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Several Prosopis species and provenances were introduced in Kenya, either as a single event or repeatedly. To date, naturally established Prosopis populations are described as pure species depending on site, despite the aforementioned introduction of several species within some sites. To determine whether naturally established stands consist of a single or mixture of species, six populations from Bamburi, Bura, Isiolo, Marigat, Taveta and Turkwel were compared for relatedness with reference to Prosopis chilensis, Prosopis juliflora and Prosopis pallida using random amplified polymorphic DNA markers. Cluster analysis based on Nei’s genetic distance clustered Kenyan populations as follows: Marigat, Bura and Isiolo with P. juliflora, Bamburi with P. pallida and Taveta with P. chilensis, whereas the Turkwel population is likely to be a hybrid between P. chileneis and P. juliflora. Four populations had private markers, revealing germplasm uniqueness. Expected heterozygosity tended to be larger for Kenyan populations (ranging from 0.091 to 0.191) than in the three reference (ranging from 0.065 to 0.144). For the six Kenyan populations and two P. juliflora provenances from the Middle East, molecular variation was larger within populations than between population. Higher molecular variance among populations is attributed to their geographical separation and the low variation within populations is due to gene flow between individuals within a population. Overall, this study shows that (1) the Kenyan Prosopis populations are genetically isolated, (2) multiple introductions enhanced genetic diversity within sites and (3) P. juliflora and its hybrid are the most aggressive invaders.Key words: Prosopis chilensis, Prosopis juliflora, Prosopis pallida, multiple introductions, genetic diversity.

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.