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Data on genetic diversity and differentiation, as well as kinship between individuals, are important for the conservation of animal and plant genetic resources. Often genetic assignment is part of law enforcement of protected endangered species. The software GDA-NT 2021 is a new, freely available user-friendly Windows program that can be used to compute various measures of genetic diversity and population genetic differentiation. It further allows genetic assignment of individuals to populations and enables the calculation of kinship-coefficients and genetic distances among pairs of individuals within populations. GDA-NT 2021 specifically computes the alternative measures for population differentiation Dj and the standardized FST of Hedrick. It has more options to compute exclusion-probabilities in assignment tests, enables self-assignment tests for variable groups of individuals, and allows for information on geographic positions to be accounted for while using permutation tests to assess statistical significance.

Local adaptation is key for ecotypic differentiation and species evolution1. Understanding the underlying genomic patterns allows the prediction of future maladaptation and ecosystem stability2. Here we report the whole-genome resequencing of 865 individuals from 100 range-wide populations of European beech (Fagus sylvatica), which is one of the most important forest tree species in Europe. We show that genetic variation closely mirrors geography. Adaptive variation identified by genotype-environment associations exhibits highly polygenic architectures, involving thousands of associated sequence variants across the genome. By modelling the ‘genomic offset’ of these sequence variants under projected future climate conditions, we identify broad- and fine-scale variation highlighting geographic regions as well as populations at potential elevated risk of mortality or local extinction. Our results emphasize the importance of considering natural genetic variation for forest conservation under climate change conditions.

Pedunculate oak is seen as an alternative to other tree species for reforestation and mitigation programs in the face of climate change. Thus, the identification of suitable, well-adapted seed sources is of high priority. We perform a genetic inventory on 970 trees from 97 locations in Russia, Belarus, Ukraine and Latvia representing the eastern part of the natural species range. All samples were screened with a set of 348 gene markers covering the nuclear (n = 327) and the organelle genomes (chloroplast: n = 14, mitochondria: n = 7) using a genotyping-by-sequencing method. We identified 10 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 600 km. After excluding 47 potentially selected markers, significant spatial genetic structure up to 800 km was also observed at the selectively neutral nuclear loci. Bayesian clustering analysis indicated a sub-division into two gene pools present at all locations but with a shift of proportion from West to East. The genetic diversity was negatively correlated with longitude, showing higher values in the West and Centre and lower values at the northern, eastern and southeastern edges of the natural distribution range. We sub-divided the sampled area into six geographic regions and used the genetic composition of all samples in each region as a genetic reference for assignment tests. Self-assignment of groups of 10 individuals to their region of origin showed an average assignment success of 93 per cent. Samples of three artificial plantations of pedunculate oak in Siberia could be clearly assigned to the East–North and Centre–South regions. We discuss the implications of our results for the forest practice and in particular the proofing of seed sources.

Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughput phenotyping enable genome-wide association studies (GWAS) and the identification of SNPs underlying traits with complex genetic architectures. The identified causal SNPs and estimated allelic effects could then be used for advanced marker-assisted selection (MAS) in breeding programs. But could such MAS compete with the broadly used genomic selection? This question is of particular interest for the lengthy tree breeding strategies. Here, with our new software SNPscan we simulated a simple tree breeding program and compared the impact of different selection criteria on genetic gain and inbreeding. Further, we assessed different genetic architectures and different levels of kinship among individuals of the breeding population. Interestingly, apart from progeny-testing, genomic selection (GS) using gBLUP performed best under almost all simulated scenarios. MAS based on GWAS results outperformed GS only if the allelic effects were estimated in large populations (ca. 10,000 individuals) of unrelated individuals. Notably, GWAS using 3,000 extreme phenotypes performed as good as the use of 10,000 phenotypes. Genomic selection increased inbreeding and thus reduced genetic diversity more strongly compared to progeny testing and GWAS-based selection. In conclusion, our analyses further support the potential of genomic selection for forest tree breeding and improvement although MAS may gain relevance with decreasing sequencing costs in the future.

The large-scale spatial genetic structure of European beech, Fagus sylvatica, has been until now poorly studied. We conducted double digest RAD sequencing (ddRADseq) on 54 beech individuals stemming from 36 provenances to discover spatially informative nuclear SNP loci. In addition, two pools derived from 14 early and 14 late flushing individuals each were sequenced with Illumina HiSeq. From an initial amount of 5,464 loci detected by ddRADseq, we selected 559 informative loci. Further 27 additional loci showing significant allelic differences among early and late flushing individuals could be identified after a genotyping on 95 test individuals. The final selection of 578 loci was submitted to probe design for targeted genotyping by sequencing, which yielded 543 loci. The new set of SNP loci should be, after validation on a larger sample size, useful for large-scale genetic studies in this economically-important species.

