Aim The origins of much Neotropical biodiversity remain a topic of debate, with both palaeogeographical and more recent climatic drivers playing a role in diversification both among and within species. Here we use a combination of molecular data to assess genetic variation within and among species in the Neotropical tree genus Cedrela, with a focus on Cedrelaodorata, to test hypotheses on the drivers of diversification, to place known ecotypic variation in context and to detect intraspecific phylogeographical structure. Location Central and South America, Cuba, Cayman Islands, Trinidad and Guadeloupe. Methods Samples were collected from the field, existing collections and herbaria from across the geographical range, including a total of 528 individuals from 72 sites. A phylogenetic framework was constructed using internal transcribed spacer (ITS) sequence data (intergenic spacers plus flanking 18S and 26S regions), and genetic structure was analysed using a combination of chloroplast DNA sequences (trnCycf6, trnHpsbA) and chloroplast and nuclear microsatellite (single sequence repeat, SSR) loci. Phylogenetic reconstruction was undertaken using a combination of Bayesian and parsimony-based approaches; divergence times were estimated for major nodes. Geographical structure in chloroplast SSR data was analysed using SAMOVA, while that in nuclear SSR data was assessed using a combination of Bayesian clustering and principal coordinates analysis. Results ITS sequence data supported phylogenetic distinctiveness of four morphologically cryptic species within C. odorata. Chloroplast sequence and microsatellite data showed geographical structuring both among and within species, suggesting the influence of climatic and geographical drivers. Intraspecific genetic divergence was also present in nuclear microsatellite data, suggesting contemporary gene flow limitation across sea and mountain barriers. Main conclusions The data support diversification of the genus Cedrela in South America with subsequent recolonization into Central America prior to the formation of the Isthmus of Panama. At least four morphologically cryptic taxa were evident within C. odorata and within-species phylogeographical divergence across the Andes and within Central America was present, the latter suggestive of Pleistocene climatic influence. Previously recognized ecotypes in Central America should be elevated to species level. The new molecular data support the recent reclassification and will support the monitoring of exploitation in the genus.

In the present work, we report the development of 11 microstallite markers (SSR) for Punica granatum. Evaluated on a set of 27 pomegranate accessions sampled in Tunisia, they displayed 25 alleles, with number of alleles per locus ranging between 1 and 4, and an observed heterozygosity from 0.037 and 0.592. This set of SSR markers can be very useful for studies dealing with genetic diversity assessment of germplasm, with cultivars/varieties fingerprinting and pedigree analysis of this economically important fruit species.

We developed eight polymorphic nuclear microsatellite markers for the Swiss stone pine (Pinus cembra L.), of which seven may be amplified in a multiplex polymerase chain reaction. Allelic polymorphism across all loci and 40 individuals representing two populations in the Swiss Alps was high (mean = 7.6 alleles). No significant linkage disequlibrium was displayed between pairs of loci. Significant deviation from Hardy-Weinberg equilibrium was revealed at three loci in one population. Cross-amplification was achieved in two related species within the genus (P. sibirica and P. pumila). Thus, the markers may be useful for population genetic studies in these three pine species. They will be applied in ongoing projects on genetic diversity and patterns of gene flow in P. cembra.

Paternal apomixis was recently reported in the endangered Mediterranean cypress, Cupressus dupreziana. This species acts as a surrogate mother for the development of all-paternal embryos from pollen grains. C. dupreziana production of Cupressus sempervirens haploid or diploid seedlings from C. sempervirens pollen was also demonstrated. The haploid progeny was derived from the embryogenic development of haploid gametes, but the origin of the diploid progeny remained unknown. To determine the ontogenic origin of the diploid C. sempervirens progeny, we analyzed the heterozygozity of 63 diploid all-paternal C. sempervirens seedlings using highly variable co-dominant nuclear microsatellite markers. The bi-parental inheritance of the markers was checked in C. sempervirens controlled crosses. A high level of polymorphism was observed among the diploid all-paternal trees. All but three individuals exhibited single-band profiles as expected for homozygotes, which may originate from natural diploidization of a C. sempervirens haploid embryo or from the fusion of two male gametes produced by the same C. sempervirens microgametophyte. The three heterozygous seedlings must be derived from the fusion of male gametes produced by two different C. sempervirens microgametophytes. These findings offer a unique opportunity in conifers to produce homozygous lines, highly valuable for genetic analyses or breeding.

