Lewanski, A. L. | bioRxiv Science

bioRxiv2025

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

Top predators have oversized influence on food webs and ecosystem dynamics, and introducing a novel predator to a naive environment can have dramatic consequences for endemic biodiversity. Using genomic data, we find that the colonization of Lake Tanganyika by Lates fishes--the top predators in this ancient lake--occurred more recently than other diverse clades within the lake. Diversification into four endemic Lates species occurred within the lake during a time of dramatic changes in lake levels driven by glacial-interglacial cycles, supporting the hypothesis that these fluctuations were a "species pump" for lacustrine taxa. These lake level fluctuations also likely contributed to multiple admixture events among Lates species during the Pleistocene ([~] 90-500 Kya). Together, our findings suggest a dynamic and environmentally-linked evolutionary history of this predator radiation, and that their colonization of the lake and subsequent diversification likely had dramatic ecosystem consequences for taxa already present in Lake Tanganyika.

evolutionary biology↗

bioRxiv2022

Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

AO_SCPLOWBSTRACTC_SCPLOWMolecular 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 to what extent 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 greatest topological accuracy when filtering sites for minor allele count >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with minor allele count >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.

bioinformatics↗