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En Andalucía se realizan diversas actuaciones para la catalogación y conservación de la biodiversidad por parte del gobierno autonómico. Con respecto a las plantas, es notable la creación de una red de Jardines Botánicos asociados a espacios naturales protegidos. Estos jardines y áreas protegidas contienen una buena representación de la flora y de las especies amenazadas andaluzas, lo que supone un gran potencial para la investigación en biodiversidad. En este artículo se exploran posibilidades que ofrecen estos jardines, dirigidas hacia la investigación y se muestran algunos resultados obtenidos. Estas investigaciones se dirigen por un lado hacia el pasado histórico que ha generado la actual diversidad evolutiva (filogenética) de la flora leñosa usando marcadores genéticos y genómicos. Por otro lado, la representación de flora amenazada en los jardines ha permitido conocer también su nivel de singularidad filogenética y compararla con su rareza basada en aspectos biogeográficos y ecológicos. Los Jardines Botánicos han proporcionado gran parte de las muestras de tejido vegetal para la extracción de ADN necesario para resolver las filogenias. Finalmente, se exponen posibilidades futuras de investigación para prevenir los efectos del cambio climático en los sistemas naturales de Andalucía, usando los jardines como estaciones de observación fenológica. La información sobre el pasado evolutivo es muy relevante para determinar su influencia en la respuesta de las plantas a los cambios que ya están aconteciendo

Sixty-six carob accessions from 19 sites throughout Algeria were analysed by leaf, pod and seed characteristics to assess their genetic diversity and identify the first Algerian carob cultivars that could be used as germplasms for breeding programmes. We compared Algerian accessions with carobs from different Mediterranean countries, and our results showed a high level of morphological similarity between Algerian and Spanish carob pods. Analysis of variance showed highly significant differences (p ˂ 0.001) between accessions for all the quantitative traits. Correlation analysis between variables indicated that seed yield could be improved by selecting light, thin and narrow carob pods. Multiple correspondence analysis explained a total variance of 30.22 % and illustrated three distinct leaf classes. Principal component analysis proposed two main groups of variables, one based on seed performance and the other targeting pod potential. Hierarchical classification with seven clusters revealed considerable genetic diversity among the Algerian carob accessions studied, and indicated that the type of bioclimate did not influence their distribution, suggesting that morphometric traits are probably controlled more by genes that by bioclimate. Linear discriminant analysis, clustering and heatmap plotting identified 11 potential cultivars, 10 female and one hermaphroditic.

Made available in DSpace on 2022-04-28T17:21:44Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-01-03 FEDER funds from the Ministerio de Ciencia e Innovacion MINECO Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) VPPI-US Flower colour has played a decisive role as an evolutionary force in many groups of plants by driving speciation. A well-known example of colour polymorphism is found across the Mediterranean populations of Lysimachia arvensis and L. monelli, in which blue- and red-flowered plants can be found. Previous studies recognized two lineages within L. arvensis differing in flower colour, but this variation has not yet been considered in a phylogenetic context. We have reconstructed the ancestral states of flower colour across Mediterranean Lysimachia spp. aiming at understanding its phylogenetic signal using the nuclear internal transcribed spacer (ITS) sequences and three plastid markers. All blue- and red-flowered specimens were nested in different clades in the ITS tree, thus supporting that L. arvensis and L. monelli are polyphyletic, whereas low phylogenetic resolution was found in plastid markers. Monophyly was reconstructed for blue-flowered L. arvensis and L. monelli samples, and similarly for red-flowered individuals of each species: (1) blue-flowered L. arvensis was reconstructed as sister to the strictly blue-flowered L. talaverae in a monophyletic clade sister to remaining Lysimachia; (2) red-flowered L. arvensis was resolved as sister to red-flowered L. monelli in a monophyletic clade; and (3) clade 2 was sister to blue-flowered L. monelli and the strictly blue-flowered L. foemina. Our results suggest that colour lineages in L. arvensis and L. monelli constitute different species, but flower colour did not promote the separation of these lineages. We propose a new name for blue-flowered L. arvensis (L. loeflingii) and a new combination for red-flowered L. monelli (L. collina), maintaining L. arvensis for red-flowered plants and L. monelli for blue-flowered plants. Univ Seville, Fac Biol, Dept Biol Vegetal & Ecol, Apdo 1095, Seville 41080, Spain Sao Paulo State Univ, Biosci Inst, Dept Biodivers, Phenol Lab,UNESP, Sao Paulo, Brazil Royal Bot Gardens, Richmond 7W9 3DS, Surrey, England Sao Paulo State Univ, Biosci Inst, Dept Biodivers, Phenol Lab,UNESP, Sao Paulo, Brazil MINECO: CGL2008-02531-E MINECO: CGL2012-33270 MINECO: CGL2015-63827 MINECO: BES-2013-062859 MINECO: EEBB-I-17-12129 CAPES: 88887.194785/2018-00

