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 sampling sites (five along the South African coastline, one each in Angola, Senegal and Portugal) were chosen to examine the population genetic structure and phylogeographic history of the cosmopolitan bluefish (Pomatomus saltatrix), distributed across a large South-east Atlantic upwelling zone. Molecular analyses were applied to mtDNA cytochrome b, intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically high genetic differentiation (F 0.15-0.20; P<0.001) between the fish sampled from South Africa and the other sites, strongly influenced by five outlier microsatellite loci located in conserved intergenic regions. In addition, differentiation among the remaining East Atlantic sites was detected, although mtDNA indicated past isolation with subsequent secondary contact between these East Atlantic populations. We further identified secondary contact, with unidirectional gene flow from South Africa to Angola. The directional contact is likely explained by a combination of the northward flowing offshore current and endogenous incompatibilities restricting integration of certain regions of the genome and limiting gene flow to the south. The results confirm that the dynamic system associated with the Benguela current upwelling zone influences species distributions and population processes in the South-east Atlantic.
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...
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 formulation of practical actions for long-term conservation of biodiversity, with the particular goal of maintaining ecological and evolutionary processes. Given the inclusion of specific goals and targets regarding DSI in the latest draft of the Global Biodiversity Framework negotiated at the 15 th Conference of the Parties (COP15) in Montreal in December 2022 and the crucial decisions on access and benefit sharing to DSI that will be taken in the coming months and future COP meetings, a southern African perspective on how and why open access to DSI is essential for the conservation of intraspecific biodiversity (genetic diversity and structure) across country borders is provided.
ASPLENIUM LOBATUM VAR. PSEUDO-ABYSSINICUM, A NEW RECORD FOR SOUTH AFRICA
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