First genomic study on Lake Tanganyika sprat Stolothrissa tanganicae: a lack of population structure calls for integrated management of this important fisheries target species

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Authors	DE KEYZER Els L. R. DE CORTE Zoe VAN STEENBERGE Maarten RAEYMAEKERS J A Joost A. M. CALBOLI F C Federico C. F. KMENTOVÁ Nikol MULIMBWA Theophile N'Sibula VIRGILIO Massimiliano VANGESTEL Carl MASILYA MULUNGULA Pascal Masilya VOLCKAERT F A Filip A. M. VANHOVE Maarten Pieterjan
Year of publication	2019
Type	Article in Periodical
Magazine / Source	BMC Evolutionary Biology
MU Faculty or unit	Faculty of Science
Citation
Web	Full Text
Doi	http://dx.doi.org/10.1186/s12862-018-1325-8
Keywords	Clupeidae; population genomics; management
Description	Clupeid fisheries in Lake Tanganyika (East Africa) provide food for millions of people in one of the world’s poorest regions. Due to climate change and overfishing, the clupeid stocks of Lake Tanganyika are declining. We investigate the population structure of the Lake Tanganyika sprat Stolothrissa tanganicae, using for the first time a genomic approach on this species. This is an important step towards knowing if the species should be managed separately or as a single stock. Population structure is important for fisheries management, yet understudied for many African freshwater species. We hypothesize that distinct stocks of S. tanganicae could be present due to the large size of the lake (isolation by distance), limnological variation (adaptive evolution), or past separation of the lake (historical subdivision). On the other hand, high mobility of the species and lack of obvious migration barriers might have resulted in a homogenous population. We performed a population genetic study on wild-caught S. tanganicae through a combination of mitochondrial genotyping (96 individuals) and RAD sequencing (83 individuals). Samples were collected at five locations along a northsouth axis of Lake Tanganyika. The mtDNA data had low global FST and, visualised in a haplotype network, did not show phylogeographic structure. RAD sequencing yielded a panel of 3504 SNPs, with low genetic differentiation (FST = 0.0054; 95% CI: 0.0046–0.0066). PCoA, fineRADstructure and global FST suggest a near-panmictic population. Two distinct groups are apparent in these analyses (FST = 0.1338 95% CI: 0.1239,0.1445), which do not correspond to sampling locations. Autocorrelation analysis showed a slight increase in genetic difference with increasing distance. No outlier loci were detected in the RADseq data.
Related projects:	ECIP - Evropské centrum ichtyoparazitologie