The marbled crayfish (Procambarus virginalis) represents a very recently evolved parthenogenetic freshwater crayfish species that has invaded diverse habitats in Europe and in Madagascar. However, population genetic analyses have been hindered by the homogeneous genetic structure of the population and the lack of suitable tools for data analysis. We have used whole-genome sequencing to characterize reference specimens from various known wild populations. In parallel, we established a whole-genome sequencing data analysis pipeline for the population genetic analysis of nearly monoclonal genomes. Our results provide evidence for systematic genetic differences between geographically separated populations and illustrate the emerging differentiation of the marbled crayfish genome. We also used mark-recapture population size estimation in combination with genetic data to model the growth pattern of marbled crayfish populations. Our findings uncover evolutionary dynamics in the marbled crayfish genome over a very short evolutionary timescale and identify the rapid growth of marbled crayfish populations as an important factor for ecological monitoring.

Chair of Hydrobiology and Fisheries Institute of Agricultural and Environment Sciences Estonian University of Life Sciences Kreutzwaldi 5D 51006 Tartu Estonia

Department of Aquaculture Institute for Natural Resources Conservation Faculty of Agriculture and Environmental Sciences Szent István University Páter Károly utca 1 2100 Gödöllő Hungary

Department of Biology Chemistry West University of Timisoara 16A Pestalozzi St 300115 Timisoara Romania

Department of Water Bioresources and Aquaculture Dnipro State Agrarian and Economic University 25 Serhii Efremov St Dnipro 49600 Ukraine

Division of Epigenetics DKFZ ZMBH Alliance German Cancer Research Center Im Neuenheimer Feld 580 69120 Heidelberg Germany

Faculty of Fisheries and Protection of Waters CENAKVA University of South Bohemia in České Budějovice Zátiší 728 2 38925 Vodňany Czech Republic

Natural Resources and Environment Department of Biological and Environmental Science University of Jyväskylä P O Box 35 40014 Jyväskylä Finland

Physical Oceanography Research Group Department of Geosciences University of Malta Msida MSD 2080 Malta

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