The aim of this study is to determine the genetic variability and differentiation among populations of pedunculate oak (Quercus robur) at the eastern margin of the species distribution range. We applied new set of 95 geographically informative nuclear SNP (single nucleotide polymorphism) loci developed using Double Digest Restriction Site Associated DNA (ddRAD), a new generation DNA sequencing technology. The study area is located in the basins of the Volga River and its two main tributaries, Kama and Belaya. Despite the strong reduction and fragmentation of pedunculate oak forests over the last several centuries and comparatively small sizes of present stands, a relatively similar genetic diversity of seven populations was observed (on average, allelic diversity υа = 1.472–1.603, observed heterozygosity HO = 0.305–0.358, expected heterozygosity HE = 0.272–0.343). The genetic distances between populations vary between 0.102 and 0.170 (on average, d0 = 0.128). We have identified the absence of a spatial genetic structure and the existence of genetically peculiar populations in the territory studied. The genetic distances of Gregorius between populations vary between 0.102 and 0.170 (on average, d0 = 0.128). Genetic differentiation among populations was statistically significant with a mean of the fixation index FST of 0.075. Populations from the Privolzhye Upplands and from northern parts of the study area make the most contribution to overall inter-population differentiation (d0 = 0.137). No significant differences exist among the samples at lowlands along the Volga river (d0 = 0.110). It was concluded that the multiplicity and different ages of local populations and the complexity of migration routes of the pedunculate oak from Pleistocene refugia and secondary Holocene shelters can cause this phenomenon.

Analysis of wolves dietary is a currently important theme because of the discussion about wolves preying on livestock as sheep or goats. We developed molecular markers to especially amplify the DNA of the prey out of wolf scat. For this purpose, we used the mitochondrial D-Loop using public available sequences for wolf and seven potential prey species (even-toed ungulates). We developed special primers amplifying either the wolves DNA or the prey DNA. In a fragment of 223-225 basepairs (bp) length we identified 21 SNPs, two 1-bp indels and one 3-bp indel, and three microsatellites to separate seven prey species from each other. Validation of the markers was performed by sequencing the PCR products of 12 fresh prey tissues and 20 wolf scat samples using the different primer pairs.

We used Double Digest Restriction site associated DNA sequencing (ddRAD) and Miseq to develop new geographically informative nuclear and plastid SNP and indel loci in Quercus robur and Q. petraea. Genotypes derived from sequence data of 95 individuals and two pools of 20 individuals each of Q. robur and Q. mongolica covering the distribution range of the species, were analysed to select geographically informative and polymorphic loci within Germany and Russia. We successfully screened a selected set of 431 nuclear single nucleotide polymorphism (nSNP), six nuclear Indel, six mitochondrial single nucleotide polymorphism (mtSNP) and ten chloroplast single nucleotide polymorphism (cpSNP) loci with a SeqSNP genotyping platform on 100 individuals Quercus petraea from 10 locations in Germany, 100 individuals Quercus robur from ten locations in Germany and 100 individuals Quercus robur from ten locations in Russia. The newly developed loci are useful for species identification and genetic studies on the genetic diversity and genetic differentiation of Quercus robur and Quercus petraea in Europe.

As for most other temperate broadleaved tree species, large-scale genetic inventories of pedunculate oak (Quercus robur L.) have focused on the plastidial genome, which showed the impact of post-glacial recolonization and manmade seed transfer. However, how have pollen mediated gene flow and introgression impacted the large-scale genetic structure? To answer these questions, we did a genetic inventory on 1970 pedunculate oak trees from 197 locations in 13 European countries. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs, and 5 mitochondrial SNPs). In a former analysis with additional 1763 putative Quercus petraea trees screened for the same gene markers we obtained estimates on the species admixture of all pedunculate oak trees. We identified 13 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 1250 km. Significant spatial genetic structure up to 1250 km was also observed at the nuclear loci. However, the differentiation at the nuclear gene markers was much lower compared to the organelle gene markers. The matrix of genetic distances among locations was partially correlated between nuclear and organelle genomes. Bayesian clustering analysis revealed the best fit to the data for a sub-division into two gene pools. One gene pool is dominating the west and the other is the most abundant in the east. The western gene pool was significantly influenced by introgression from Quercus petraea in the past. In Germany, we identified a contact zone of pedunculate oaks with different introgression intensity, likely resulting from different historical levels of introgression in glacial refugia or during postglacial recolonization. The main directions of postglacial recolonization were south to north and south to northwest in West and Central Europe, and for the eastern haplotypes also east to west in Central Europe. By contrast, the pollen mediated gene flow and introgression from Q. petraea modified the large-scale structure at the nuclear gene markers with significant west–east direction.

