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The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the “core Nymphaeaceae”—comprising the genera Euryale, Nymphaea and Victoria—is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogeneti

1. DNA barcoding aids in rapidly identifying specimens in various contexts by comparing short stretches of DNA to a reference database. Barcoding initiatives generate large reference databases of carefully curated high-quality sequences to maximize identification success. 2. BarKeeper provides a flexible tool for barcoding initiatives and in the context of phylogenetic studies to foster shared work on large datasets of raw sequence and associated metadata. It is free, open-source and available as a set of Docker containers for easy setup. After setting it up once, all project members can use it independently of their operating system or location. 3. BarKeeper offers features to collect and manage data and metadata about specimens, taxa and DNA sequences from Sanger sequencing and high-throughput sequencing (HTS) technologies. It provides excellent flexibility by not being restricted to specific markers or taxon groups. Users can view and edit records and associated metadata while the app assists them by trimming and assembling reads. It automatically checks the quality of generated barcodes with a taxonomy-based tool and offers a wide range of options for data analysis. Extensive search features allow querying the database for specific groups of records and saving the search results in the user's profile or downloading them in various file formats. 4. BarKeeper combines multiple tools to aid barcoding projects in every step, from a reference taxa list to finished barcode sequences, thereby minimizing the number of laborious, potentially error-prone manual steps and enabling efficient collaborative workflows., Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347, Deutscher Akademischer Austauschdienst http://dx.doi.org/10.13039/501100001655, University of Muenster, Peer Reviewed

Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense compared to congeners. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and seven levels of sequencing coverage across the plastid genome (original sequencing depth, 2,000x, 1,000x, 500x, 250x, 100x, and 50x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic reconstruction is assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produces the most consistent assemblies for C. bakuense. Moreover, we demonstrate that a sequencing coverage between 500x and 100x can reduce both the sequence variability across assembly contigs and computation time. When comparing the most reliable plastid genome assemblies of C. bakuense, a sequence difference in only three nucleotide positions is detected, which is less than the difference potentially introduced through software choice.

Premise The genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it. Methods We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference. Results Our results indicate that the inclusion of all plastid genome partitions is needed to infer well-supported phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia. Conclusions The concatenation and combined analysis of all plastid genome partitions and the construction of manually-curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of well-supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence data sets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.

Plants, fungi and algae are important components of global biodiversity and are fundamental to all ecosystems. They are the basis for human well-being, providing food, materials and medicines. Specimens of all three groups of organisms are accommodated in herbaria, where they are commonly referred to as botanical specimens.The large number of specimens in herbaria provides an ample, permanent and continuously improving knowledge base on these organisms and an indispensable source for the analysis of the distribution of species in space and time critical for current and future research relating to global biodiversity. In order to make full use of this resource, a research infrastructure has to be built that grants comprehensive and free access to the information in herbaria and botanical collections in general. This can be achieved through digitization of the botanical objects and associated data.The botanical research community can count on a long-standing tradition of collaboration among institutions and individuals. It agreed on data standards and standard services even before the advent of computerization and information networking, an example being the Index Herbariorum as a global registry of herbaria helping towards the unique identification of specimens cited in the literature.In the spirit of this collaborative history, 51 representatives from 30 institutions advocate to start the digitization of botanical collections with the overall wall-to-wall digitization of the flat objects stored in German herbaria. Germany has 70 herbaria holding almost 23 million specimens according to a national survey carried out in 2019. 87% of these specimens are not yet digitized. Experiences from other countries like France, the Netherlands, Finland, the US and Australia show that herbaria can be comprehensively and cost-efficiently digitized in a relatively short time due to established workflows and protocols for the high-throughput digitization of flat objects.Most of the h

