Phylogenetic relationships in southern African Bryde’s whales inferred from mitochondrial DNA: further support for subspecies delineation between the two allopatric populations

DNA Barcoding Technology Used to Successfully Sub-Classify a Museum Whale Specimen as Balaenoptera edeni edeni

DNA barcoding technology is becoming an increasingly powerful tool in resolving issues of detailed species identification based on morphology, as commonly employed by museums. In the present study, we aimed to identify a stranded Bryde’s whale on Hainan Island, China by extracting DNA from a vertebra pre-treated by physical and/or chemical processes. Based on morphological characteristics, this Bryde’s whale was initially determined as Balaenoptera edeni. Then, DNA was efficiently extracted using ancient DNA techniques. The mitochondrial gene (COI) phylogenetic analysis further revealed that this museum whale specimen belonged to the sub-species B. e. edeni. This study provides a testable and rapid method for museum species verification, by using ancient DNA extraction methods to compensate the disadvantage of traditional DNA extraction methods that are difficult to extract valid DNA.

Discriminating lineages of Batrachochytrium dendrobatidis using quantitative PCR

The ability to detect and monitor infectious disease in a phylogenetically informative manner is critical for their management. Phylogenetically informative diagnostic tests enable patterns of pathogen introduction or changes in the distribution of genotypes to be measured, enabling research into the ecology of the pathogen. Batrachochytrium dendrobatidis (Bd), a causative agent of chytridiomycosis in amphibian populations, emerged worldwide in the 21st century and is composed of six lineages which are display varying levels of virulence in their hosts. Research into the distribution, ecology and pathogenicity of these lineages has been hampered by an inability to type lineage efficiently. Here, we describe a lineage‐specific TaqMan qPCR assay that differentiates the two lineages of Bd most commonly associated with chytridiomycosis: BdGPL and BdCAPE. We demonstrate how this assay can be used for the surveillance of wild populations of amphibians in Southern Africa using skin swabs, tissue samples and cultured isolates.

see also the Perspective by Claudio Azat

Species distribution modelling of Bryde's whales, humpback whales, southern right whales, and sperm whales in the southern African region to inform their conservation in expanding economies

In southern African waters, information about species distribution and habitat preferences of many cetacean species is limited, despite the recent economic growth that may affect them. We determined the relative importance of eight environmental variables (bathymetry, distance to shore, slope, chlorophyll-a, salinity, eastwards sea water velocity, northwards sea water velocity and sea surface temperature) as drivers of seasonal habitat preferences of Bryde's whales (Balaenoptera brydei), humpback whales (Megaptera novaeangliae), southern right whales (Eubalaena australis) and sperm whales (Physeter macrocephalus). Using presence only data from multiple sources, we constructed predictive species distribution models (SDMs) consisting of ensembles of seven algorithms for these species during both summer and winter. Predicted distribution for all cetaceans was high in southern Africa and, in particular, within the South African Exclusive Economic Zone (EEZ). Predictive models indicated a more pronounced seasonal variation for humpback, sperm and southern right whales than for Bryde's whales. Southern right whales occurred closer to shore during winter, humpback whales were more likely to occur along the east coast in winter and the west coast in summer, and sperm whales were more concentrated off the shelf in winter. Our study shows that ensemble models using historical, incidental and scientific data, in conjunction with modern environmental variables, can provide baseline knowledge on important environmental drivers of cetacean distribution for conservation purposes. Results of this study can further be used to help develop marine spatial plans and identify important marine mammal areas.