysophilus Aethomys kaiseri Mus minutoides Lemniscomys zebra/rosalia Same geographic pattern, different divergence times 2.5‐3 Mya 0.5‐1 Mya (1) How long‐term evolution of forest‐savanna mosaic has shaped diversity of small mammals? • detailed sampling in main biogeographical zones in Tanzania (+ other available data) – spatial distribution of genetic lineages • ecological niche modelling – identification of environmental variables • comparative (community) phylogeography – dating of divergence, hypothesis testing, etc. (2) How genetically divergent rodents evolve on the contact zones? S. Baird • detailed sampling across the contact zone(s) • analysis of introgression in M. natalensis – genomic and morphometric approaches • development of nuclear SNP markers by using commercial mouse chips Many similarities with house mouse hybrid zone t B MAL G G er assignmen t G BUF G G NIR G GGG G GG G GGGG XY G SOM GGXYGGGGGG CDI GHA GG XYGGGGGGGGGG XY GGGGGXYGGGGG G ETH e clus XYGG GGG G G GG SSD t GXYG GG G GG G G CAR XY G elli CAM t KEN CNG DRC G Human Lassa fever cases GAB G 6" 6" Mastomys natalensis range 6" XYXY TANZANIA M. natalensis mt-lineage: 6" Average microsa ANG Shinyanga Mbulu / ZAM A-I B-IV MOZ A-II B-V XYXY 6" 6" A-III B-VI XY XY Itigi NAM XY Arenavirus detected in M. natalensis: ZIM 6" BOT XY Landscape resistancebetween Landscape neightbouring localities ype frequency frequency ype LASV MOPV t GAIV LUNV SOU 0 1020304050 Geno Lihale 0.0 0.2 0.4 0.6 0.8 1.0 MORV 6" 0 11 35 46 67 87 102 116 135 147 162 180 Widescale localities A B C D E F G H I J K L A B C D E F G H I G K L One-Dimensional Distance (km) Proportion M. natalensis Cline center Cline width mt-lineage B-I V / B-V T A 38.7 25.1 Host SMCY haplotype (35.2-42.6) (14.8-41.8) B-V B-IV Chakwale Legend 37.1 22.54 Majawanga Host cytochrome b lineage (35.2-39.5) (10.8-37.0) Berega Agriculture B C1 C2 A 36.5 21.4 M aguha Natural vegetation C umila Host microsatellite cluster assignment (36.3-36.7) (19.3-23.4) Natural aquatic vegetation Dumila Dakawa D M kundiUrban MORV GAIV Dakawa Uben 38.0 6.4 Water body Arenavirus (32.0-64.0) (1.0-55.0) E M ikese C F M kundi J Bwawani Ubena L Chalinze G Mikese K M or ogor o I H microsatellites, Y‐chromosom, mtDNA GAIV MORV-IV MORV-II MORV-III MORV-I 06030 Km Transect localities Gryseels et al., submitted Species delimitations (analyses of reproductive barriers, taxonomic revisions) (3) Evolution of parasites in the contact zone of differentiated hosts? • arenaviruses • Pneumocystis J. Goüy de Bellocq Arenavirus phylogeography (sisters to Lassa virus –non pathogenic to human) Mobala4_Stenocephalemys.albipes_Ethiopia Mobala1_Praomys.sp_Central.Africa.Republic Mobala3_Mastomys.awashensis_Ethiopia 1 Mobala2_Mastomys.awashensis_Ethiopia Mbulu_MBL3020 1Mbulu_MBL2091 A_Maj_27423 virus contact zone A_Maj_MW12 Gairo virus 0.68 A_Maj_MW6 A_Maj_MW5 A_Maj_27430 1 A_Maj_27425 A_Maj_MW19 GAIV S1 1 A_Maj_MW18 A_Maj_27431 1 A_Maj_27429 Gairo A_Maj_27428 A_Maj_27421 Virus A_Maj_27380 GAIV S2 B A_Maj_27402 Morogoro virus A_Maj_27371 A A_Maj_27367 C_Ber_27457 GAIV S3 C 1 C_Ber_TA1192 C_Ber_27306 C_Ber_25189 A_Maj_27370 D B_Chk_27317 GAIV S4 C_Ber_25161 LunaLSK_Mastomys.natalensis_Zambia E 1 LunaNMW_Mastomys.natalensis_Zambia C_Ber_TA62 F