INISEFOR Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™ genotyping. These markers can be used for population genetic studies and timber tracking purposes. Las especies de Swietenia son las maderas tropicales estadounidenses más valiosas y han sido muy sobreexplotadas durante décadas. los Tres especies están incluidas como vulnerables o en peligro de extinción por la UICN y están incluidas en el Apéndice II de la CITES, pero son ilegales. la explotación continúa. Aquí, utilizamos la secuenciación de ADN asociada a la restricción para desarrollar un nuevo conjunto de 120 marcadores SNP para Swietenia sp., Adecuada para el genotipado MassARRAY®iPLEX ™. Estos marcadores se pueden utilizar para estudios genéticos de poblaciones. y seguimiento de la madera. As espécies de Swietenia são as madeiras tropicais americanas mais valiosas e têm sido fortemente superexploradas por décadas. As três espécies estão listadas como vulneráveis ​​ou em perigo pela IUCN e estão incluídas no Apêndice II da CITES, mas a exploração ilegal continua. Aqui, usamos o sequenciamento de DNA associado à restrição para desenvolver um novo conjunto de 120 marcadores SNP para Swietenia sp., Adequado para genotipagem MassARRAY®iPLEX ™. Esses marcadores podem ser usados ​​para estudos de genética populacional e fins de rastreamento de madeira. Thünen Institute of Forest Genetics, Germany Instituto Nacional de Pesquisas da Amazônia, Brazil Universidad Nacional, Costa Rica Centre for Ecology & Hydrology, United Kingdom Instituto Florestal de São Paulo, Brazil University of Bordeaux, France Mahogany for the Future Inc., USA Bush Estate, United Kingdom Instituto de Investigación y Servicios Forestales

Made available in DSpace on 2019-10-06T15:52:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01 Illegal logging and trade of timber are major worldwide concerns, resulting in biodiversity and economic losses. Tropical tree species in the genus Cedrela, which have historically been heavily exploited, are still often illegally traded and there is an urgent need to develop tools to verify the origin of Cedrela products. A set of 351 SNP loci for Cedrela species from Bolivia, Brazil, Costa Rica, Cuba, Ecuador, French Guiana, Mexico, and Peru was developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing, and adapted for MassARRAY genotyping. After screening of 94 individuals covering most of the distribution of Cedrela, a final set of 136 SNP loci which included 92 nuclear SNPs, 22 chloroplast markers (20 SNPs and 2 INDELs), and 22 mitochondrial markers (19 SNPs and 3 INDELs) was selected and tested for potential to verify Cedrela timber origin. Carrera de Ingeniería Forestal Laboratorio de Dendrocronología Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito Thünen Institute of Forest Genetics, Sieker Landstrasse 2 Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5 Instituto Florestal de São Paulo, CP 1322 Faculdade de Engenharia Universidade Estadual Paulista (Unesp) INRA UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane, Campus Agronomique, Avenue de France Centre for Ecology & Hydrology Edinburgh, Bush Estate Faculdade de Engenharia Universidade Estadual Paulista (Unesp)

We studied the genetic composition of 200 pedunculate oak (Quercus robur) trees at nine nuclear microsatellite gene loci. We sampled nine locations in an area of 1100 km by 400 km in the South-Ural. The question was to analyse the genetic differentiation of the oaks at the south-east edge of the species distribution area. We observed relatively high values of genetic differentiation and fixation (delta=0.387, F ST =0.0652, F ST(Hedrick) =0.407) compared to values from the centre of the species distribution range. Bayesian clustering analysis revealed three genetic groups. Presence of all genetic groups was detected at all locations, but oak trees in the extreme east of the Ural Mountains were genetically most different. We hypothesise that genetic drift influenced the observed pattern.

We developed a new set of 25 nuclear (nc), 12 chloroplast (cp) and 7 mitochondrial (mt) SNPs and used it to genotype 371 Mongolian oak (Quercus mongolica Fisch. ex Ledeb.) trees from seven locations in a 200 km by 400 km area in the Russian Far East. One of the locations in an area of 15 km by 25 km east of the city Ussuriusk was analyzed more intensively with 188 collected trees. The genetic differentiation at the nuclear SNPs was small to moderate and for the plastid SNPs it was high when considering all trees from the seven locations. The gene pool distances between locations were for 19 out of 21 pairs statistically highly significant. There was no correlation of genetic and spatial distances. Only three different multilocus-haplotypes could be identified and 42 two-loci-combinations of plastid SNPs could be used to identify them. Conclusions for the practical application such as timber tracking and gene conservation are discussed.

The timber of the species Lophira alata (azobe) is very popular for outdoor constructions, which favours its overexploitation and illegal logging. We sampled individuals from Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, Congo Brazzaville and Republic Democratic of Congo to discover new nuclear and plastidial SNP and INDEL loci through restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. From an initial set of 397 loci, a final set of 126 loci was selected for timber tracking purposes., SCOPUS: ar.j, info:eu-repo/semantics/published

