Paulette Bloomer

• PhD
• Professor (Full) at University of Pretoria

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...

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...

Environmental DNA (eDNA) sampling has attracted worldwide attention over the past few years as an emerging approach to characterising and monitoring biodiversity, and has become particularly important for species that are rare, elusive or endangered. Most animal studies to date have focused on aquatic taxa; studies on other metazoan taxa, particula...

Many recent contributions have made a compelling case that genetic diversity is not adequately reflected in international frameworks and policies, as well as in local governmental processes implementing such frameworks. Using digital sequence information (DSI) and other publicly available data is supported to assess genetic diversity, toward formul...

The reduced costs 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 marke...

Pseudobarbus quathlambae (Barnard, 1938) is a cyprinid minnow with a disjunct distribution divided into tributaries of the Upper Orange River system in the Lesotho Highlands and the Mzimkhulu River system in KwaZulu Natal Province (KZN), South Africa. Recent records in the Mzimkhulu River system extended the species’ geographic range, and this coul...

Background Non-random associations within and among groups of social animals can provide valuable insight into the function of group living and the evolution of social behaviour. Damaraland mole-rats ( Fukomys damarensis ) demonstrate extremely high levels of reproductive skew, and dispersal is considered to be male-biased in onset and frequency, a...

Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7...

The Spike-heeled Lark Chersomanes albofasciata is a peculiar, short-tailed lark confined to southern, central and East Africa. Typical of resident larks, it exhibits marked geographic variation in plumage colour, which has historically resulted in large numbers of subspecies being described. This variation was examined by sequencing 630 base pairs...

Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Synce...

Hybridisation caused by anthropogenic movements of animals is a conservation concern. Black-faced impala (Aepyceros melampus petersi) are endemic to north-western Namibia and south-western Angola and are geographically isolated from common impala (A. m. melampus). Common impala have been translocated into the black-faced impala range creating a hyb...

The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework...

Fragmented wildlife populations are challenged by limited gene flow that can lead to significant inbreeding. The lion (Panthera leo) population in South Africa’s Hluhluwe-iMfolozi Park (HiP) started from a small founder population of one adult male (1958), one adult female, followed by two lionesses and three cubs (two females and one male; 1965; u...

Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub-Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have rela...

Wildlife ranching including the hunting, collection, sales and husbandry of wild animals in captivity, is practised worldwide and is advocated as an approach towards the conservation of wild species. While many authors have explored the biological impacts of intensive wild population management, primarily with respect to disease transmission (espec...

Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years; however, recent trends focus on genome‐wide analyses. One method proposed for calibrating inferences from noisy next‐generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this...

Rabbitfishes are reef-associated fishes that support local fisheries throughout the Indo-West Pacific region. Sound management of the resource requires the development of molecular tools for appropriate stock delimitation of the different species in the family. Microsatellite markers were developed for the cordonnier, Siganus sutor, and their poten...

The KwaZulu-Natal yellowfish (Labeobarbus natalensis) is an abundant cyprinid, endemic to KwaZulu-Natal Province, South Africa. In this study, we developed a single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing of samples across the distribution. We addressed several hidden challenges, p...

Habitat loss and fragmentation are major drivers of biodiversity loss, with large carnivores being particularly vulnerable due to their large home ranges. These species were once widespread across the African continent but over the past 100 years their ranges have decreased by more than 75% and there is continued pressure on the remaining free-roam...

The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic s...

Understanding the role of geography and climatic cycles in determining patterns of biodiversity is important in comparative and evolutionary biology and conservation. We studied the phylogeographic pattern and historical demography of a rock-dwelling small mammal species from southern Africa, the rock hyrax Procavia capensis. Using a multilocus coa...

White steenbras Lithognathus lithognathus (Teleostei: Sparidae) is an overexploited marine fish species endemic to South Africa. Overexploitation in recreational, subsistence and commercial fisheries has resulted in stock collapse and the need for improved management of the species. Adults are thought to undertake large-scale annual spawning migrat...