Background and aims. Among the numerous pantropical species of the yam genus, Dioscorea, only a small group occurs in the Mediterranean basin, including two narrow Pyrenean endemics (Borderea clade), and two Mediterranean-wide species (D. communis and D. orientalis, Tamus clade). However, several currently unrecognized species and infraspecific taxa have been described in the Tamus clade due to significant morphological variation associated with D. communis. Our overarching aim was to investigate taxon delimitation in the Tamus clade using an integrative approach combining phylogenomic, spatial and morphological data. Methods. We analysed 76 herbarium samples using Hyb-Seq genomic capture to sequence 260 low-copy nuclear genes and plastomes, together with morphometric and environmental modelling approaches. Key results. Phylogenomic reconstructions confirmed that the two previously accepted species of the Tamus clade, D. communis and D. orientalis, are monophyletic and form sister clades. Three subclades showing distinctive geographic patters were identified within D. communis. These subclades were also identifiable from morphometric and climatic data, and introgression patterns were inferred between subclades in the eastern part of the distribution of D. communis. Conclusions. We propose a taxonomy that maintains D. orientalis, endemic to the eastern Mediterranean region, and splits D. communissensu lato into three species: D. edulis, endemic to Macaronesia (Canary Islands and Madeira); D. cretica, endemic to the eastern Mediterranean region; and D. communissensu stricto, widespread across western and central Europe. Introgression inferred between D. communis s.s. and D. cretica is likely to be explained by their relatively recent speciation at the end of the Miocene, disjunct isolation in eastern and western Mediterranean glacial refugia and a subsequent westward recolonization of D. communis s.s. Our study shows that the use of integrated genomic, spatial and morphological approaches allows a more robust definition of species boundaries and the identification of species that previous systematic studies failed to uncover.

Here we study a challenging group of karyotypically highly variable Epidendrum spp. using phylogenetic methods to help understand how hybridization/introgression contributes to karyotype evolution. We hypothesize that species with great chromosome number variation are a result of past hybridization/introgression. Conflicting topologies in trees constructed using separate plastid and nuclear datasets suggest past hybridization events that occurred most probably at least 3.7 Mya. A basic number x = 14 and substantial karyotype change followed by species divergence are suggested. Descending dysploidy and polyploidy were the most frequent changes estimated across the phylogenetic tree of the group. Two species, Epidendrum secundum and E. xanthinum, have probably experienced unidirectional gene flow involving their ancestors (the pollen recipients) and ancestors of E. puniceoluteum and E. denticulatum/E. flammeum, respectively, the pollen donors. However, it is not possible to say whether hybridization participated in the origin of E. secundum and E. xanthinum or merely contributed to their genomic divergence and karyotype change through introgression as has been observed in modern hybrid zones in Epidendrum. This pattern of introgression causing karyotype disruption and divergence could help explain the enigma of some highly diverse genera, such as Epidendrum. Further studies using a wider sampling of the genus could test if gene flow and karyotype variability are associated with the increase of speciation rates.

Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives (Asphodelaceae, subfamily Alooideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With >600 species and an origin of ±15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.

Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.La captura selectiva de secuencias de ADN ha surgido como una herramienta importante para la filogenética y la genética de poblaciones en taxones no-modelo. Mientras que el desarrollo de sondas de captura específicas para cada taxón requiere un esfuerzo sostenido, las colecciones de sondas universales disponibles pueden tener una potencia disminuida para la reconstrucción de relaciones filogenéticas poco profundas o de radiaciones rápidas. Presentamos aquí un conjunto de sondas para la captura selectiva desarrollado recientemente para Bromeliaceae, una familia de plantas extensa, ecológicamente diversa y con tasas de diversificación muy variables. El conjunto de sondas se centra en 1776 regiones de codificación, incluyendo genes supuestamente implicados en rasgos de innovación clave, con el objetivo de potenciar la comprobación de una amplia gama de hipótesis evolutivas. Comparamos la potencia relativa de este conjunto de sondas diseñado para un taxón específico, Bromeliad1776, con la colección universal Angiosperms353. El conjunto específico da lugar a un mayor éxito de captura en toda la familia. Sin embargo, el rendimiento global de ambos kits para reconstruir árboles filogenéticos es relativamente comparable, lo que pone de manifiesto el gran potencial de los kits universales para resolver las relaciones evolutivas. Para análisis filogenéticos o de genética de poblaciones más detallados, como por ejemplo la exploración de la congruencia de los árboles de genes, la diversidad de nucleótidos o la estructura de la población, el conjunto de captura específico para Bromeliaceae presenta claras ventajas. Discutimos las lecciones potenciales que este estudio comparativo proporciona para futuras investigaciones filogenéticas y de genética de poblaciones, en particular para el estudio de las radiaciones evolutivas.

