Use of Highly Specific Molecular Markers Reveals Positive Correlation between Abundances of Mesodinium cf. major and Its Preferred Prey,Teleaulax amphioxeia,During Red Water Blooms in the Columbia River Estuary

In a previous study, Teleaulax amphioxeia—the preferred prey of Mesodinium in the Columbia River estuary—were undetectable within intense annual blooms, suggesting blooms are prey‐limited or prey are acquired outside of bloom patches. We used a novel molecular approach specifically targeting the prey (i.e., Unique Sequence Element [USE] within the ribosomal RNA 28S D2 regions of T. amphioxeia nucleus and nucleomorph) in estuarine water samples acquired autonomously with an Environmental Sample Processor integrated within a monitoring network (ESP‐SATURN). This new approach allowed for both more specific detection of the prey and better constraint of sample variability. A positive correlation was observed between abundances of M. cf. major and T. amphioxeia during bloom periods. The correlation was stronger at depth (> 8.2 m) and weak or nonexistent in the surface, suggesting that predator–prey dynamics become uncoupled when stratification is strong. We confirmed exclusive selectivity for T. amphioxeia by M. cf. major and observed the incorporation of the prey nucleus into a 4‐nuclei complex, where it remained functionally active. The specific biomarker for T. amphioxeia was also recovered in M. cf. major samples from a Namibian coastal bloom, suggesting that a specific predator–prey relationship might be widespread between M. cf. major and T. amphioxeia.     

Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations

Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half‐siblings or cousins) is strongly suggested.     

Genetic heterogeneity in sable antelope (Hippotragus niger Harris 1838) from four Southern African regions

Allozyme variability in four populations of sable antelope Hippotragus niger from southern Africa was determined by protein gel electrophoresis. Eighteen protein-coding loci, of which four displayed polymorphism, were resolved in blood samples obtained from 54 animals. Average heterozygosity ranged from 3.78% in a control group to as low as 1.53% in a small, isolated population. Within-population diversity constituted the major part of total gene diversity at 92.27%. Genetic distances confirmed that comparatively little divergence has occurred between the populations sampled, with a maximum genetic distance value of only 0.0044. We discuss the influence of early histories on current genetic characteristics in the populations sampled and present some guidlines towards optimal genetic management of H. niger.     

Stability, activity and flexibility in alpha-lactalbumin.

alpha-Lactalbumins and the type-c lysozymes are homologues with similar folds that differ in function and stability. To determine if the lower stability of alpha-lactalbumin results from specific substitutions required for its adaptation to a new function, the effects of lysozyme-based and other substitutions on thermal stability were determined. Unblocking the upper cleft in alpha-lactalbumin by replacing Tyr103 with Ala, perturbs stability and structure but Pro, which also generates an open cleft, is compatible with normal structure and activity. These effects appear to reflect alternative enthalpic and entropic forms of structural stabilization by Tyr and Pro. Of 23 mutations, only three, which involve substitutions for residues in flexible substructures adjacent to the functional site, increase stability. Two are lysozyme-based substitutions for Leu110, a component of a region with alternative helix and loop conformations, and one is Asn for Lys114, a residue whose microenvironment changes when alpha-lactalbumin interacts with its target enzyme. While all substitutions for Leu110 perturb activity, a Lys114 to Asn mutation increases T(m) by more than 10 degrees C and reduces activity, but two other destabilizing substitutions do not affect activity. It is proposed that increased stability and reduced activity in Lys114Asn result from reduced flexibility in the functional site of alpha-lactalbumin.     