We present a first study of the diversity and community composition of lichens in seasonally dry tropical forest (DTF) remnants in the Atlántico department, Colombia. Lichens were sampled in two of the three protected areas of the department: Distrito de Manejo Integrado (DMI) Luriza and Reserva Forestal Protectora (RFP) El Palomar. The inventory revealed 61 species, including four new to science: Fissurina linoana Lücking, Moncada & G. Rodr. sp. nov., Graphis lurizana Lücking, Moncada & Celis sp. nov., G. mokanarum Lücking, Moncada & M.C. Martínez sp. nov., and Phaeographis galeanoae Lücking, Moncada & B. Salgado-N. sp. nov. Arthonia erupta and Coenogonium saepincola are new to South America, whereas thirteen species are recorded for Colombia for the first time. Further 37 species are new records for Atlántico, raising the total of species known from the department from 27 to 84. With 42 species at Luriza and 31 at El Palomar, species richness was comparable to that of other DTF sites in the Neotropics. Overlap in species composition between the two sites was remarkably low, with only twelve shared species (20 %), indicating a high level of heterogeneity. Biogeographical affinities lie with Central American DTF, which is in line with those of woody plants. These results underline the importance of the remaining fragments of DTF in Colombia in conserving partially unknown biodiversity and the necessity for their continuing conservation., Presentamos un primer estudio de la diversidad y composición de comunidades de líquenes en remanentes de bosque seco tropical (bs-T) en el departamento de Atlántico, Colombia. Se muestrearon líquenes en dos de las tres áreas protegidas del departamento: Distrito de Manejo Integrado (DMI) Luriza y Reserva Forestal Protectora (RFP) El Palomar. El inventario registró 61 especies, incluyendo cuatro especies nuevas para la ciencia: Fissurina linoana Lücking, Moncada & G. Rodr. sp. nov., Graphis lurizana Lücking, Moncada & Celis sp. nov., Graphis mokanarum Lücking, Moncada & M.C. Martínez sp. nov. y Phaeographis galeanoae Lücking, Moncada & B. Salgado-N. sp. nov. Arthonia erupta y Coenogonium saepincola son nuevos registros para América del Sur, mientras que trece especies son reportadas por primera vez para Colombia. Unas 37 especies adicionales son nuevos reportes para Atlántico, incrementando el total de especies conocidas para el departamento de 27 a 84. Con 42 especies en Luriza y 31 en El Palomar, la riqueza de especies fue comparable con la de otros sitios de bs-T en el Neotrópico. El traslape en la composición de especies entre los dos sitios es bajo, con solamente doce (20 %) compartidas, indicando un alto nivel de heterogeneidad. Las afinidades biogeográficas son mayores con los bs-T de Centroamérica, lo que coincide con las de plantas leñosas. Estos resultados enfatizan la importancia de los remanentes de bs-T en Colombia para la conservación de una biodiversidad poco conocida.

We present a first study of the diversity and community composition of lichens in seasonally dry tropical forest (DTF) remnants in the Atlántico department, Colombia. Lichens were sampled in two of the three protected areas of the department: Distrito de Manejo Integrado (DMI) Luriza and Reserva Forestal Protectora (RFP) El Palomar. The inventory revealed 61 species, including four new to science: Fissurina linoana Lücking, Moncada & G. Rodr. sp. nov., Graphis lurizana Lücking, Moncada & Celis sp. nov., G. mokanarum Lücking, Moncada & M.C. Martínez sp. nov., and Phaeographis galeanoae Lücking, Moncada & B. Salgado-N. sp. nov. Arthonia erupta and Coenogonium saepincola are new to South America, whereas thirteen species are recorded for Colombia for the first time. Further 37 species are new records for Atlántico, raising the total of species known from the department from 27 to 84. With 42 species at Luriza and 31 at El Palomar, species richness was comparable to that of other DTF sites in the Neotropics. Overlap in species composition between the two sites was remarkably low, with only twelve shared species (20 %), indicating a high level of heterogeneity. Biogeographical affinities lie with Central American DTF, which is in line with those of woody plants. These results underline the importance of the remaining fragments of DTF in Colombia in conserving partially unknown biodiversity and the necessity for their continuing conservation., Presentamos un primer estudio de la diversidad y composición de comunidades de líquenes en remanentes de bosque seco tropical (bs-T) en el departamento de Atlántico, Colombia. Se muestrearon líquenes en dos de las tres áreas protegidas del departamento: Distrito de Manejo Integrado (DMI) Luriza y Reserva Forestal Protectora (RFP) El Palomar. El inventario registró 61 especies, incluyendo cuatro especies nuevas para la ciencia: Fissurina linoana Lücking, Moncada & G. Rodr. sp. nov., Graphis lurizana Lücking, Moncada & Celis sp. nov., Graphis mokanarum Lücking, Moncada & M.C. Martínez sp. nov. y Phaeographis galeanoae Lücking, Moncada & B. Salgado-N. sp. nov. Arthonia erupta y Coenogonium saepincola son nuevos registros para América del Sur, mientras que trece especies son reportadas por primera vez para Colombia. Unas 37 especies adicionales son nuevos reportes para Atlántico, incrementando el total de especies conocidas para el departamento de 27 a 84. Con 42 especies en Luriza y 31 en El Palomar, la riqueza de especies fue comparable con la de otros sitios de bs-T en el Neotrópico. El traslape en la composición de especies entre los dos sitios es bajo, con solamente doce (20 %) compartidas, indicando un alto nivel de heterogeneidad. Las afinidades biogeográficas son mayores con los bs-T de Centroamérica, lo que coincide con las de plantas leñosas. Estos resultados enfatizan la importancia de los remanentes de bs-T en Colombia para la conservación de una biodiversidad poco conocida.

