African lates perches (Teleostei, Latidae, Lates): Paraphyly of Nile perch and recent colonization of Lake Tanganyika

Admixture and environmental fluctuations shape the evolutionary history of a predator radiation in East Africa's Lake Tanganyika

Top predators have oversized impacts on food webs and ecosystem dynamics, and introducing a novel predator to a naive environment can have dramatic consequences for endemic biodiversity. Lake Tanganyika is unique among African lakes in the diversity of the pelagic top predators in the genus Lates, where four species are endemic to the lake. Using a combination of reduced-representation and whole genome resequencing data, and pairing these with phylogenetic and demographic modeling approaches, we find that Lates colonization of Lake Tanganyika was much more recent (~1-2 Mya) than other major and diverse clades within the lake. Demographic modeling suggests that diversification among Lates species within the lake occurred during a time period of dramatic changes in lake levels driven by glacial-interglacial cycles, supporting a role of these fluctuations as a "species pump" for lacustrine taxa. We further find that these lake level fluctuations likely contributed to multiple bouts of admixture among Lates species during the mid- to late-Pleistocene (~90-500 Kya). Together, our findings suggest a dynamic and environmentally linked evolutionary history of the Lates radiation with the potential for dramatic ecosystem consequences for the taxa already present in Lake Tanganyika prior to Lates colonization and diversification.

Significance Statement

When introduced to novel ecosystems, top predators can cause major alterations to biodiversity and food webs. Species introductions to novel habitats can also provide invading taxa with ecological opportunities that facilitate evolutionary diversification. Here, we find evidence that the radiation of endemic top predators in East Africa's Lake Tanganyika originated surprisingly recently, and that these species have experienced periods of hybridization with a widespread riverine relative throughout their history. These findings have major implications for the history of the lake and suggest that the introduction of Nile perch into Lake Victoria, which caused dramatic ecosystem and food web changes, may be a contemporary analog to the historical events in Lake Tanganyika.

Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses

Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate the extent to which the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find the greatest topological accuracy when filtering sites for minor allele count (MAC) >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with MAC >1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short-read genomic data for phylogenetic inference.

Monogeneans from Catfishes in Lake Tanganyika. II: New Infection Site, New Record, and Additional Details on the Morphology of the Male Copulatory Organ of Gyrodactylus transvaalensis Prudhoe and Hussey, 1977

The ichthyofauna of Lake Tanganyika consists of 12 families of fish of which five belong to Siluriformes (catfishes). Studies on Siluriformes and their parasites in this lake are very fragmentary. The present study was carried out to help fill the knowledge gap on the monogeneans infesting the siluriform fishes of Lake Tanganyika in general and, more particularly, Clarias gariepinus. Samples of gills of Clarias gariepinus (Clariidae) were examined for ectoparasites. We identified the monogenean Gyrodactylus transvaalensis (Gyrodactylidae). This is the first time this parasite was found infecting gills. We are the first to observe a large spine in the male copulatory organ of this species and to provide measurements of its genital spines; this completes the description of the male copulatory organ, which is important in standard monogenean identification. This is the first monogenean species reported in C. gariepinus at Lake Tanganyika and the third known species on a representative of Siluriformes of this lake. It brings the total number of species of Gyrodactylus recorded in Lake Tanganyika to four. Knowing that other locations where this species has been reported are geographically remote from Lake Tanganyika, we propose a "failure to diverge" phenomenon for G. transvaalensis.

Co-introduction of Dolicirroplectanum lacustre, a monogenean gill parasite of the invasive Nile perch Lates niloticus: intraspecific diversification and mitonuclear discordance in native versus introduced areas

The Nile perch (Lates niloticus) is a notorious invasive species. The introductions of Nile perch into several lakes and rivers in the Lake Victoria region led to the impoverishment of trophic food webs, particularly well documented in Lake Victoria. Additionally, its parasites were co-introduced, including Dolicirroplectanum lacustre (Monogenea, Diplectanidae). Dolicirroplectanum lacustre is the single monogenean gill parasite of latid fishes (Lates spp.) inhabiting several major African freshwater systems. We examined the intra-specific diversification of D. lacustre from Lates niloticus in Lake Albert, Uganda (native range) and Lake Victoria (introduced range) by assessing morphological and genetic differentiation, and microhabitat preference. We expected reduced morphological and genetic diversity for D. lacustre in Lake Victoria compared with Lake Albert, as a result of the historical introductions. We found that D. lacustre displayed high morphological variability within and between African freshwaters, with two morphotypes identified, as in former studies. The single shared morphotype between Lake Albert and Lake Victoria displayed similar levels of haplotype and nucleotide diversity between the lakes. Mitonuclear discordance within the morphotypes of D. lacustre indicates an incomplete reproductive barrier between the morphotypes. The diversification in the mitochondrial gene portion is directly linked with the morphotypes, while the nuclear gene portions indicate conspecificity. Based on our results, we reported reduced genetic and morphological diversity, potentially being a result of a founder effect in Lake Victoria.

The Genetic Population Structure of Lake Tanganyika's Lates Species Flock, an Endemic Radiation of Pelagic Top Predators

Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae, and L. angustifrons) using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST = 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure within L. mariae, with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis, and L. angustifrons). Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species-particularly that of L. mariae-which may be important for conservation and management of this culturally and economically important clade of fishes.