Phylogeographic reconstruction of the marbled crayfish origin

The marbled crayfish (Procambarus virginalis) is a triploid and parthenogenetic freshwater crayfish species that has colonized diverse habitats around the world. Previous studies suggested that the clonal marbled crayfish population descended as recently as 25 years ago from a single specimen of P. fallax, the sexually reproducing parent species. However, the genetic, phylogeographic, and mechanistic origins of the species have remained enigmatic. We have now constructed a new genome assembly for P. virginalis to support a detailed phylogeographic analysis of the diploid parent species, Procambarus fallax. Our results strongly suggest that both parental haplotypes of P. virginalis were inherited from the Everglades subpopulation of P. fallax. Comprehensive whole-genome sequencing also detected triploid specimens in the same subpopulation, which either represent evolutionarily important intermediate genotypes or independent parthenogenetic lineages arising among the sexual parent population. Our findings thus clarify the geographic origin of the marbled crayfish and identify potential mechanisms of parthenogenetic speciation

Origination, Monoclonality and Evolution of the Marbled Crayfish Genome Procambarus virginalis

The parthenogenetic marbled crayfish (Procambarus virginalis) sparked interest within the scientific community due to its unique features. Its polyploid and monoclonal genome, high environmental adaptability and phenotypic diversity made the marbled crayfish a suitable laboratory model for genomics, epigenetics and ecology research. The previously established marbled crayfish genome sequence of 3.5 Gbp represents a highly fragmented draft assembly. Initial comparative genomic analyses resulted in confirmation of P. virginalis genome origination from the sexually reproducing freshwater crayfish P. fallax. However, in-depth genomic analysis and interspecies genome comparisons require further refinement of the fragmented genome reference of the marbled crayfish. In this PhD thesis, the first refinement of the marbled crayfish genome has been performed with application of the PacBio Single Molecule Real Time (SMRT) sequencing technology. The new and improved genome assembly of the marbled crayfish resulted in 3.7 Gbp of sequence length and an N50 of 144kb. The refined genome assembly enabled searching parental haplotypes and understanding species origination. The absence of evidence for loss of heterozygosity in the various monoclonal marbled crayfish generations suggests the lack of recombination process during oogenesis. Thus, marbled crayfish suggest to be apomictic parthenogens which are characterized by generating identical copies of the maternal genotype. Moreover, despite of the limited genome variability, monoclonal marbled crayfish genomes consisted of population-specific genetic polymorphisms within the global population. Comparative genomic analysis between geographically distant populations resulted in the identification of population-specific mutational signatures. The calculation of genomic variability of marbled crayfish from the growing population in Lake Reilingen allowed to estimate population dynamics. Thus, the population in Lake Reilingen demonstrates a rapid growth, following the density-independent exponential model. This PhD thesis provides fundamental insights into marbled crayfish research, particularly via making use of an improved genome assembly for comparative genomic analyses, epigenetic studies, and for research on the evolution and genomic adaptation to asexuality

Genome analysis of the monoclonal marbled crayfish reveals genetic separation over a short evolutionary timescale

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.peerReviewe