The African Wildcat is listed as Least Concern because it is the most common and widely distributed wild felid within the assessment region. However, extensive hybridisation and introgression with domestic cats across its global distribution range has been recorded. Recent studies suggest lower levels of introgression than expected in South Africa....

Physical and/or physiological constraints are assumed to isolate fish populations confined to or dependent on estuarine habitats. Strong isolation by distance is thus expected to affect connectivity. Such structuring has important implications for sustainable utilisation and replenishment of estuarine stocks that are heavily exploited. Here we pres...

Environmental gradients have been shown to disrupt gene flow in marine species, yet their influence in structuring populations at depth remains poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis) are demersal species co-occurring in the Benguela Current system, where decades of intense fishing resulted in severely depleted stoc...

Wildlife is a multi-million dollar industry in South Africa ranging from intensively farmed animals on small properties to free-roaming animals in large functional ecosystems. Specific concerns surrounding the conservation value of the intensively managed wildlife have been raised. Increasingly it is recognised that genetics must be considered when...

The combination of oceanographic barriers and habitat heterogeneity are known to reduce connectivity and leave specific genetic signatures in the demographic history of marine species. However, barriers to gene flow in the marine environment are almost never impermeable which inevitably allows secondary contact to occur. In this study, eight sampli...

Due to their geographic isolation, biotas of oceanic islands are likely influenced by episodic long distance dispersal events, but such observations are scarce. In June 2012, fishermen from Réunion Island caught an unknown specimen of grouper, identified as dusky grouper Epinephelus marginatus (Lowe, 1834). This was highly unexpected considering th...

In western Africa, multiple species of marine fish are exploited by a large fishing community. The exploitation of this resource calls for the establishment of appropriate management and conservation strategies at national and regional levels, which must start with the correct species identification of catches at fish landing sites. To improve fish...

Population fragmentation is threatening biodiversity worldwide. Species that once roamed vast areas are increasingly being conserved in small, isolated areas. Modern management approaches must adapt to ensure the continued survival and conservation value of these populations. In South Africa, a managed metapopulation approach has been adopted for s...

The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied s...

Maximum Likelihood and Bayesian gene trees. (DOCX)

Divergence dating tree with outgroups included. (DOCX)

Sample information for all Amblysomus samples used in this study. (DOCX)

Estimates of evolutionary divergence over sequence pairs between clades. (DOCX)

Population-level coalescent analyses. (DOCX)

The utility of 15 new and 17 previously published microsatellite markers was evaluated for species identification and stock delimitation in the deep-water hake Merluccius paradoxus and the shallow-water hake Merluccius capensis. A total of 14 microsatellites were polymorphic in M. paradoxus and 10 in M. capensis. Two markers could individually disc...

Overfishing has led to the collapse of many marine fish stocks along the South African coast, particularly species characterised by predictable distribution patterns and vulnerable life-history traits. Dusky kob (Argyrosomus japonicus) is an estuarine-dependent sciaenid fish that has been severely depleted by overfishing and is currently managed by...

Understanding the degree of genetic population differentiation is important in conservation genetics for inferring gene flow between populations and for identifying small and isolated threatened populations. We evaluated the genetic variation within and between three populations of the rock firefinch (Lagonosticta sanguinodorsalis), a range restric...

The South African lion (Panthera leo) population is highly fragmented. One-third of its wild lions occur in small (<1000 km2) reserves. These lions were reintroduced from other areas of the species’ historical range. Management practices on these reserves have not prioritized genetic provenance or heterozygosity. These trends potentially constrain...

Hybridization between fish species can play a significant role in evolutionary processes and can influence management and conservation planning, however, this phenomenon has been widely understudied, especially in marine organisms. The distribution limits of two sciaenid species (silver kob, Argyrosomus inodorus, and dusky kob, A. japonicus) partly...