This study represents the first large-scale analysis using nuclear molecular markers to assess genetic diversity and structure of Cupressus sempervirens L.. Genetic and fossil data were combined to infer the possible role of human activity and evolutionary history in shaping the diversity of cypress populations. We analysed 30 populations with six polymorphic nuclear microsatellite markers. Dramatic reductions in heterozygosity and allelic richness were observed from east to west across the species range. Structure analysis assigned individuals to two main groups separating central Mediterranean and eastern populations. The two main groups could be further divided into five subgroups which showed the following geographical distributions: Turkey with the Greek islands Rhodes and Samos, Greece (Crete), Southern Italy, Northern Italy, Tunisia with Central Italy. This pattern of genetic structure is also supported by SAMOVA and Barrier analyses. Palaeobotanical data indicated that Cupressus was present in Italy in the Pliocene, Pleistocene and Holocene. Furthermore, our molecular survey showed that Italian cypress populations experienced bottlenecks that resulted in reduced genetic diversity and allelic richness and greater genetic differentiation. Recent colonization or introduction may also have influenced levels of diversity detected in the Italian populations, as most individuals found in this range today have multilocus genotypes that are also present in the eastern range of the species. The data reveal a new interpretation of the history of cypress distribution characterized by ancient eastern populations (Turkey and Greek islands) and a mosaic of recently introduced trees and remnants of ancient, depauperate populations in the central Mediterranean range.

This article documents the addition of 283 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Agalinis acuta; Ambrosia artemisiifolia; Berula erecta; Casuarius casuarius; Cercospora zeae-maydis; Chorthippus parallelus; Conyza canadensis; Cotesia sesamiae; Epinephelus acanthistius; Ficedula hypoleuca; Grindelia hirsutula; Guadua angustifolia; Leucadendron rubrum; Maritrema novaezealandensis; Meretrix meretrix; Nilaparvata lugens; Oxyeleotris marmoratus; Phoxinus neogaeus; Pristomyrmex punctatus; Pseudobagrus brevicorpus; Seiridium cardinale; Stenopsyche marmorata; Tetranychus evansi and Xerus inauris. These loci were cross-tested on the following species: Agalinis decemloba; Agalinis tenella; Agalinis obtusifolia; Agalinis setacea; Agalinis skinneriana; Cercospora zeina; Cercospora kikuchii; Cercospora sorghi; Mycosphaerella graminicola; Setosphaeria turcica; Magnaporthe oryzae; Cotesia flavipes; Cotesia marginiventris; Grindelia Xpaludosa; Grindelia chiloensis; Grindelia fastigiata; Grindelia lanceolata; Grindelia squarrosa; Leucadendron coniferum; Leucadendron salicifolium; Leucadendron tinctum; Leucadendron meridianum; Laodelphax striatellus; Sogatella furcifera; Phoxinus eos; Phoxinus rigidus; Phoxinus brevispinosus; Phoxinus bicolor; Tetranychus urticae; Tetranychus turkestani; Tetranychus ludeni; Tetranychus neocaledonicus; Tetranychus amicus; Amphitetranychus viennensis; Eotetranychus rubiphilus; Eotetranychus tiliarium; Oligonychus perseae; Panonychus citri; Bryobia rubrioculus; Schizonobia bundi; Petrobia harti; Xerus princeps; Spermophilus tridecemlineatus and Sciurus carolinensis.

Landraces are domesticated local plant varieties that did not experience a deliberate and intensive selection during a formal breeding programme. In Europe, maize landraces are still cultivated, particularly in marginal areas where traditional farming is often practiced. Here, we have studied the evolution of flint maize landraces from central Italy over 50 years of on‐farm cultivation, when dent hybrid varieties were introduced and their use was widespread. We have compared an ‘old’ collection, obtained during the 1950s, before the introduction of hybrids, and a recent collection of maize landraces. For comparison, a sample of maize landraces from north Italy, and of improved germplasm, including hybrids and inbred lines were also used. A total of 296 genotypes were analysed using 21 microsatellites. Our results show that the maize landraces collected in the last 5–10 years have evolved directly from the flint landrace gene pool cultivated in central Italy before the introduction of modern hybrids. The population structure, diversity and linkage disequilibrium analyses indicate a significant amount of introgression from hybrid varieties into the recent landrace populations. No evidence of genetic erosion of the maize landraces was seen, suggesting that in situ conservation of landraces is an efficient strategy for preserving genetic diversity. Finally, the level of introgression detected was very variable among recent landraces, with most of them showing a low level of introgression; this suggests that coexistence between different types of agriculture is possible, with the adoption of correct practices that are aimed at avoiding introgression from undesired genetic sources.

We have developed a set of eight polymorphic nuclear microsatellite markers for the Mediterranean shrub Pistacia lentiscus by means of an enriched library method. Characterization for the eight loci was carried out on 42 individuals from two populations sampled in southern Spain. The overall number of alleles detected was 59, ranging from three to 13 per locus. Expected heterozygosity per locus and population ranged from 0.139 to 0.895. Two loci albeit only in one population (Seville) departed significantly from Hardy–Weinberg equilibrium expectations and no linkage disequilibrium between pairs of loci was detected. These markers will be used in studies of gene flow across a fragmented landscape.