Biology subjects

Jansen van Vuuren, B.

Publications and source records attributed to Jansen van Vuuren, B..

5 recordsLinked to original sources

bioRxiv2021

Dietary specialisation in a Critically Endangered pipefish revealed by faecal eDNA metabarcoding

Understanding the dietary preferences of endangered species can be useful in implementing conservation strategies, including habitat restoration, translocation, and captive breeding. Environmental DNA (eDNA) from feces provides a non-invasive method for analyzing animal diets. Currently, metabarcoding, a PCR-based method, is the method of choice for analyzing such data. However, this method has limitations, specifically PCR bias, which can result in the overestimation of the importance of certain taxa and the failure to detect other taxa because they do not amplify. The present study compared metabarcoding with metagenomics, a marker-free method, to assess the diversity of prey items in the feces of a critically endangered South African estuarine pipefish, Syngnathus watermeyeri, and its widely distributed congener (S. temminckii) to investigate the potential dietary competition. Our results showed a distinct difference between the diets of S. watermeyeri and S. temminckii, with the former mainly consuming calanoid copepods and the latter preferring caridean shrimp. Metagenomics produced more species identifications than metabarcoding; however, most of the species identified are not present in South Africa. The identifications made by both methods mostly belonged to the same families, but some prey items were identified only by either method. Both methods would benefit from a complete reference database of South African estuarine macroinvertebrates.

ecology↗

bioRxiv2020

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 22 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

evolutionary biology↗

bioRxiv2020

Genomic divergence and differential gene expression between crustacean ecotypes across a marine thermal gradient

Environmental gradients between marine biogeographical provinces separate distinct faunal communities; in the absence of absolute dispersal barriers numerous species nonetheless occur on either side of such boundaries. While the regional populations of such widespread species tend to be morphologically indistinguishable from each other, genetic evidence suggests that they represent unique ecotypes, and likely even cryptic species, that may be uniquely adapted to their local environment. Here, we explored genomic divergence in four sympatric southern African decapod crustaceans whose ranges span the boundary between the cool-temperate west coast (south-eastern Atlantic) and the warm-temperate south coast (south-western Indian Ocean) near the southern tip of the African continent. Using genome-wide data, we found that all four species comprise distinct west- and south coast ecotypes, with molecular dating suggesting divergence during the Pleistocene. Using transcriptomic data from one of the decapod crustaceans, we further found a clear difference in gene expression profiles between the west- and south coast ecotypes. This was particularly clear in the individual from the south coast, which experienced a transcriptomic shock at low temperatures that are more typical of the west coast and may explain their absence from that coastline. Our results shed new light on the processes involved in driving genomic divergence and incipient speciation.

genomics↗

bioRxiv2019

Assessing introgressive hybridization in roan antelope (Hippotragus equinus): Lessons from South Africa

Biological diversity is being lost at unprecedented rates, with admixture and introgression presenting major threats to species conservation. To this end, our ability to accurately identify introgression is critical to manage species, obtain insights into evolutionary processes, and ultimately contribute to the Aichi Targets developed under the Convention on Biological Diversity. A case in hand concerns roan antelope, one of Africas most iconic large mammal species. Despite their large size, these antelope are sensitive to habitat disturbance and interspecific competition, leading to the species being listed as Least Concern but with decreasing population trends, and as extinct over parts of its range. Molecular research identified the presence of two evolutionary significant units across their sub-Saharan range, corresponding to a West African lineage and a second larger group which includes animals from East, Central and Southern Africa. Within South Africa, one of the remaining bastions with increasing population sizes, there are a number of West African roan antelope populations on private farms, and concerns are that these animals hybridize with roan that naturally occur in the southern African region. We used a suite of 27 microsatellite markers to conduct admixture analysis. Our results unequivocally indicate evidence of hybridization, with our developed tests able to accurately identify F1, F2 and non-admixed individuals at threshold values of qi = 0.20 and qi = 0.15, although further backcrosses were not always detectable. Our study is the first to confirm ongoing hybridization in this iconic African antelope, and we provide recommendations for the future conservation and management of this species.

zoology↗

bioRxiv2018

Context-dependent spatial sorting of dispersal-related traits in the invasive starlings (Sturnus vulgaris) of South Africa and Australia.

Species undergoing range expansion frequently experience increased dispersal rates, especially among invasive alien species. Such increased dispersal rates have been attributed to spatial sorting, where traits enhancing dispersal assort towards the expanding range edge while traits enhacing competitiveness are favoured within the core range. To date no single study has compared patterns of spatial sorting across multiple continents for the same species. Here we compared patterns of spatial sorting in Sturnus vulgaris, the European starling (hereafter referred to as starlings), in its invasive ranges in South Africa and Australia. Starlings have experienced similar residence times in these two countries. Using multi-scale pattern analyses and generalized additive models, we determine whether dispersal and foraging traits (i.e. the morphological attributes of wings and bills) were sorted along the distance from introduction site. We found apparent patterns of spatial sorting in Australia, but not in South Africa. This difference may be attributed to differences in dispersal rates, clinal variation, environmental heterogeneity, and thus population demography on the two continents. Genetic data suggests that starlings in South Africa have experienced frequent long distance dispersal events, which could have diluted or overridden patterns of spatial sorting.

evolutionary biology↗