The primary freshwater fish Pseudobarbus burchelli (Smith 1841) occurs across four presently isolated river systems in the south-western cape floristic region of South Africa. Mitochondrial DNA cytochrome b (701 base pairs) and control region (601 base pairs) genes were sequenced to assess the evolutionary history of P. burchelli and evaluate the r...

Aim A river hierarchy model has been proposed for stream‐dwelling taxa, where genetic structure is expected to reflect geographical proximity and connectivity of river systems. However, many exceptions and deviations from this model have been detected. The present study tested three biogeographical hypotheses (River Hierarchy, Palaeoriver Systems a...

The dusky kob (Argyrosomus japonicus) is a large, estuarine-dependent sciaenid fish that has been severely depleted in South African waters and that, in recent years, has received considerable attention from the local fish farming industry. Discovery and application of appropriate molecular markers is necessary to improve the understanding of wild...

Background The major histocompatibility complex (MHC) is an important component of the vertebrate immune system and is frequently used to characterise adaptive variation in wild populations due to its co-evolution with pathogens. Passerine birds have an exceptionally diverse MHC with multiple gene copies and large numbers of alleles compared to oth...

Table S1. List of 23 major histocompatibility complex class II ß (MHCIIß) exon 2 Nesospiza bunting sequences used in the present study.

Behavioural observations of reproduction and mate choice in wild fossorial rodents are extremely limited and consequently indirect methods are typically used to infer mating strategies. We use a combination of morphological, reproductive, spatial, and genetic data to investigate the reproductive strategy of a solitary endemic species, the Cape dune...

Summary information for each locus including number of alleles (A), frequency of null alleles (Null), expected and observed heterozygosity (HO, HE), and FIS (Probability of significant deviation from Hardy-Weinberg equilibrium; P<0.05 = *, P<0.01 = **, P<0.001 = ***). (DOCX)

Sire assignments for regions 1 (a) and 2 (b) across all models showing sire identity (sire-progeny distances in metres), probability of assignment, and number of mismatches between sire and progeny genotypes (NA denotes no sire assignment made). (DOCX)

Plots showing the shape and number of either equal (E) or variable (V) volume components; (a) male length, the best BIC values were: V,2 (-6255), V,3 (-6264), E,2 (-6270), and (b) male mass, the best BIC values were:E,2 (-8853.623), V,2(-8858), E,3 (-8866). (TIF)

Recently, 454 sequencing has emerged as a popular method for isolating microsatellites owing to cost-effectiveness and time saving. In this study, repeat-enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7370 sequences containing repeats (SCRs) we...

Chronogram generated using LSU sequence data to determine a secondary calibration date for the divergence between the Agaricales and Boletales from the Basidiomycota matrix. Asterisks indicate nodes with PP<0.95. (TIF)

Chronogram generated using DNA sequence data from the SSU and LSU genes as well as RPB2 amino acid sequence data to determine a secondary calibration date for the divergence between the Agaricales and Boletales from the Ascomycota - Basidiomycota matrix. Asterisks indicate nodes with PP<0.95. (TIF)

Culture numbers and GenBank accessions of Armillaria strains used in this study. (DOC)

Data sets and calibration dates used to determine the time of divergence between the Boletales and Agaricales, and the tMRCA of A. fuscipes, A. mellea and A. novae-zealandiae , as well as their node ages, heights and confidence intervals. (DOC)

GenBank accession numbers and genome project sources for DNA and amino acid sequence data used in the Ascomycota – Basidiomycota data. (DOC)

List of species included in the Basidiomycota matrix and their GenBank accession numbers. (DOC)

Substitution models determined from jModelTest and ProtTest during the study. (DOC)

The global movement and speciation of fungal plant pathogens is important, especially because of the economic losses they cause and the ease with which they are able to spread across large areas. Understanding the biogeography and origin of these plant pathogens can provide insights regarding their dispersal and current day distribution. We tested...