The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and results of sequencing, assembling, annotating and quality-checking of three complete plastid genomes of the aquatic plant genus Cabomba as well as subsequent gene alignment and phylogenetic tree inference. We accompany our findings by a detailed description of the bioinformatic workflow employed. Importantly, we share a total of eleven software scripts for each of these bioinformatic processes, enabling other researchers to evaluate and replicate our analyses step by step. The results of our analyses illustrate that the plastid genomes of Cabomba are highly conserved in both structure and gene content.

The Caryophyllales constitute a major lineage of flowering plants with approximately 12500 species in 39 families. A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the order. A detailed review of the literature of the past two decades shows that enormous progress has been made in understanding overall phylogenetic relationships in Caryophyllales. The process of re-circumscribing families in order to be monophyletic appears to be largely complete and has led to the recognition of eight new families (Anacampserotaceae, Kewaceae, Limeaceae, Lophiocarpaceae, Macarthuriaceae, Microteaceae, Montiaceae and Talinaceae), while the phylogenetic evaluation of generic concepts is still well underway. As a result of this, the number of genera has increased by more than ten percent in comparison to the last complete treatments in the Families and genera of vascular plants” series. A checklist with all currently accepted genus names in Caryophyllales, as well as nomenclatural references, type names and synonymy is presented. Notes indicate how extensively the respective genera have been studied in a phylogenetic context. The most diverse families at the generic level are Cactaceae and Aizoaceae, but 28 families comprise only one to six genera. This synopsis represents a first step towards the aim of creating a global synthesis of the species diversity in the angiosperm order Caryophyllales integrating the work of numerous specialists around the world.

Premise of the study: The Caucasus represents one of the world’s biodiversity hotspots and includes the climatic refugia Hyrcan on the southern coast of the Caspian Sea and Colchis on the eastern coast of the Black Sea, where different species survived during the Quaternary climatic oscillations. We evaluated the genetic diversity of the relict tree Zelkova carpinifolia shared between the two refugia and distributed throughout the Caucasus and adjacent areas.Methods: Specimens were collected from 30 geographical sites in Azerbaijan, Georgia, Iran, and Turkey and screened for variability at eight nuclear microsatellite loci. The genetic diversity among and within populations was assessed using a set of statistical measures.Key results: We detected 379 different genotypes from a total of 495 individuals with varying degrees of clonal reproduction at the different sites. Low to intermediate levels of genetic diversity were observed at all sites, and strong differentiation between sampling sites was absent. In addition, we observed no clear genetic differentiation between the Colchis and Hyrcan. Bayesian clustering of the genotypes revealed three populations with high levels of admixture between the sampling sites.Conclusions: The lack of strong genetic structure of studied populations of Z. carpinifolia contrasts with a previous study based on chloroplast markers and suggests that long-distance pollen dispersal is an important factor of gene flow among populations of Z. carpinifolia. The present study does not reveal any particular site with particularly isolated genotypes that would deserve more attention for conservation purposes than others, although some sites should be considered for further investigation.