Made available in DSpace on 2021-06-25T12:22:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-06-01 German Federal Ministry of Food and Agriculture (BMEL) by the LargeScale-project (Forderkennzeichen) Programa Nacional de Innovacion para la Competitividad y Productividad (Innovate Peru) Conseil Regional d'Aquitaine European Union, FEDER Investissements d'avenir Dipteryx timber has been heavily exploited in South America since 2000s due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to 6 different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial single nucleotide polymorphisms (SNPs), and 2 chloroplast and 5 mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78-96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in Dipteryx odorata and Dipteryx ferrea, obtaining self-assignment success rates of 91-100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbor approach (69-92%) compared to the Bayesian approach (33-80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber. Inst Invest Amazonia Peruana IIAP, Av Jose A Quinones Km 2-5, Iquitos, Peru Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745,EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRAE, BIOGECO, F-33610 Cestas, France Escola Nacl Bot Trop, Rua Pacheco Leao 2040, BR-22460030 Rio De Janeiro, RJ, Brazil Inst Pesquisas Jardim Bot Rio de Janeiro, Rua Pacheco Leao 915, BR-22460030 Rio De Janeiro, RJ, Brazil Univ Fed Bahia, Inst Biol, Rua Barao de Jeremoabo S-N, BR-40170115 Salvador, BA, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil German Federal Ministry of Food and Agriculture (BMEL) by the LargeScale-project (Forderkennzeichen): 281-001-01 Programa Nacional de Innovacion para la Competitividad y Productividad (Innovate Peru): 381-PNICP-PIAP-2014 Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01

There is a high international demand for timber from the genus Dipteryx, or “shihuahuaco” as it is known in Peru. Developing tools that allow the identification and discrimination of Dipteryx species is therefore important for supporting management of natural populations and to underpin legal trade of its timber. The objective of this study was the molecular characterization of Dipteryx species in the Peruvian Amazonia. Two plastid regions (cpDNA: trnH–psbA and matK) were sequenced and 11 microsatellite markers (nDNA) were genotyped for 32 individuals identified as Dipteryx charapilla, D. micrantha morphotype 1 and D. micrantha morphotype 2. Using the concatenated sequences of the plastid genes, we identified ten haplotypes that were not shared between the species or between the D. micrantha morphotypes. Haplotypic diversity was greater in D. micrantha morphotype 2 and D. charapilla than in D. micrantha morphotype 1, which presented only one haplotype with a wide distribution in Peru. The microsatellites allowed the discrimination of the same three clades and identified diagnostic alleles for each clade. These results allowed us to demonstrate that the two morphotypes of D. micrantha are different at both the plastid and nuclear markers, which supports the existence of three genetically distinct species in Peru. This study provides information for the genetic discrimination of Dipteryx species and emphasises the importance of conserving the genetic variability of this genus in the Peruvian Amazonia. Programa Nacional de Innovación para la Competitividad y Productividad Innóvate-Perú (contrato 381-PNICP-PIAP-2014); German Federal Ministry of Food and Agriculture (BMEL, Large Scale Project, Grant 28I-001-01) Revisión por pares.

We used double digest restriction site associated DNA sequencing (ddRAD) to develop new geographically informative nuclear SNP loci in Quercus robur and Quercus petraea. Genotypes derived from sequence data of 95 individuals covering the distribution range of the species were analysed to select geographically informative and polymorphic loci within Russia and Germany. We successfully screened a selected set of 119 loci on a MassARRAY® iPLEX™ platform on 190 individuals from 19 locations in Russia. The newly developed loci will be useful for genetic studies over the whole distribution range of both species.

Development of agriculture in the forest and forest-steppe zones of the vast East European plain over the past millennium has resulted to a significant decrease of broad-leaved forests habitat. It is expected that the disintegration of the forest tree species distribution ranges will lead to the erosion of the population genetic diversity of due to limited gene flow, impacts on gene pools of genetic drift and inbreeding. To investigate this threat, we analyzed the genetic diversity and differentiation among 20 populations of pedunculate oak (Quercus robur L.) from the Ural Mountains (Russia) and neighboring lowlands and foothills. A set of 412 nuclear SNPs loci was used for our study. A positive correlation (r = 0.168, p

Mit Auslaufen der im §40(4) Bundesnaturschutzgesetz (BNatSchG) gewahrten Ubergangsfrist im Jahr 2020 ergibt sich fur die Produzenten von Vermehrungsgut gebietseigener Geholze die Herausforderung, geeignete Saatgutquellen zu finden. Die Gewinnung von Saatgut in Samenplantagen kann eine wichtige Alternative zur Ernte in geeigneten Spenderpopulationen sein. Weder das BNatSchG noch der 'Leitfaden zur Verwendung gebietseigener Geholze' machen explizit Vorgaben fur die Anlage von Samenplantagen. Deshalb hat die Bund-Lander-Arbeitsgruppe 'Forstliche Genressourcen und Forstsaatgutrecht' einen Vorschlag fur Mindeststandards fur Plantagen auf der Basis populationsgenetischer Uberlegungen und vorhandener Regelungen in einzelnen Bundeslandern und in benachbarten europaischen Landern erarbeitet. Es werden Empfehlungen zu der Art und dem Umfang des Ausgangsmaterials, geeigneten Standorten einschlieslich der Isolation von einkreuzbaren Vorkommen, der Anlage von Plantagen und deren Beerntung formuliert.

