Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species

List of individuals. For each individual, the country, district, and absolute coordinates in decimal degrees are given. (PDF 29 kb

Multivariate analysis of anatomical characters confirms the differentiation of two morphologically close species, Melanohalea olivacea (L.) O. Blanco et al. and M. septentrionalis (Lynge) O. Blanco et al

This study investigates how anatomical characters can be used to differentiate two morphologically close species, Melanohalea olivacea (L.) O. Blanco et al. and M. septentrionalis (Lynge) O. Blanco et al. Although the two species are morphologically differentiated, mainly based on the position and shape of pseudocyphellae on the lobes, poorly-developed specimens can be difficult to identify based on morphology alone. For example, in Switzerland, both species are at the south-west limit of their distribution range and most specimens are small and not fully developed. In such cases, anatomical characters are particularly useful in separating the two species. Five anatomical characters were studied: spore length and width; hymenium, subhymenium and hypothecium height. A nested ANOVA showed that variation of spore length was 155 times greater between species than between individuals of the same species, itself 5 times higher than within individuals. In a Principal Component Analysis, despite a substantial variation of the anatomical characters within both species, a significant species differentiation appeared distinctly on the first axis (P < 0·001), which accounted for 62·35% of the total variance, and the type specimens nested within each species. Finally, a Discriminant Linear Analysis assigned 100% of the individuals to their species class, the best predictors to discriminate between the two species being subhymenium height and spore length. These characters proved to be powerful in identifying specimens with a poorly-developed morphology and confirmed the presence of M. olivacea in Switzerlan

Allelic configuration and polysomic inheritance of highly variable microsatellites in tetraploid gynodioecious Thymus praecox agg

Polyploidy plays a pivotal role in plant evolution. However, polyploids with polysomic inheritance have hitherto been severely underrepresented in plant population genetic studies, mainly due to a lack of appropriate molecular genetic markers. Here we report the establishment and experimental validation of six fully informative microsatellite markers in tetraploid gynodioecious Thymus praecox agg. Sequence data of 150 microsatellite alleles and their flanking regions revealed high variation, which may be characteristic for polyploids with a reticulate evolutionary history. Understanding the patterns of mutation (indels and substitutions) in microsatellite flanking-sequences was a prerequisite for the development of co-dominant markers for fragment analyses. Allelic segregation patterns among progeny arrays from ten test crosses revealed tetrasomic inheritance in T. praecox agg. No evidence of frequent double reduction was detected. Polymerase chain reaction (PCR) based dosage effects allowed for precise assignment of allelic configuration at all six microsatellite loci. The quantification of allele copy numbers in PCR was verified by comparisons of observed and expected gametic allele frequencies and heterozygosities in test crosses. Our study illustrates how PCR based markers can provide reliable estimates of heterozygosity and, thus, powerful tools for breeding system and population genetic analyses in polyploid organism

Genetical lmprovement of Marine Fish and Shellfish: a French Perspective

Absrracr In France, marine fish and shellfish farming is based mainly on the breeding of wild species, whose natural populations are traditionally exploited. Research programs are conducted by IFREMER, in co-operation with INRA and Universities. French research programs for the genetical improvement of marine fish and shellfish concern primarily seabass (Dicentrarchus labrax) and oysters (Ostrea edulis and Crassostrea gigas). The following programs are developed: • The knowledge of wild and farmed populations. The most recent prodjects involve the highly variable microsatellite markers. Seven markers are presently available for seabass and the work is now initiated on turbot (Scophthalmus maximus). In molluscs, microsatellite markers have been developed for the European fJat oyster (O.edulis). • The control of sex-ratios. Research programs in physiology and developmental genetics are initiated in order to control sex-ratios in seabass. These programs include the production of gynogenetic progenies and the study of the sex-ratios of progenies issued from the crossing of hormonally feminised or masculinised breeders with normal ones. • The production of polyploids. Triploid seabass have been produced using high pressure and thermal shocks. The results after 6 months show a lower survival and growth compared with diploid controls. Triploid oysters, produced using chemical treatments (cytochalasin B or 6-DMAP), show better performances compared to doploids. • The establishment of breeding programs for traits of commercial interest

