Phylogenomics and population genomics of Nothobranchius in lowland Tanzania: species delimitation and comparative genetic structure

Abstract

Annual killifishes of the genus Nothobranchius are widespread across East Africa, with a particularly high biodiversity in lowland Tanzania. While they are typically found in ephemeral pools, the pools vary greatly in size, connectivity and inundation patterns. It was previously suggested that main river channels formed significant barriers to Nothobranchius dispersal. Here, we study the distribution of genetic lineages in an equatorial part of their range where main river channels that may act as barriers occur and closely related lineages frequently coexist in secondary contact zones. We used single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing to investigate how genetic diversity is structured in Nothobranchius species from the coastal lowlands of Tanzania. Our analyses resolved some uncertain phylogenetic relationships within the N. melanospilus and N. guentheri species groups and placed N. flammicomantis outside the Coastal clade. Rather than a shared intraspecific genetic diversity pattern across four coexisting and widely distributed species, we found highly diverse patterns of intra-specific genetic structure among N. eggersi, N. janpapi, N. melanospilus and N. ocellatus. Populations of Nothobranchius species from the humid coastal lowlands of Tanzania are therefore structured, but not constrained by barriers formed by river channels or by basins – in contrast to Nothobranchius species from the dry part of their distribution. Some of the genetic relationships determined call for a re-evaluation of taxonomic delimitations.