During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregates and intend to identify the most likely group of origin. Often this grouping does not have a biological but rather a historical or political justification, such as "country of origin". In this paper, we present a new nearest neighbour approach to individual assignment or classification within a given but potentially imperfect grouping of reference samples. This method, which is based on the genetic distance between individuals, functions better in many cases than commonly used methods. We demonstrate the operation of our assignment method using two data sets. One set is simulated for a large number of trees distributed in a 120km by 120km landscape with individual genotypes at 150 SNPs, and the other set comprises experimental data of 1221 individuals of the African tropical tree species Entandrophragma cylindricum (Sapelli) genotyped at 61 SNPs. Judging by the level of correct self-assignment, our approach outperformed the commonly used frequency and Bayesian approaches by 15% for the simulated data set and by 5-7% for the Sapelli data set. Our new approach is less sensitive to overlapping sources of genetic differentiation, such as genetic differences among closely-related species, phylogeographic lineages and isolation by distance, and thus operates better even for suboptimal grouping of individuals.

Made available in DSpace on 2019-10-04T12:40:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture (BMEL) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest European Union, FEDER We developed nuclear and chloroplastic single nucleotide polymorphism (SNP) and INDEL (insertion/deletion) markers using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing to set up a genetic tracking method of the geographical origin of Hymenaea sp. From two initial sets of 358 and 32 loci used to genotype at least 94 individuals, a final set of 75 nSNPs, 50 cpSNPs and 6 INDELs identifying significant population structure was developed. Univ Sao Paulo, Luiz de Queiroz Coll Agr, Dept Forest Sci, Ave Padua Dias,11,POB 9, BR-13418900 Sao Paulo, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia IIAP, LBGM, Ave Jose A Quinones Km 2-5, Iquitos, Peru Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRA, BIOGECO, 69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Dept Fitotecnia, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Univ Estadual Paulista, Dept Fitotecnia, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest: ANR-10-EQPX-16-01 European Union, FEDER: ANR-10-EQPX-16-01 European Union, FEDER: 2003227 European Union, FEDER: ANR-10-LABX-25-01

International audience; The genus Khaya includes some of the highest-value timber species in natural forests in Africa, which are under heavy exploitation pressure. Genetic identification of Khaya species is important to confirm the taxonomic classification for biodiversity conservation purposes and as a forensic tool aiding law enforcement in the fight against illegal logging. We collected samples from a total of 2222 trees belonging to five or six (depending on classification) different Khaya species (K. ivorensis, K. anthotheca/K. nyasica, K. grandifoliola, K. senegalensis, K. madagascariensis). Representative sampling was conducted over the natural ranges of all sampled Khaya species, in humid tropical forest and savanna zones. We genotyped individuals based on 101 molecular markers (67 nuclear, 11 chloroplast and 22 mitochondrial SNPs, 1 chloroplast indel). Bayesian clustering produced three main genetic groups assigning all K. ivorensis and all K. senegalensis trees, respectively, in two different clusters and all remaining individuals in a third cluster. Genetic self-assignment tests with all 101 SNPs had success rates of 97-100% for all species except for K. nyasica and K. madagascariensis, which could not be clearly distinguished from each other. A success rate for species identification nearly as high was observed using a subset of 15 highly differentiated SNPs. There was only very little evidence for hybridization among species and the vast majority (> 97%) of individuals were assigned to the same species group as identified based on morphological characters.

Made available in DSpace on 2019-10-04T12:40:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture Conseil Regional d'Aquitaine European Union FEDER Investissements d'avenir Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin. Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia IIAP, Ave Jose A Quinones Km 2-5, Iquitos, Peru Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRA, BIOGECO, F-33610 Cestas, France Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01 : 001-2016-SERFOR-DGGSPFFS-DGSPF

Made available in DSpace on 2019-10-06T15:45:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-15 Bundesministerium für Ernährung und Landwirtschaft Conseil Régional Aquitaine Agence Nationale de la Recherche Low coverage MiSeq genome sequencing and restriction associated DNA sequencing (RADseq) were used to identify nuclear and plastid SNP and INDEL genetic markers in Carapa guianensis. 261 genetic markers including 237 nuclear SNPs, 22 plastid SNPs, and 2 plastid INDELs are described based on 96 genotyped individuals from French Guiana, Brazil, Peru, and Bolivia. The best 117 SNPs for identifying population structure and performing individual assignment are assembled into four multiplexes for MassARRAY genotyping. INRA UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane, Campus Agronomique, Avenue de France Thünen Institute of Forest Genetics, Sieker Landstrasse 2 School of Natural Sciences and Engineering São Paulo State University (UNESP) Carrera de Ingeniería Forestal Laboratorio de Dendrocronología Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5 Instituto Florestal de São Paulo, CP 1322 BIOGECO INRA University Bordeaux School of Natural Sciences and Engineering São Paulo State University (UNESP) Conseil Régional Aquitaine: 20030304002FA Conseil Régional Aquitaine: 20040305003FA Agence Nationale de la Recherche: ANR-10-EQPX-16-01 Agence Nationale de la Recherche: ANR-10-LABX-25-01