Hybridization between introduced and endemic ungulates, resulting from anthropogenic actions, has been reported for several species. Several studies of such events contain the common themes of extralimital movements, problematic phenotypic and genetic detection, and imperfect management. In southern Africa, the endemic black wildebeest (Connochaete...

Biogeographic boundaries are the meeting zone of broadly distributed faunas, or the actual cause of a faunal break. In the latter case, closely related sister species should be found across such a boundary. To achieve such a situation, preliminary stages are expected, where phylogeographic breaks followed by genetic cryptic speciation would be obse...

Eight microsatellite markers were developed for African mole-rats using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol and pyrosequencing. The markers were developed in Bathyergus suillus and applied to a selection of individuals from seven related taxa: Bathyergus janetta, Cryptomys hottentotus hottentotus, C. h. pret...

Ophiostoma species such as O. quercus are the most frequent causal agents of sapstain of freshly felled hardwood timber and pulpwood. Many species are regarded as economically important agents of wood degradation. The aim of this study was to identify a collection of Ophiostoma isolates, resembling O. quercus, found on stained Eucalyptus pulpwood c...

Ophiostoma species such as O. quercus are the most frequent causal agents of sapstain of freshly felled hardwood timber and pulpwood. Many species are regarded as economically important agents of wood degradation. The aim of this study was to identify a collection of Ophiostoma isolates, resembling O. quercus, found on stained Eucalyptus pulpwood c...

Intraspecific variation within the diverse southern African murine rodents has not been extensively investigated, yet cryptic diversity is evident in several taxa studied to date. The Namaqua rock mouse, Micaelamys namaquensis Smith, 1834 is a widespread endemic murine rodent from the subregion. Currently, a single species with four subspecies is r...

Over the past decade, numerous molecular phylogenetic studies uncovered cryptic diversity within the Copepoda, yet very few investigations focused on symbiotic copepods. Here we report mitochondrial DNA cytochrome oxidase I diversity in the cosmopolitan elasmobranch symbiont Nesippus orientalis off the KwaZulu-Natal coast of South Africa. Analysis...

Polymorphic sequence-characterised marker assays from a recent diversity study on the Ascomycete fungus Ophiostoma quercus reported that some isolates from Africa were genetically distinct from O. quercus. In the present study, these African isolates were compared with authentic O. quercus isolates by evaluating morphological characters, growth in...

Combined data nexus file. GHR alignment, indel, and morphological character data, plus 8 optimal MP trees and MrBayes command block, in nexus format, entitled "gmole-comb-feb10.nex".

Morphological data nexus file. Morphological characters with character and state names in nexus format entitled "gmole-morph-feb10.nex".

Table of Blast results. BLAST results for GHR sequences obtained from museum skulls. All fragments recovered maximum similarity to GHR sequences of Chrysospalax trevelyani (AF392877 [30]).

Golden moles (Chrysochloridae) are small, subterranean, afrotherian mammals from South Africa and neighboring regions. Of the 21 species now recognized, some (e.g., Chrysochloris asiatica, Amblysomus hottentotus) are relatively common, whereas others (e.g., species of Chrysospalax, Cryptochloris, Neamblysomus) are rare and endangered. Here, we use...

Ophiostoma quercus is a morphologically variable species that causes sapstain on mostly hardwood hosts worldwide. Several species have been suggested as synonyms of O. quercus in the past, including O. fagi, O. roboris, O. valachicum, O. kubanicum, and O. catonianum. A recent collection of isolates resembling O. quercus from Azerbaijan provided the...

Non-geographic morphometric variation, particularly at the level of sexual dimorphism and ontogenetic (age-related) variation, has been documented in rodents, and useful for establishing whether to analyse sexes separately or together, and for selecting adult specimens for subsequent data recording and analysis. However, such studies have largely b...