DOI: 10.5061/dryad.f1vhhmgt4
title: Summary of the microsatellite genotyping analysis of 280 C. gariepinus samples originating from eight locations in the Congo basin using five microsatellite markers

description: Aim The formation history of Africa’s current river basins remains largely
 unknown. In order to date changes in landscape and climate, we studied the
 biogeography of the African freshwater fish with the largest natural
 distribution. We also validated biogeographic units. Location Continental
 Africa. Taxon Clarias gariepinus sl. Methods We investigated mitochondrial
 cytb sequences of 443 individuals from 97 localities, using a haplotype
 network and a genetic landscape analysis. We inferred a dated phylogeny
 using maximum likelihood and Bayesian inference approaches and
 reconstructed ancestral areas with S-DEC and S-DIVA models. Microsatellite
 genotyping complemented the mitochondrial approach in the Congo basin,
 where the latter revealed complex patterns. Results Limited
 differentiation is found in northern and south-western Africa, and sharp
 genetic differentiation in the continent’s East and Centre. Populations
 with affinities to neighbouring basins occur at the edges of the Congo
 province. High diversity exists in the South of the Congo basin. The
 Zambezi province is partitioned into eastern, central and western sectors.
 In the East, specimens were related to those from the Congo. In the West,
 they were similar to Southern representatives. Phylogenetic inference
 placed the origin of C. gariepinus in the East Coast, with intraspecific
 diversification starting around the Great Lakes. These events occurred ca.
 4.8-1.65 and 2.3-0.8 MYA, respectively. Main conclusions Clades of C.
 gariepinus sl. show a clear geographic signature. The origin of C.
 gariepinus in the East Coast and diversification around the Great Lakes
 coincided with periods of increased aridity. Low genetic differentiation
 in northern and southern Africa may result from connectivity during recent
 periods of higher rainfall. In contrast to other widespread African
 freshwater fishes, colonisation rather than extinction seemed to mediate
 distribution patterns. This can be explained by a high ecological
 tolerance. We highlight the species’ suitability to study landscape and
 climate evolution at various scales.
description: We genotyped 280 adult <i>C. gariepinus</i> from
 eight sites at seven loci, <i>Cga01</i>,<i>
 Cga02</i>,<i> Cga05</i>,<i>
 Cga09</i>,<i> Cga11 </i>(Galbusera, Volckaert,
 Hellemans, & Ollevier<i>, </i>1996), <i>Cba
 19</i> and <i>Cba 20</i> (Yue, Kovacs, & Orban,
 2003). We amplified all loci using the QIAGEN Multiplex PCR kit (QIAGEN,
 Venlo, the Netherlands) in two multiplex and one singleplex
 reaction. Multiplex 1: <i>Cba 19</i> and
 <i>Cba 20</i>; Annealing temp 58-52 °C (TD) and 52°C ; Number
 of cycles: 7 (TD) and 28; Primer concentrations: 0.05 µm (both)
 Multiplex 2: <i>Cga 01, Cga 05, Cga 09 and Cga
 11</i> ; Annealing temp 54°C ; Number of cycles: 25; Primer
 concentrations: 0.1 µm (<i>Cga 01</i>), 0.05 µm
 (others) Singleplex: <i>Cga
 02</i>; Annealing temp 54°C ; Number of cycles: 25; Primer
 concentration: 0.2 µm We ran multiplex PCR products
 with an internal size standard (500LIZ, Applied Biosystems), on an ABI
 3130 automated capillary DNA sequencer (Applied Biosystems, Foster City,
 USA). We conducted fragment analysis in GENEMAPPER v4.0 (Applied
 Biosystems) and checked for the potential occurrence of null alleles and
 scoring errors, with MICRO-CHECKER v2.2.3 and DROPOUT v2.0. Scoring errors
 were detected at loci <i>Cga09</i> and
 <i>Cba19</i>, which were excluded from further analyses. We
 ran 10-30% of the samples twice for all markers to verify
 reproducibility.  
description: codes: KIN; Kinshasa; Lower Congo; -04°18’N;
 15°20’E KIS; Kisangani; Middle Congo; 00°31’N;
 25°11’E DBL; Bukama; Upper Congo; -09°11’N;
 25°51’E KAD; Dianda; Kando, Lulua; -10°45’N;
 25°50’E LUF; Kapolowe; Upper Lufira; -11°21’N;
 26°46’E KYU; Kyubo; Middle Lufira; -09°31’N;
 27°02’ KAF; Lubumbasi; Kafubu, Luapula; -11°42’N;
 27°29’E LUT; Mwaba; Lutshipuka, Luapula; -10°14’N;
 28°20’E