Made available in DSpace on 2019-10-04T12:40:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture (BMEL) Programa Nacional de Innovacion para la Competitividad y Productividad Conseil Regional d'Aquitaine European Union, FEDER We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia. IIAP, Ave Jose A Quinones Km 2-5, Iquitos, Peru Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France INRA, Plateforme Genome Transcriptome Bordeaux, Site Pierroton Batiment Artiga,69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Programa Nacional de Innovacion para la Competitividad y Productividad: 381-PNICP-PIAP-2014 Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 European Union, FEDER: ANR-10-EQPX-16-01 European Union, FEDER: ANR-10-LABX-25-01

100 SNP and one Indel markers were developed for Khaya using a combination of restriction associated DNA sequencing and low coverage MiSeq genome sequencing. The marker set was successfully used to genotype a set of 1919 individuals, representing 5 Khaya species from 18 African countries, using MassARRAY®iPLEX™ genotyping.

182 SNP markers were developed for Ayous (Triplochiton scleroxylon K. Schum) by incorporating information from two next generation sequencing approaches (RADseq Floragenex and AFLPseq IonTorrent PGM) into a single genotyping panel for MassARRAY® iPLEX™. This set of markers was successfully used to genotype 753 individuals from 43 populations in five Tropical West and Central African Countries. These loci have an expected heterozygosity range of 0.007–0.501 and F ST from 0 to 0.306.

Made available in DSpace on 2019-10-04T12:34:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-12-01 German Federal Ministry of Food and Agriculture Conseil Regional d'Aquitaine European Union, FEDER Investissements d'avenir Chico Mendes Biodiversity Institute A combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing was used for the development of single nucleotide polymorphisms (SNP) and INDEL (insertion/deletions) genetic markers for Ipe (Handroanthus sp.). Of the 402 putative loci identified, 389 SNPs and INDELs (315 nuclear SPNs, six chloroplast INDELs, 15 chloroplast SNPs, 12 mitochondrial INDELs and 41 mitochondrial SNPs) were successfully genotyped at 93 individuals from Brazil, Bolivia and French Guiana using a - MassARRAY (R) iPLEX (TM) platform. This set of markers will be invaluable for population genetics, phylogeography and DNA fingerprinting studies. Univ Estadual Paulista, Dept Fitotecnia Tecnol Alimentos & Socioecon, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Carrera Ingn Forestal, Lab Dendrocronol, Km 6 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, INRA, UMR0745 EcoFoG,AgroParisTech,Cirad,CNRS, Campus Agron,Ave France,BP97387, Kourou, France Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil INRA Pierroton, Plateforme Genome Transcriptome Bordeaux, 69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Dept Fitotecnia Tecnol Alimentos & Socioecon, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01 Chico Mendes Biodiversity Institute: 47960 Chico Mendes Biodiversity Institute: 49369

International audience; We describe the development of new nuclear SNP markers for the genetic timber tracking of the geographical origin of Sapelli, Entandrophragma cylindricum (Meliaceae). Restriction associated DNA sequencing (RADseq) of two reference individuals yielded 1131 putative SNPs. Among those, 131 were selected to design four MassARRAY multiplexes and screened at 178 individuals. Seventy-two loci were selected for further use in genetic tracking.

International audience; Deforestation-reinforced by illegal logging-is a serious problem in many tropical regions and causes pervasive environmental and economic damage. Existing laws that intend to reduce illegal logging need efficient, fraud resistant control methods. We developed a genetic reference database for Jatoba (Hymenaea courbaril), an important, high value timber species from the Neotropics. The data set can be used for controls on declarations of wood origin. Samples from 308 Hymenaea trees from 12 locations in Brazil, Bolivia, Peru, and French Guiana have been collected and genotyped on 10 nuclear microsatellites (nSSRs), 13 chloroplast SNPs (cpSNP), and 1 chloroplast indel marker. The chloroplast gene markers have been developed using Illumina DNA sequencing. Bayesian cluster analysis divided the individuals based on the nSSRs into 8 genetic groups. Using self-assignment tests, the power of the genetic reference database to judge on declarations on the location has been tested for 3 different assignment methods. We observed a strong genetic differentiation among locations leading to high and reliable self-assignment rates for the locations between 50% to 100% (average of 88%). Although all 3 assignment methods came up with similar mean self-assignment rates, there were differences for some locations linked to the level of genetic diversity, differentiation, and heterozygosity. Our results show that the nuclear and chloroplast gene markers are effective to be used for a genetic certification system and can provide national and international authorities with a robust tool to confirm legality of timber.

