Bloomer, P. | bioRxiv Science

bioRxiv2024

DNA barcoding affirms the presence of invasive Parachanna obscura and new records of some species in the Mweru-Luapula fishery

DNA barcoding has recently been instrumental in identifying both invasive and undetected species in aquatic environments. This study aimed at analysing collected fish fin clips to ascertain the identity of native species and the Parachanna species that have invaded the Mweru-Luapula (ML) fishery of Zambia. The identification process was carried out through field phenotypic analysis using species guides and DNA barcoding, with the mitochondrial DNA (mtDNA) cytochrome C oxidase 1 (COI) gene fragment. Of the 28 specimens for which DNA was successfully PCR amplified, five matched the reference sequences of species and 22 matched the reference sequences of genera on the NCBI GenBank. Five unexpected species, namely Oreochromis niloticus, Coptodon zillii, Mormyrus kannume, Thoracochromis buysi and Tylochromis polylepis were identified. The study further affirmed the presence of invasive Parachanna obscura in the fishery and its interconnected water bodies. Parachanna obscura invaded the fishery through annual flooding from aquacultural facilities in the Democratic Republic of Congo (DRC). There is a need to investigate this invasion further by using large sample sizes and also by applying the gonadosomatic index (GSI) to determine invasive species occupancy and impact on native species throughout the fishery. This study provides a platform for further detailed taxonomic verification and species inventory of the entire ML fishery. This will facilitate the development of a viable and sustainable strategy to appropriately curb the impact of invasive species, and will thus contribute to the conservation of the ML aquatic biodiversity.

genetics↗

bioRxiv2023

A highly divergent mitochondrial genome in extant Cape buffalo from Addo Elephant National Park, South Africa

The reduced cost of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history, and biology of non-model species. While the Cape buffalo (Syncerus caffer caffer) has been well-studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population-level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154-1,036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe-iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known from previous studies to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochrome b gene. Using a fossil-calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, either S. acoelotus or S. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.

genetics↗