Aim  The genus Prosopis includes 44 species and has a pseudoamphitropical, disjunct distribution. We aimed to determine whether American Prosopis sections arose in North or South America, and to explain the current distribution of their species on the basis of their genetic relationships. Location  South‐western USA, Mexico, Caribbean Antilles, Peru–Ecuador, central and northern Argentina, south‐western Argentina (Patagonia) and Cuyo, south‐western Asia and northern Africa. Methods  Internal transcribed spacer fragments from 21 species of Prosopis were sequenced and the data were used to analyse the phylogenetic relationships using Microlobius and Mimosa as outgroups. Genetic distances were calculated to estimate the degree of divergence. Dispersal–vicariance (DIVA) analysis was conducted to help understand the biogeographical history of the genus. Main conclusions  The sections Strombocarpa and Algarobia are not monophyletic. Prosopis argentina (section Monilicarpa) and the species of Algarobia are included in single clade. The phylogeny, DIVA analysis, and the pattern of genetic distances indicate that the ancestral area for the American species was wide, from south‐western USA to Central and northern Argentina. Successive vicariance events split this area, and long‐distance dispersal episodes (perhaps mediated by birds) led to recolonizations from North to South America, and vice versa.

The section Algarobia of genus Prosopis involves important natural resources in arid and semiarid regions of the world. Their rationale use requires a better knowledge of their biology, genetics and mating system. There are contradictory information about their mating system. Some authors claim they are protogynous and obligate outcrosser. However, some evidence have been shown indicating that they might not be protogynous and that they might be somewhat self-fertile. The current paper analyses genetic structure and mating system parameters in populations of seven species of this section from South and North America based on isozyme data. In all species a significant homozygote excess was found in the offspring population but not in mother plant genotypes. Multilocus and mean single locus outcrossing rates (tm, ts) indicated that about 15% selfing can occur in the studied populations. The heterogeneity between pollen and ovule allele frequencies was low suggesting population structuration, in agreement with the estimates of correlation of tm within progeny (rt) and correlation of outcrossed paternity (rp). The difference of FIS estimates between offspring and mother plants suggest some selection favouring heterozygotes between seedling and adult stages.

Prosopis represents a valuable forest resource in arid and semiarid regions. Management of promising species requires information about genetic parameters, mainly the heritability (h(2)) of quantitative profitable traits. This parameter is traditionally estimated from progeny tests or half-sib analysis conducted in experimental stands. Such an approach estimates h(2) from the ratio of between-family/total phenotypic variance. These analyses are difficult to apply to natural populations of species with a long life cycle, overlapping generations, and a mixed mating system, without genealogical information. A promising alternative is the use of molecular marker information to infer relatedness between individuals and to estimate h(2) from the regression of phenotypic similarity on inferred relatedness. In the current study we compared h(2) of 13 quantitative traits estimated by these two methods in an experimental stand of P. alba, where genealogical information was available. We inferred pairwise relatedness by Ritland's method using six microsatellite loci. Relatedness and heritability estimates from molecular information were highly correlated to the values obtained from genealogical data. Although Ritland's method yields lower h(2) estimates and tends to overestimate genetic correlations between traits, this approach is useful to predict the expected relative gain of different quantitative traits under selection without genealogical information.

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• Premise of the study: As only six useful microsatellite loci that exhibit broad cross-amplification are so far available for Prosopis species, it is necessary to develop a larger number of codominant markers for population genetic studies. Simple sequence repeat (SSR) markers obtained for Prosopis species from a 454 pyrosequencing run were optimized and characterized for studies in P. alba and P. chilensis.• Methods and Results: Twelve markers that were successfully amplified showed polymorphism in P. alba and P. chilensis. The number of alleles per locus ranged between two and seven and heterozygosity estimates ranged from 0.2 to 0.8. Most of these loci cross-amplify in P. ruscifolia, P. flexuosa, P. kuntzei, P. glandulosa, and P. pallida.• Conclusions: These loci will enable genetic diversity studies of P. alba and P. chilensis and contribute to fine-scale population structure, indirect estimation of relatedness among individuals, and marker-assisted selection.

In the present work, isoenzyme electrophoresis was used to analyze the variability and phenetic relationships among seven American species of genus Prosopis belonging to three different sections: P. argentina (Monilicarpa), P. glandulosa, P. velutina, P. flexuosa, P. ruscifolia, P. kuntzei (Algarobia), and P. reptans (Strombocarpa). The genetic variability in P. argentina, P. reptans, and P. kuntzei was significantly lower than in the rest of the species analyzed. The species belonging to different sections are highly differentiated, but the relationships retrieved among species belonging to the section Algarobia suggested that the series of this section are not natural groups. P. kuntzei is as differentiated from the remaining species of Algarobia as from P. reptans or P. argentina, suggesting that this species might be included in a different section. The series within section Algarobia are not supported by the clusters retrieved in the phenogram based on isoenzymatic data. The results suggest that the two North American species (P. velutina and P. glandulosa) would have originated in different founder events.

Allozyme and random amplified polymorphic DNA (RAPD) techniques have been compared for their usefulness for genetic and taxonomic studies in Prosopis glandulosa and P. velutina populations. Isozymes and RAPDs yielded similarly high estimates of genetic variability. Genetic structure and differentiation were analyzed through non-hierarchical Wright's F DT . For all populations considered, both markers produced low gene flow (Nm < 1) estimates. When only P. glandulosa populations were analyzed, isozyme data yielded higher gene flow estimates (Nm > 1), in agreement with that expected for conspecific populations. However, in RAPD data the expected reduction in F DT and the increase in Nm were not observed. Correlation between F DT and geographical distance matrices (Mantel test) for all populations was significant (P = 0.02) when based on isozymes, but not so (P = 0.33) when based on RAPDs. No significant associations among genetic and geographical or climatic variables were observed. Two isoenzyme systems (GOT and PRX) enabled us to distinguish between P. glandulosa and P. velutina, but no diagnostic band for recognition of populations or species studied here were detected by RAPD. However, RAPD markers showed higher values for genetic differentiation among conspecific populations of P. glandulosa and a lower coefficient of variation than those obtained from isozymes.