Species delimitation in the East Asian species of the relict tree genus Zelkova (Ulmaceae): A complex history of diversification and admixture among species

Zelkova species, trees of the elm family (Ulmaceae), are part of the Cenozoic relict flora. In western Eurasia, the genus comprises three species that are restricted to disjunct areas (Z. sicula on Sicily, Z. abelicea on Crete and Z. carpinifolia in Transcaucasia). The situation is different in East Asia, where three species (Z. serrata, Z. schneideriana and Z. sinica) have at least partly overlapping distributions. The phylogenetic and phylogeographic status of these East Asian species is still not well understood, mainly since all previous studies used almost exclusively plant material collected in botanical gardens and were based on very small numbers of individuals. Our study is the first based on 33 natural populations covering all important areas with Zelkova species in the Sino-Japanese Floristic Region. Chloroplast and microsatellite markers were used, and Bayesian analyses were run for both types of markers. East Asian Zelkova species cluster into two groups that partially overlap when comparing the two types of markers. For chloroplast markers, the two groups coincide with all Japanese, some Korean and northern Chinese Z. serrata in one group and all other individuals in the other group, regardless of whether they are attributed to Z. serrata, Z. sinica or Z. schneideriana from Korea, mainland China and Taiwan. At the nuclear level, however, the clustering clearly groups all the Z. serrata individuals together, regardless of whether they are from Japan, Korea or China, and the two other species in a second group. This complex genetic pattern in East Asian Zelkova species is most likely due to a combination of ancient diversification and speciation events and more recent hybridization during the last glacial/interglacial retractions and recolonizations. One of the surprising results of our study concerns the populations from Taiwan, which are genetically similar to Z. schneideriana. Thus, their assignation to a separate taxon (Z. tarokoensis) or to a variety of Z. serrata (Z. serrata var. tarokoensis), as currently reported in all local and national floras, might be in need of revision. Furthermore, our results indicate that the East Asian species are more closely related to Z. carpinifolia than to any other Western European species. Haplotypes of Z. sicula and Z. abelicea (Mediterranean region) as well as those of Z. sinica and Z. schneideriana (East Asia) seem to have diversified more recently. The most ancient haplotypes are found among the western Eurasian Z. carpinifolia and the East Asian Z. serrata. This result is in agreement with the carpinifolia and serrata-like morphotypes commonly found in the fossil record

Do living ex situ collections capture the genetic variation of wild populations? A molecular analysis of two relict tree species, Zelkova abelica and Zelkova carpinifolia

Botanic gardens and arboreta, particularly in regions where iconic relict trees naturally occur, play a vital role in the conservation of these species. Maintaining well-managed living ex situ collections of rare and threatened relict tree species provides an immediate insurance policy for the future species conservation. The aim of this research was to investigate the origin, representativeness and genetic diversity of relict trees kept in botanic gardens and arboreta. We used as a model two ecologically and biogeographically distinct members of the prominent relict genus Zelkova (Ulmaceae), which survived the last glaciation in disjunct and isolated refugial regions: Z. carpinifolia in Transcaucasia and Z. abelicea endemic to Crete (Greece) in the Mediterranean. Our study revealed substantial differences in the genetic diversity and the origin of living ex situ collections of the two investigated taxa. The living ex situ collections of Z. carpinifolia have relatively high representativeness compared with the global genetic variability of natural stands identified in a previous study. In contrast, Z. abelicea, which possesses an extraordinarily high genetic variability in natural populations, is clearly underrepresented in botanic garden collections. Moreover, all Z. abelicea trees investigated in this study most probably originated from a single region, the Levka Ori in western Crete. Thus, the ex situ conservation of Z. abelicea requires major planning and coordination efforts, including the establishment of well-documented collections in botanic gardens in Greece and especially on Crete. New living ex situ collections should be created using plant material collected from all of the mountain regions where Z. abelicea still occurs. Our study highlights the need for re-evaluating the existing living ex situ collections of trees and the development of new strategies for future conservation efforts in botanic gardens and arboreta. The coordination of conservation efforts between gardens must be enhanced to prioritize actions for the most threatened relict tree species

Contribution a l'etude de la variabilite phenotypique et genetique chez le millet Setaria italica (L. P. Beauv.)

