Population genomic analysis reveals cryptic population structure in the commercially important Lake Malawi cichlid Copadichromis mloto

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Fish is an important source of animal protein for many people living around Lake Malawi. The evaluation of population structure and genetic diversity can yield useful information for management and conservation of fish species but is complicated in Lake Malawi by the close genetic relatedness of species of the recent cichlid adaptive radiation. In this study, we analysed whole-genome sequencing data of “true utaka”, a group of cichlids previously common in fisheries, but that has faced strong decline due to overfishing. Our analysis of 223 individuals collected from fishermen’s catches along the western shoreline of Lake Malawi confirmed that Copadichromis mloto ( C. sp . “virginalis kajose”) is the true utaka most targeted by fisheries. Genetic principal component analysis, phylogenetic inference, and admixture analysis revealed complex patterns of population structure. The presence of at least three geographically widespread genetic clades that have remained separate despite gene flow and partial sympatry hints at the presence of currently undescribed, cryptic species diversity in C. mloto . This result leads us to suggest that, despite the lack of obvious habitat barriers, benthic and pelagic species of Malawi cichlids might harbour unidentified species diversity and calls for further genetic and taxonomic research to define appropriate conservation units.

Authors 9

1. Wilson Sawasawa

   University of Antwerp

   Affiliation as printed

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium;

2. Alexander Hooft van Huysduynen

   University of Antwerp

   Affiliation as printed

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium;

3. Sophie Gresham

   University of Antwerp

   Affiliation as printed

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium;

   Department of Fisheries, Monkey Bay Capture Fisheries Station (MFRS)

4. Harold Sungani

   University of Malawi · Malawi Government

   Affiliation as printed

   Department of Fisheries, Monkey Bay Capture Fisheries Station (MFRS), P.O. Box 27, Monkey Bay, Malawi

   Department of Fisheries, Monkey Bay Capture Fisheries Station (MFRS);

   Department of Biological Sciences, Chancellor College, University of Malawi, P.O. Box 280, Zomba, Malawi

5. Bosco Rusuwa

   University of Antwerp · University of Malawi

   Affiliation as printed

   Department of Biological Sciences, Chancellor College, University of Malawi, P.O. Box 280, Zomba, Malawi

   Department of Biological Sciences, Chancellor College, University of Malawi, P.O. Box 280, Zomba, Malawi;

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium,

6. Gudrun De Boeck

   University of Antwerp · Bangor University

   Affiliation as printed

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium,;

   Bangor University

7. George F. Turner

   Bangor University · Malawi Government

   Affiliation as printed

   Bangor University;

   School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK

   Department of Fisheries, Ministry of Natural Resources & Climate change, P.O. Box 593, Lilongwe, Malawi

8. Maxon J. Ngochera

   University of Antwerp · Malawi Government

   Affiliation as printed

   Department of Fisheries, Ministry of Natural Resources & Climate change, P.O. Box 593, Lilongwe, Malawi

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium

9. Hannes Svardal corresponding Aachen Naturalis Biodiversity Center

   Naturalis Biodiversity Center · University of Antwerp

   Affiliation as printed

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium

   Department of Biology, University of Antwerp, 2020 Antwerp, Belgium;

   Naturalis Biodiversity Center, 2333 Leiden, The Netherlands