We combined evidence from biogeography, craniodental traits, linear and geometric morphometrics (233 skulls), cytogenetics (karyotypes of 18 individuals) and mitochondrial DNA sequences (44 cytochrome b and 21 12S rRNA sequences) to test species limits within Otomys typus s.l. (Muridae: Murinae: Otomyini), a complex that is patchily distributed across alpine zones of Ethiopia and East Africa. Our results confirm the specific validity of O. dartmouthi, O. jacksoni, O. orestes, and O. uzungwensis, forms recently removed from synonymy under typus s.l.; support elevation of four other alpine forms to species (O. fortior, O. helleri, O. thomasi, and O. zinki); identify three additional new species (O. cheesmani sp. nov., O. simiensis sp. nov., O. yaldeni sp. nov.); and enable redefinition of O. typus s.s. as a species restricted to certain mountains west of the Great Rift Valley in Ethiopia (Simien and Guna Mountains in the north, extending to the highlands of the western rim of the Rift Valley). Phylogenetic interpretation of the cytochrome b data clearly demonstrates that the alpine morphotype once united under O. typus s.l. has originated independently at high elevations on several mountain ranges in eastern and northeastern Africa; although generally adapted to high-elevation vegetation, such alpine species are ecologically segregated from one another. Patterns of morphometric, genetic, and ecological differentiation among populations once misassigned to nominal O. tropicalis and O. typus more parsimoniously reflect regional cladogenesis along elevational gradients, rather than multiple, successive colonization by different ancestral forms from southern Africa as earlier supposed. Although incomplete and preliminary, information gathered for O. tropicalis indicates that it too is a species composite; several lines of research are discussed to redress its polyphyletic content. Our results, together with other recent taxonomic studies of Otomys, appreciably elevate the level of endemism within eastern Africa and underscore the significance of Africa's eastern highlands to the continental diversification of Otomyini.

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, primarily focusing on proper filtering of RAD data and selecting optimal parameters for data processing in polyploid lineages. We used the resulting high‐quality SNP dataset to investigate the population genetic structure of L. natalensis. A small number of mitochondrial markers present in these data had disproportionate influence on the recovered genetic structure. The presence of singleton SNPs also confounded genetic structure. We found a well‐supported division into northern and southern lineages, with further subdivision into five populations, one of which reflects north–south admixture. Approximate Bayesian Computation scenario testing supported a scenario where an ancestral population diverged into northern and southern lineages, which then diverged to yield the current five populations. All river systems showed similar levels of genetic diversity, which appears unrelated to drainage system size. Nucleotide diversity was highest in the smallest river system, the Mbokodweni, which, together with adjacent small coastal systems, should be considered as a key catchment for conservation.

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 approach appear to be unaware that many single nucleotide polymorphisms (SNPs) identified from genome-wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses.

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Eight polymorphic microsatellite loci, containing simple tetranucleotide repeats, were isolated de novo from a Pomatomus saltatrix partial genomic library using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol. These loci were further characterized in 100 individuals from two putative populations off the South African east coast. The loci are highly polymorphic with 18-37 alleles (on average 24 alleles/locus) and the observed heterozygosity in both populations was high (0.79). These loci will be used to assess population structuring in P. saltatrix along the southern African coast with consideration of implications for future management of this important linefish species.

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 was polymorphic in M. paradoxus and 10 in M. capensis. Two markers could individually discriminate the species using Bayesian clustering methods and a statistical power analysis showed that the set of markers for each species is likely to detect subtle genetic differentiation (F ST < 0.006), which will be valuable to delimit and characterise genetic stocks.Key words: Bayesian methods; cross-species amplification; genetic markers; genomic library; power analysis 1 Both the shallow-water hake Merluccius capensis Castelnau, 1861 and the deep-water hake M.paradoxus Franca, 1960 are targeted by a valuable demersal fishery along the west coasts of Southern Africa (>100 million USD annually; Butterworth & Rademeyer, 2005), but the intensification of exploitation over recent decades caused a resource decline (Payne & Punt, 1995). Due to their morphological similarity and overlapping distribution, the two species are not distinguished in the commercial landings records (von der Heyden et al., 2007b) and they are combined into geographic managements units, namely Namibia, west coast and south coast of South Africa (Butterworth & Rademeyer, 2005). Previous genetic surveys successfully distinguished the two species (Grant et al., 1987; von der Heyden et al., 2007b; Garcia-Vazquez et al., 2012) and detected population differentiation (Grant et al., 1987; von der Heyden et al., 2007a) using mtDNA markers and allozymes. Since these markers are inadequate to draw final conclusions regarding stock delimitation, highly informative markers such as microsatellites are necessary (Selkoe et al., 2006).To provide reliable genetic markers for species identification and stock delimitation in the two Cape hake species, the resolution power of newly developed and previously published microsatellites is assessed. The development of de novo microsatellite markers is presented.The discriminating power of each microsatellite for the correct identification of species was evaluated. A simulation approach was used to assess the robustness of each set of markers in detecting subtle genetic differentiation. 2Total genomic DNA was isolated using the DNeasy tissue extraction kit (Qiagen, www.qiagen.com). A partial genomic library enriched using two sets of four tetranucleotide repeat probes (TATC/AGCA/GCGA/CAGC and GATA/GTCT/GAAA/ACGT) was generated for M.paradoxus following Zane et al. (2002). A total of 585 clones was selected and sequenced and Msatcommander 0.8.2 (Faircloth, 2008) was used to identify 213 sequences containing repeats and design 141 primers after exclusion of duplicates (Table SI each genotype to the correct species with high accuracy ( Fig. 1; Fig. 2). All the other markers cannot individually discriminate the species even though some show 100% private all...

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Mangrove forests are among the most important ecosystems with high ecological and economic value. In order to better understand and conserve this ecosystem, we aim to provide an overview of mangrove structure along the southern, central and northern parts of Mozambique, in Costa do Sol (CS), Bons Sinais Estuary (BSE) and Pemba-Metuge (PM), respectively. A total of 10 plots/site (10 × 10 m) along a transect perpendicular to the seashore were used. Inside the plots, the stem diameter and height were measured, and the species identified. The phenology and deforestation were categorized, and dead stumps were identified by species and its diameter measured. A total of five mangrove CONTACT Faura M. C.