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate

Magnoliales, consisting of six families of tropical to warm-temperate woody angiosperms, were long considered the most archaic order of flowering plants, but molecular analyses nest them among other eumagnoliids. Based on separate and combined analyses of a morphological matrix (115 characters) and multiple molecular data sets (seven variable chloroplast loci and five more conserved genes; 14 536 aligned nucleotides), phylogenetic relationships were investigated simultaneously within Magnoliales and Myristicaceae, using Laurales, Winterales, and Piperales as outgroups. Despite apparent conflicts among data sets, parsimony and maximum likelihood analyses of combined data converged towards a fully resolved and well-supported topology, consistent with higher-level molecular analyses except for the position of Magnoliaceae: Myristicaceae + (Magnoliaceae + ((Degeneria+Galbulimima) + (Eupomatia+ Annonaceae))). Based on these results, we discuss morphological evolution in Magnoliales and show that several supposedly plesiomorphic traits are synapomorphies of Magnoliineae, the sister group of Myristicaceae (e.g. laminar stamens). Relationships within Annonaceae are also resolved with strong support (Anaxagorea basal, then ambavioids). In contrast, resolution of relationships within Myristicaceae is difficult and still incomplete, due to a very low level of molecular divergence within the family and a long stem lineage. However, our data provide good evidence that Mauloutchia is nested among other Afro-Malagasy genera, contradicting the view that its androecium and pollen are plesiomorphic © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 142, 125–186.

Thomas Borsch, Zusammenfassung auf Deutsch und Englisch

Das Vegetationsmosaik eines extensiv genutzten Wiesengebietes im Vortaunus (Hessen) wird untersucht. Die oft kleinräumig abweichenden Ausbildungen der Pflanzengesellschaften (Arrhenatheretum elatioris, Juncetum acutiflori, Molinia-caerulea-Gesellschaften, Caricetum gracilis, Filipendula-ulmaria-Gesellschaft und andere) und die Prinzipien ihrer Verteilung werden möglichst wirklichkeitsnah dargestellt. Aus dem Juncetum acutiflori entwickelt sich nach Brachfallen die Filipendula-ulmaria-Gesellschaft. Dabei treten starke Änderungen des Artenspektrums und der Dominanzverhältnisse auf. Es wird vermutet, daß interne Nährstoffverlagerungen bei Filipendula ulmaria eine Schlüsselrolle bei der sekundären Sukzession spielen. Die gewonnenen Daten lassen auf eine starke pflanzeninterne Stickstoffverlagerung bei der Art schließen. Das Stickstoffnachlieferungsvermögen des Bodens unter der Hochstauden-Gesellschaft unterscheidet sich gering von dem unter dem Juncetum acutiflori. Abschließend werden die Ergebnisse in Bezug auf die Anwendung für Naturschutzzwecke diskutiert., The vegetation of minimum management meadows in the Lower Taunus in Hesse was investigated. The species composition and distribution patterns of the plant communities (Arrhenatheretum elatioris, Juncetum acutiflori, Caricetum gracilis, the Molinia caerulea, Filipendula ulmaria and other communities) are presented as realistically as possible. The Juncetum acutiflori develops into the Filipendula ulmaria community in line with the changes in species composition and plant dominances following abandonement. It seems that nutrient shifting which causes increased competitive ability in Filipendula, plays a key role in secondary succession. The data point to strong internal nitrogen shifts in the Filipendula plant. The net nitrogen mineralization capacity of the soil bearing the tall-herb community appears to differ slightly from that bearing the Juncetum acutiflori. Finally, the results are discussed, applying them to nature conservation purposes.

Premise of the study: The Caucasus represents one of the world’s biodiversity hotspots and includes the climatic refugia Hyrcan on the southern coast of the Caspian Sea and Colchis on the eastern coast of the Black Sea, where different species survived during the Quaternary climatic oscillations. We evaluated the genetic diversity of the relict tree Zelkova carpinifolia shared between the two refugia and distributed throughout the Caucasus and adjacent areas.Methods: Specimens were collected from 30 geographical sites in Azerbaijan, Georgia, Iran, and Turkey and screened for variability at eight nuclear microsatellite loci. The genetic diversity among and within populations was assessed using a set of statistical measures.Key results: We detected 379 different genotypes from a total of 495 individuals with varying degrees of clonal reproduction at the different sites. Low to intermediate levels of genetic diversity were observed at all sites, and strong differentiation between sampling sites was absent. In addition, we observed no clear genetic differentiation between the Colchis and Hyrcan. Bayesian clustering of the genotypes revealed three populations with high levels of admixture between the sampling sites.Conclusions: The lack of strong genetic structure of studied populations of Z. carpinifolia contrasts with a previous study based on chloroplast markers and suggests that long-distance pollen dispersal is an important factor of gene flow among populations of Z. carpinifolia. The present study does not reveal any particular site with particularly isolated genotypes that would deserve more attention for conservation purposes than others, although some sites should be considered for further investigation.