The prosecution of illegal logging crimes is hampered by a lack of available forensic timber identification tools, both for screening of suspect material and definitive identification of illegally sourced wood. Reputable timber traders are also struggling to police their own supply chains and comply with the growing requirement for due diligence with respect to timber origins and legality. A range of scientific methods have been developed independently with the potential to provide the required identification information, but little attention has been given to how these tools can be applied synergistically to support the legal timber trade. Here we review the use of visual identification methods (wood anatomy, dendrochronology), chemical methods (mass spectrometry, near infrared spectroscopy, stable isotopes, radio-carbon), and genetic methods (DNA barcoding, population genetics/phylogeography, DNA fingerprinting) each with potential application to forensic timber identification. We further highlight where future research and development are required to identify illegal logging crimes using these methods and suggest ways in which multiple methods can be used together to answer specific identification questions. We argue that a new integrated field of forensic timber identification should be a global investment priority, for which the ongoing collection, curation and taxonomic study of appropriate reference material is a critical part. Consideration of the specific legal requirements for method development and the application of identification methodologies to criminal evidence are also imperative to achieve robust scientific support for illegal logging crime prosecutions and prevention.

DNA-based techniques are helpful in characterising hybridisation patterns in plant species. To be efficient in disentangling species boundaries and interspecific gene flow, it is recommended to combine various methodologies and types of markers. Here, we used different analytical tools (algorithms implemented in Structure, Tess, NewHybrids and HIest, and the haploweb approach) and three nuclear genetic markers (7 nuclear simple sequence repeat loci (SSRs), 62 single-nucleotide polymorphism loci (SNPs) and a single-copy gene region, At103) to revisit hybridisation patterns in the commercially important African tree genus Milicia. Samples were collected in the natural ranges of Milicia regia and Milicia excelsa in West Africa. Using real data sets, simulated purebreds and hybrid genotypes, we found that SNPs yielded results more consistent than SSRs; outputs from the Bayesian and maximum-likelihood analyses differed significantly using the SSRs, whereas they were perfectly congruent using SNPs. A proportion of 12.4% hybrids were detected amongst the SNP genotype samples. A haploweb analysis of At103 gene sequences confirmed the existence of interspecific hybrids. There was also a clear evidence of advanced generations of hybrids (backcrossed individuals) but only towards M. regia. Although more investigation is required for understanding the mechanisms responsible for this asymmetric introgression, we suggest that it may be due to the differences in flowering time between species and between sexes, combined with a maternal inheritance of flowering time.

Restriction associated DNA sequencing was conducted on two genetically independent individuals of Iroko, Milicia excelsa, for the discovery of nuclear SNPs. Ninety-four samples, well-distributed over the natural range and including timber DNA, were screened at 138 loci on a MassARRAY iPLEX system. Amplification success was high and 77 loci were selected to design a set of markers for genetic timber tracking purposes.

Conservation of forest genetic resources has drawn much attention in the last decades, as it prevents negative effects of genetic erosion on adaptability potential of material used for afforestation. According to the German Act on Forest Reproductive Material, seed harvesting must occur in certified stands. Seed lots must stem from a minimum number of seed-trees, although the effect of this limit on genetic diversity has not been addressed. In this study, we aimed at understanding the effect of seed harvesting strategies on genetic diversity. We used the simulation model Eco-Gene and real molecular data to disentangle the effects of number of seed-trees and harvesting method in three wild cherry (Prunus avium) stands. Our results outline the importance of harvesting genetically different or distant seed-trees in maintaining genetic diversity. Besides optimal sampling strategy, we also recommend minimum harvesting of 25 seed-trees to reach 90 % of genetic diversity available within the stand. The outcomes of these results for the practice are also discussed.

Illegal logging is one of the main causes of ongoing worldwide deforestation and needs to be eradicated. The trade in illegal timber and wood products creates market disadvantages for products from sustainable forestry. Although various measures have been established to counter illegal logging and the subsequent trade, there is a lack of practical mechanisms for identifying the origin of timber and wood products. In this study, six nuclear microsatellites were used to generate DNA fingerprints for a genetic reference database characterising the populations of origin of a large set of mahogany (Swietenia macrophylla King, Meliaceae) samples. For the database, leaves and/or cambium from 1971 mahogany trees sampled in 31 stands from Mexico to Bolivia were genotyped. A total of 145 different alleles were found, showing strong genetic differentiation (δ(Gregorious)=0.52, F(ST)=0.18, G(ST(Hedrick))=0.65) and clear correlation between genetic and spatial distances among stands (r=0.82, P

Background: Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species' divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure. Results: West African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination' corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance. Conclusions: Our genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species., SCOPUS: ar.j, info:eu-repo/semantics/published

