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

Penry, Gwenith S.; Hammond, Philip S.; Cockcroft, Victor G.; Best, Peter B.; Graves, Jeff A.

doi:10.1007/s10592-018-1105-4

Cited by 16 publications

(25 citation statements)

References 37 publications

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“…Bryde's whales Recent genetic work by Penry et al (2018) suggests that, in South African waters, there are two forms of B. brydei consisting of the inshore and offshore stocks. They recommend that the B. brydei forms should be separated entirely from B. edeni as they appear to be morphologically and genetically different in South African waters.…”

Section: Key Findingsmentioning

confidence: 99%

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

Purdon

Shabangu²,

Yemane

et al. 2020

PeerJ

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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.

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Section: Key Findingsmentioning

confidence: 99%

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

Purdon

Shabangu²,

Yemane

et al. 2020

PeerJ

View full text Add to dashboard Cite

show abstract

“…For instance, we kept the required minimum distance on sighting of the individual. The individual was identified each time it was sighted based on its features as discussed in [26]. Most times, recordings were carried out when a single individual is sighted.…”

Section: Recordings and Preprocessingmentioning

confidence: 99%

“…Subsequently, it was affirmed that the B. brydei described by Olsen [21] include characteristics from the inshore and offshore forms of B. edeni [23]- [25]. Much recently, different literature have described the genetic and phylogenetic features of Bryde's whales off South Africa [26], [27]. However, no work has previously documented the Brdye's whales calls off South Africa.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Template-Based Detection Algorithms for Inshore Bryde’s Whale Short Pulse Calls

Ogundile

Versfeld

2020

IEEE Access

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Marine mammals use sound for communication and echolocation within their ecosystems. The detection of these sounds is an important aspect of signal processing, such that we can estimate the spatial position and direction of arrival of these mammals, and have an understanding of their ecology. Passive acoustic monitoring (PAM) is widely used to understand marine mammal movement and vocal repertoire. In PAM, datasets are accumulated over days, months or years. Thus, it is impracticable to manually analyse the datasets because it is very large. This motivated the development of automated sound detection techniques for marine mammals, which most often varies depending on the vocal duration, frequency range and call type. In this paper, continuous recordings of Bryde's whale (Balaenoptera edeni edeni) short pulse calls (< 3.1s long) were collected on a weekly basis from December 2018 to April 2019 on sighting of the individual in a single site in the endmost SouthWest of South Africa. The sound, previously not documented off South Africa, was observed on visual confirmation of the presence of inshore Brydes's whale. In addition, the paper develops and analyses two automated template-based detection algorithms for this short pulse call, employing dynamic time warping (DTW) and linear predictive coding (LPC) techniques. These proposed template-based detectors are novel, as they have not being previously used in Bryde's whale sound detection in the literature. When applied to the continuous recordings of the short pulse calls, the DTW-based and LPC-based detection algorithms obtained a sensitivity of 96.04% and 97.14% respectively for high signal-tonoise ratio (about 10dB above the ambient sound). Otherwise, for low SNR, the DTW-based and LPC-based detection algorithms obtained a sensitivity of 94.98% and 96.00% respectively. These detection algorithms exhibit low computational time complexity and can be modified to analyse the movement of obscure but vocal marine species instead of manual identification.

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“…The Bd mitochondrial genome has recently been fully sequenced, has a low rate of recombination relative the nuclear genome, and is present at high copy number so is likely to be detectable at low infection burdens. There is also a precedent for using mtDNA for phylogenetic studies across a wide range of taxa (Barr et al, 2011;Li et al, 2016;Penry et al, 2018;Schreeg et al, 2016;Song et al, 2016). Here, we report a lineage-specific qPCR assay for Bd based on mtDNA which detects the two lineages of Bd most commonly associated with chytridiomycosis in wild populations -BdGPL and BdCAPE -with high specificity and sensitivity.…”

Section: Introductionmentioning

confidence: 99%

Discriminating Lineages ofBatrachochytrium dendrobatidisusing quantitative PCR

Ghosh

Verster

Sewell

et al. 2020

Preprint

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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.

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

Cited by 16 publications

References 37 publications

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

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

Analysis of Template-Based Detection Algorithms for Inshore Bryde’s Whale Short Pulse Calls

Discriminating Lineages ofBatrachochytrium dendrobatidisusing quantitative PCR

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