The complete sequence of the mitochondrial genome of the African Penguin (Spheniscus demersus)

The complete mitochondrial genome of the African Penguin (Spheniscus demersus) was sequenced. The molecule was sequenced via next generation sequencing and primer walking. The size of the genome is 17,346 bp in length. Comparison with the mitochondrial DNA of two other penguin genomes that have so far been reported was conducted namely; Little blue penguin (Eudyptula minor) and the Rockhopper penguin (Eudyptes chrysocome). This analysis made it possible to identify common penguin mitochondrial DNA characteristics. The S. demersus mtDNA genome is very similar, both in composition and length to both the E. chrysocome and E. minor genomes. The gene content of the African penguin mitochondrial genome is typical of vertebrates and all three penguin species have the standard gene order originally identified in the chicken. The control region for S. demersus is located between tRNA-Glu and tRNA-Phe and all three species of penguins contain two sets of similar repeats with varying copy numbers towards the 3′ end of the control region, accounting for the size variance. This is the first report of the complete nucleotide sequence for the mitochondrial genome of the African penguin, S. demersus. These results can be subsequently used to provide information for penguin phylogenetic studies and insights into the evolution of genomes.     

Molecular and morphometric assessment of the taxonomic status of Ectemnorhinus weevil species (Coleoptera: Curculionidae, Entiminae) from the sub-Antarctic Prince Edward Islands

There are long‐standing controversies on the taxonomic status of Ectemnorhinus weevil species occurring on the sub‐Antarctic Prince Edward Islands. Since the two islands that constitute the Prince Edward Islands archipelago (PEIA), Marion Island (MI) and Prince Edward Island (PEI), differ in terms of alien invasive species such as the introduced house mouse Mus musculus and conservation management strategies, it is important to consider inter‐island dynamics when investigating inter‐specific relationships. Using a combined molecular phylogenetic and morphometric approach, we attempted to resolve the taxonomic status of the PEIA Ectemnorhinus weevil species. A COI gene phylogeny was inferred following the genetic characterization of 52 Ectemnorhinus weevils from both islands, and morphometric assessment using a set of 15 linear, external measurements was used to differentiate between the two currently recognized species, Ectemnorhinus similis and Ectemnorhinus marioni. Analyses revealed the presence of two genetically and morphometrically distinct species on PEI, whilst evidence for a single species, comprising diverse genetically discrete populations was found on MI. Based on these results, the species unique to PEI has been designated Ectemnorhinus kuscheli n. sp. whilst we confirm the synonymy between E. similis and E. marioni, the two species originally described from MI. E. kuscheli appears to be restricted to PEI, whereas E. similis occurs on both MI and PEI.     

The effect of sample age and storage method on DNA yield and microsatellite amplification from baboon (Papio ursinus) faecal samples

Sampling methods that allow DNA collection without the physical handling of animals are popular in conservation genetics, but DNA isolated from faecal samples may be degraded, potentially leading to erroneous microsatellite genotyping results. We collected baboon faecal samples from fresh to 1-week post-defecation in a controlled sampling environment and preserved these using three storage techniques. After DNA isolation and quantification, the samples were genotyped at eight microsatellite loci. Quantitatively, DNA yield was highest when using silica as storage medium. However, microsatellite amplification from samples stored in 95% ETOH were most successful, with 100% success for fresh samples and dropping only marginally to 87.5% of loci for samples collected after 1 week. This disparity between quantitative and qualitative results suggests that total DNA concentrations do not necessarily provide a reliable indication of the amount of target DNA present in a DNA isolate. Our results nevertheless confirm that microsatellite fragments can successfully be amplified from faecal samples up to 1 week post-defecation, with careful selection of storage protocols and loci.     

Modelling the effectiveness of contraception for controlling introduced populations of elephant in South Africa

Re‐introduced African elephant (Loxodonta africana Blumenbach) populations are growing at very high rates in many of southern Africa’s reserves, have attained densities higher than previously thought possible and may be exhibiting irruptive growth. Active management of such populations is necessary to prevent the potentially negative effects on habitat and biodiversity that are associated with elephant overpopulation. One potentially feasible method of elephant management is immunocontraception, but very little is known about the long‐term effectiveness of this method. Using demographic data from three South African elephant populations, we made model projections of the effects of contraception on population growth rates to determine whether contraception may be a feasible management tool for elephant. In comparison with noncontracepted populations, realistic reductions in population growth rate after 20 years of contraception were projected to be up to c. 64%, with 50% being a very feasible target. Through its ability to reduce population growth rates, immunocontraception should be an effective tool for preventing or minimizing irruption in elephants and, perhaps, other introduced ungulate species.