An increasing number of genomic studies are showing that genetic introgression between closely related species is surprisingly common across the tree of life, thus making the description of biodiversity and understanding the process of speciation complex and challenging. The adaptive radiation of cichlid fishes in Lake Malawi, with hybrid origins and recent cases of introgression, provides an important model system to study the evolutionary implications of introgression. However, many potential sources of introgression into the radiation have not yet been investigated. Here we use whole genome data from 239 cichlid species from Lake Malawi and a comprehensive dataset of 76 species from surrounding African river and lake systems to discover and map previously unknown introgression events involving the Malawi cichlid radiation. Using genome-wide excess allele sharing (ABBA BABA statistics) and window-based analyses, we found that three independent riverine cichlid lineages are significantly closer to the Malawi radiation than to its sister group, suggesting historical genetic exchange between these lineages and the Malawi radiation. Across Malawi species, we found low variability in the levels of excess allele sharing with non-Malawi species, suggesting that introgressed haplotypes are distributed relatively uniformly across the radiation and that most hybrid-derived polymorphism was acquired and sorted before the formation of the contemporary Malawi cichlid radiation. Our results point towards several previously unknown contributors to the Malawi hybrid swarm, suggesting that the history of one of the largest vertebrate radiations was even more complex than previously thought.

1 Gravel beaches in the Mediterranean ecoregion represent an economically important and unique habitat type. Yet, burgeoning tourism, intensive coastal development and artificial nourishment of beaches may jeopardize their ecological communities. To date, species that reside on gravel beaches and the consequences of beach alterations are poorly understood, which hampers the development of a sustainable coastal tourism industry along the region’s shorelines. 2 Using a simple collection method based on dredging buckets through the intertidal section of beaches, we quantified the microhabitat association of two sympatric clingfish species in the genus Gouania at seven natural and an artificial gravel beach based on sediment characteristics. We hypothesized that slender (G. pigra) and stout (G. adriatica) morphotypes would partition interstitial niche space based on sediment size, which may affect the vulnerability of the species to changes in gravel beach composition due to coastal development. 3 We detected substantial differences in gravel composition within and among the sampled beaches which suggests scope for microhabitat partitioning in Gouania. Indeed, we found significant relationships between species identity and the presence/absence and abundance of individuals in hauls based on their positioning on PC1. 4 Our results suggest that modifications of gravel beaches through coastal development, including beach nourishment, intensifying coastal erosion, or artificial beach creation, may have detrimental consequences for the two species if sediment types or sizes are altered. We posit that, given the simplicity and efficacy of our sampling method and the sensitivity of Gouania species to prevailing gravel composition, the genus could serve as an important indicator for gravel beach management in the Mediterranean ecoregion.