SIGLEAvailable from INIST (FR), Document Supply Service, under shelf-number : T 82858 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Usnea dasopoga (Ach.) Nyl. and U. barbata (L.) F. H. Wigg. (Ascomycetes, Parmeliaceae) are two different species: a plea for reliable identifications in molecular studies

Using molecular data to delimit species or reconstruct their evolutionary history is now widely used across all organisms. However, such analyses can suffer from poor or false specimen identifications leading to incorrect conclusions. Here we show that the use of misidentified specimens in a phylogenetic framework resulted in questionable conclusions in a previously published study (Mark et al. 2016). Using morphological, chemical and statistical analyses on the specimens used in that study, we found support for Usnea barbata and U. dasopoga being morphologically and anatomically distinct species with separate clusters in the molecular phylogeny. Furthermore, our revision of specimen identifications refutes the synonymization of U. substerilis with U. lapponica. In conclusion, we discuss the issue of correct identification of voucher specimens in DNA databases and conclude with some general suggestions to avoid false specimen identifications in phylogenetic studies. </p

Le millet Setaria italica, une plante à découvrir (étude bibliographique)

Foxtail millet Setaria italica is an autogamous plant of Panicoïdés tribe, which seems to be one of the first cultivated cereal in Europe and Asia. Although China seems to be the oldest birthplace of foxtail millet, recent studies would point out that this part of the world is not its only center of origin (with Harlan's meaning). Indeed, foxtail millet would not only have been domesticated in Europe and China, but also in India, Japan and South of Russia, at different times and independantly. Migrations and introgressions would have occured afterwards ; and so have been created the current geographical groups. The extension of foxtail millet is due to its agronomical (autogamy, hardiness...) and nutritional advantages (high protein and fatty acid contents...). Actually, foxtail millet is, among other uses, a cereal of high nutritive value. Foxtail millet is still widely cultivated in Asia for human food, but it has nearly disappeared in Europe except for bird food because of maize introduction and because of a lack in genetic improvment. Nevertheless, in the current context of overproduction and diversification, a wide and unused variability and a high nutritive value make of foxtail millet an interesting culture for the futur.Le millet Setaria italica, plante autogame de la tribu des Panicoïdés, semble avoir été une des premières céréales cultivées dans le périmètre euro-asiatique. Bien que la Chine semble être le berceau le plus ancien du millet, les études récentes tendent à démontrer que cette région du monde ne serait pas le seul centre d'origine (au sens de Harlan) de la céréale. En effet, elle aurait été domestiquée de façon indépendante à des périodes différentes en Europe et en Chine mais aussi en Inde, au Japon ou dans le Sud de la Russie, migrations et introgressions s'étant produites par la suite, permettant ainsi la formation des groupes géographiques actuels. L'extension passée et actuelle du millet s'explique par des avantages agronomiques (pouvoir de multiplication, autogamie, rusticité...) et nutritionnels (forte teneur en protéines, en acides gras, etc..) : entre autres utilisations, le millet est une céréale alimentaire de bonne valeur. Si le millet est toujours cultivé de façon importante en Asie pour l'alimentation humaine, sa culture a presque disparu en Europe, concurrencée par l'extension du maïs et par une absence de travaux d'amélioration génétique. Cependant l'existence d'une variabilité non exploitée et le contexte actuel de diversification des productions associés aux qualités de la céréale en font une culture intéressante pour l'avenir.Naciri Yamama, Belliard Jacques. Le millet Setaria italica, une plante à découvrir (étude bibliographique). In: Journal d'agriculture traditionnelle et de botanique appliquée, 34ᵉ année,1987. pp. 65-87