During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregates and intend to identify the most likely group of origin. Often this grouping does not have a biological but rather a historical or political justification, such as “country of origin”.In this paper, we present a new nearest neighbour approach to individual assignment or classification within a given but potentially imperfect grouping of reference samples. This method, which is based on the genic distance between individuals, functions better in many cases than commonly used methods. We demonstrate the operation of our assignment method using two data sets. One set is simulated for a large number of trees distributed in a 120 km by 120 km landscape with individual genotypes at 150 SNPs, and the other set comprises experimental data of 1221 individuals of the African tropical tree speciesEntandrophragma cylindricum(Sapelli) genotyped at 61 SNPs. Judging by the level of correct self-assignment, our approach outperformed the commonly used frequency and Bayesian approaches by 15% for the simulated data set and by 5 to 7% for the Sapelli data set.Our new approach is less sensitive to overlapping sources of genetic differentiation, such as genic differences among closely-related species, phylogeographic lineages and isolation by distance, and thus operates better even for suboptimal grouping of individuals.

To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for insertion/deletion (indel) polymorphisms to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indel and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.

Genetic diversity strongly influences populations' adaptability to changing environments and therefore survival. Sustainable forest management practices have multiple roles including conservation of genetic resources and timber production. In this study, we aimed at better understanding the variation in genetic diversity among adult and offspring individuals, and the effects of mating system on offspring survival and growth in wild cherry, Prunus avium. We analysed adult trees and open pollinated seed-families from three stands in Germany at eight microsatellite loci and one incompatibility system locus and conducted paternity analyses. Seed viability testing and seed sowing in a nursery allowed further testing for the effects of pollen donor diversity and genetic similarity between mates on the offspring performance at the seed and seedling stages. Our results were contrasting across stands. Loss of genetic diversity from adult to seedling stages and positive effect of mate diversity on offspring performance occurred in one stand only, whereas biparental inbreeding depression and significant decrease in fixation index from adults to seedlings was detected in two stands. We discussed the effects of stand genetic diversity on the magnitude of biparental inbreeding depression at several life-stages and its consequences on the management of genetic resources in P. avium.

Pollen and seed movement among and within populations connect individuals and populations, and therefore are among the most important evolutionary processes determining the genetic structure of populations. Seven microsatellite loci were used to investigate the realized pollen dispersal and intra-population spatial genetic structure (SGS) in four permanent plots located in an overexploited big-leaf mahogany (Swietenia macrophylla King) population in the Bolivian Amazon. All adult trees found in the plots were mapped, sampled and genotyped. Seedlings were sampled below the canopy of reproductive trees. Private alleles in the sub-population of the adults and the seedlings were observed. The observed heterozygosity was significantly lower and fixation index was significantly higher for the seedlings (Ho=0.697, F=0.068) compared to the adults (Ho=0.761, F=-0.023). In one plot, seed immigration was observed (18%). Realized pollen immigration ranged among the plots from zero to 41% and selfing ranged from zero to 5.8%. We observed an average pollen dispersal distance from 75 to 255 m, with the maximum reaching 576 m. We found a significant SGS up to 150 m, showing that near neighbour individuals are relatives. The observed data on pollen- and seed dispersal provides important information for the sustainable management of the endangered mahogany species.

Illegal logging and associated trade are the cause of many economic and ecological problems both in producer and in consumer countries. There are an increasing number of national and international regulations in place that call for efficient timber tracking systems. We present results of a pilot study of a DNA-based method to control the geographical origin of timber in forest concessions in Cameroon. We addressed genetic differentiation at five nuclear microsatellite loci in seven sapelli (Entandrophragma cylindricum, Meliaceae) populations located in three forest concessions in Eastern Cameroon. In the framework of a blind test, seven anonymous timber sample sets were analysed at three microsatellite loci and compared to the genetic reference data of the forest concessions in Cameroon. Our results show that genetic differentiation was low within and among concessions. Combining the results of Bayesian genetic assignment method and exclusion test, we could determine that the timber stemmed or did not stem from the focus forest concession in six out of the seven blind sample sets. We further discuss the accuracy of the presented method and draw conclusions for a better sampling and genotyping strategy. Our work provides clear evidence that the use of genetic fingerprints is a useful tool to fight against illegal logging.

Although pollen dispersal has been extensively studied in trees, parameters influencing between-population variation are still poorly understood. In this study, we conducted paternity analyses on open-pollinated seeds in four natural populations of wild cherry (Prunus avium) with contrasting density and clonal propagation, using eight microsatellite loci and one self-incompatibility system locus. We also measured four quantitative traits and spatial positions as potential correlates of reproductive success. Levels of polyandry differed among populations and 30% of the seed families exhibited unequal paternal contributions, suggesting variation in reproductive success rather than variation in mate availability. Mating occurred preferentially among neighbours in all populations, suggesting that it is a common pattern in wild cherry and probably results from pollinator behaviour. Paternal success was positively correlated with diameter at breast height, as indicated in previous studies and tree dominance only resulted in higher paternal success in low density plots. Mating patterns were thus also affected by both density and tree size. Large-scale studies are needed to disentangle relative influences of these factors on the mating system and pollination success.