Biology subjects

Emami-Khoyi, A.

Publications and source records attributed to Emami-Khoyi, A..

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

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↗

bioRxiv2020

A globally threatened shark, Carcharias taurus, shows no population decline in South Africa

Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark Carcharias taurus (also known as the sandtiger or grey nurse shark) is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, it was found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. Taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.

genetics↗

bioRxiv2018

Thermal selection drives biodiversity origination across the Atlantic/Indian Ocean boundary

Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive the evolution of new biodiversity. Ecological speciation scenarios are often invoked to explain such patterns, but the fact that adaptation is usually only identified when phylogenetic splits are already evident makes it impossible to rule out the alternative scenario of allopatric speciation with subsequent adaptation. We integrated large-scale genomic and environmental datasets along one of the worlds best defined marine thermal gradients (the South African coastline) to test the hypothesis that incipient speciation in the sea is due to divergence linked to the thermal environment. We identified temperature-associated gene regions in a coastal fish species that is spatially homogeneous throughout several temperature-defined biogeographical regions on the basis of selectively neutral markers. Based on these gene regions, the species is divided into geographically distinct regional populations. Importantly, the ranges of these populations are delimited by the same ecological boundaries that define distinct infraspecific genetic lineages in co-distributed marine the species, and biogeographical disjunctions in species assemblages. Our results indicate that ecologically-mediated selection represents an early stage of marine speciation in coastal regions that lack physical dispersal barriers.

evolutionary biology↗

bioRxiv2018

Blood, sweat and tears: a review of non-invasive DNA sampling

AO_SCPLOWBSTRACTC_SCPLOWThe use of DNA data is ubiquitous across animal sciences. DNA may be obtained from an organism for a myriad of reasons including identification and distinction between cryptic species, sex identification, comparisons of different morphocryptic genotypes or assessments of relatedness between organisms prior to a behavioural study. DNA should be obtained while minimizing the impact on the fitness, behaviour or welfare of the subject being tested, as this can bias experimental results and cause long-lasting effects on wild animals. Furthermore, minimizing impact on experimental animals is a key Refinement principle within the 3Rs framework which aims to ensure that animal welfare during experimentation is optimised. The term non-invasive DNA sampling has been defined to indicate collection methods that do not require capture or cause disturbance to the animal, including any effects on behaviour or fitness. In practice this is not always the case, as the term non-invasive is commonly used in the literature to describe studies where animals are restrained or subjected to aversive procedures. We reviewed the non-invasive DNA sampling literature for the past six years (380 papers published in 2013-2018) and uncovered the existence of a significant gap between the current use of this terminology (i.e. non-invasive DNA sampling) and its original definition. We show that 58% of the reviewed papers did not comply with the original definition. We discuss the main experimental and ethical issues surrounding the potential confusion or misuse of the phrase non-invasive DNA sampling in the current literature and provide potential solutions. In addition, we introduce the terms non-disruptive and minimally disruptive DNA sampling, to indicate methods that eliminate or minimise impacts not on the physical integrity/structure of the animal, but on its behaviour, fitness and welfare, which in the literature reviewed corresponds to the situation for which an accurate term is clearly missing. Furthermore, we outline when these methods are appropriate to use.

ecology↗