E_Dum_23382 F_Dak_23235 MORV S1 E_Dum_E9 L 1 E_Dum_23310 E_Dum_E10 G J Morogoro_Mastomys.natalensis_Tanzania H_Mor_24548 K H_Mor_24557 H_Mor_24174 H_Mor_M1_17 I H_Mor_23087 1 H_Mor_23120 MORV S2 H_Mor_23124 H H_Mor_24167 I_Mik_24760 Legend 1 G_Mku_23211 Morogoro I_Mik_24742 L_Chal_24598 Virus 1 L_Chal_Cha26 MORV S3 J_Bwa_24888 J_Bwa_25017 1 J_Bwa_24981 K_Ube_24831 MORV S4 K_Ube_24838 K_Ube_24835 Mopeia1_Mastomys.natalensis_Mozambique 1 Mopeia2_Mastomys.natalensis_Mozambique Gbagroube_Mus.setulosus_Cote.d.Ivoire Lassa_Mastomys.natalensis_Guinea ons/site Gryseels et al., submitted Pneumocystis • subspecies‐specific lineages in HMHZ – is this general pattern? • which parts of Pneumocystis genome introgress better than others; is the pattern concordant in different hosts • exome sequencing of Pneumocystis in both Mus musculus and Mastomys natalensis hybrid zones – bait design and NGS Few additional news from Eastern Africa (if there is still time ...) Myomyscus • gather typical Praomys‐like rodents (partly arboricolous), which are not true „Praomys“ • currently four species: • M. verreauxi – South Africa („type species“) • M. brockmani (= Myomys fumatus) –East Africa • M. yemeni – Yemen, Saudi Arabia • M. angolensis –Angola (no genetic data) • formerly also Praomys daltoni/derooi or Stenocephalemys albipes –bothas Myomys 99 Mastomys M. yemeni 5 99 Mastomys kollmanspergeri 99 Stenocephalemys 5 99 Myomyscus brockmani_South 20 0 99 Myomyscus brockmani_North1 99 MYOMYSCUS BROCKMANI 99 Myomyscus brockmani_North2a 96 85 Myomyscus brockmani_North2b 99 1667 Inegawa forestETH. 1140 nucleotides. 0 99 4 Praomys delectorum M. sp. n. 16 Hylomyscus deniae 91 99 New genus (?) Myomyscus yemeni 70 ETH1019. 1132 nucleotides. 99 ETH1021. 1132 nucleotides. 27 ETH1022. 1132 nucleotides. MYOMYSCUS YEMENI GROUP 0 99 ET205 Mymyscus Harar 99 Myomyscus sp.n. ETH ET204 Mymyscus Harar 69 MET2599Myomyscus AlamataET 99 MET2631Myomyscus AlamataET 46 MET2627Myomyscus AlamataET 2 Hylomyscus M. brockmani 7 24 ‐ phylogeography 0 Praomys daltoni group 88 Praomys tullbergi group 3 similar to 25 Praomys jacksoni group 88 Gerbilliscus 3 99 Praomys lukolelae group 84 Colom goslAF518372 15 Zelotom hildegAF518375 25 MYOMYSCUS VERREAUXI - Cape Region 99 gi|70948312|gb|DQ022380.1| Malacomys longipes voucher MNHN 2001-070 cytochrome b (cytb) gene partial cds mitochondrial 23 V01556 Rattus norvegicus gi|5732716|gb|AF159394.1| Apodemus mystacinus cytochrome b gene partial cds mitochondrial gene for mitochondrial product KE539. 1140 nucleotides. 34 Hylomyscus baeri (GenBank) 99 0.02 All East African Myomyscus should have different genus name Mastomys • probably the most important rodent genus for human in Africa (abundant, agricultural pest, diseases) • while intensively studied in some parts of Africa (e.g. western Africa or Tanzania), in other regions even basic data (i.e. distribution of species) are missing • 1671 Mastomys collected in Eastern Africa in last six years Mastomys in Eastern Africa H. Leirs Acknowledgements S. Baird S. Gryseels E. Verheyen R. Makundi Y. Meheretu V. Nicolas A. Konečný J. Goüy de Bellocq M. McDonough J. Těšíková T. Aghová R. Šumbera and V. Mazoch Supported by the Czech Science Foundation J. Mbau O. Mikula and many others ....