To contribute to what is known about involvement of vegetation dynamics in Neotropical speciation, we used the Epidendrum latilabre complex, a taxonomically well-defined species group, to investigate past connections between Amazonian (AM) and Atlantic (AF) forests and address the following topics: (1) divergence times between sister species currently distributed in AM and AF; (2) distribution patterns of ancestral species of the E. latilabre complex and (3) potential routes connecting ancestral ranges between AM and AF. We developed a robust phylogenetic estimate for species of the E. latilabre complex by sequencing two nuclear and six plastid loci. Then, we combined divergence time estimation, ancestral range reconstruction and ecological niche modelling. Our biogeographic reconstruction exhibits a complex pattern of connections among tropical forests east of the Andes in South America. The AM and AF species of the E. latilabre complex are intermixed in the results, and climatic shifts during the Pleistocene (Chibanian) are suggested here as a major force promoting speciation. Sister species tend to be ecologically distinct in their climate niche spaces, and vicariance and peripheral isolation are reconstructed as the main drivers of speciation. There is evidence to suggest that the south-east/north-west bridge and the northern/north-eastern coastal route have been occupied by the ancestors of the E. latilabre complex, and alternative routes across the South American dry diagonal were unlikely. Further studies on Neotropical epiphytic taxa are still necessary for understanding the dynamics of historical connections between AM and AF.

The jewel orchids (Goodyerinae), named after their often colourful leaves, have a pantropical distribution with a clear Asian centre of diversity. However, the Nearctic and Neotropical America together form a second centre of diversity, with one-third of known species of Goodyerinae. Previously, only a few American samples have been included in phylogenetic studies, and their putatively Asian origins and American divergence times were poorly known. To elucidate these topics, we inferred phylogenetic trees, performed molecular dating and reconstructed biogeographic history using nuclear ribosomal ITS and plastid matK sequences for 34 species of Goodyerinae from the New World and 76 previously published accessions of Cranichideae. Our well-supported phylogenetic topology suggests two independent dispersal events to the New World from the Indomalesian region during the Miocene. The first inferred dispersal of a Neotropical clade diverged c. 11 Mya from their most recent common ancestor (MRCA), comprising three highly supported subclades that do not match the limits of Aspidogyne, Kreodanthus and Microchilus as previously circumscribed. The second dispersal involved a largely Nearctic clade of Goodyera s.l. diverging c. 8.4 Mya from the MRCA and exhibiting a complex biogeographic history with subsequent dispersals between the Nearctic and Indomalesia. The occurrence of these species in gallery forests putatively prevented vicariance events imposed by the expansion of the Chacoan region as previously detected for epiphytic Orchidaceae. Eighty-nine nomenclatural combinations and three new names in Microchilus are proposed.

Characterizing genetic diversity and structure of populations is essential for the effective conservation of threatened species.Orchis patenssensu lato is a narrowly distributed tetraploid species with a disjunct distribution (i.e., Northern Italy, North Africa and the Canary Islands), which is facing a severe decline. In this study, we evaluated levels of genetic diversity and population structuring using 12 new nuclear microsatellite markers. Our analyses of genetic differentiation based on multiple approaches (Structure analysis, PCA analysis, andF-statistics using the ploidy-independentRho-index) showed that gene flow is low across the range ofO. patens s.l., particularly in the Canary Islands. Clear differences in allele frequencies between Italy, Algeria and the Canary Islands underlie the genetic differentiation retrieved. Our study provides support for the recognition ofO. canariensisas a sister species toO. patensand the separation of the Italian populations as a new subspecies ofO. patens. Despite the high heterozygosity values found in all populations (ranging from 0.4 to 0.7), compatible with the tetraploid status of the species, small population sizes and reduced gene flow will be likely detrimental for the different populations in the long term, and we recommend immediate conservation actions to counteract further fragmentation and population decline.

Societal Impact Statement We rely on plants and fungi for most aspects of our lives. Yet plants and fungi are under threat, and we risk losing species before we know their identity, roles, and potential uses. Knowing names, distributions, and threats are first steps toward effective conservation action. Accessible products like field guides and online resources engage society, harnessing collective support for conservation. Here, we review current knowledge of the plants and fungi of the UK and UK Overseas Territories, highlighting gaps to help direct future research efforts toward conserving these vital elements of biodiversity. Summary This review summarizes current knowledge of the status and threats to the plants and fungi of Great Britain and the UK Overseas Territories (UKOTs). Although the body of knowledge is considerable, the distribution of information varies substantially, and we highlight knowledge gaps. The UK vascular flora is the most well studied and we have a relatively clear picture of its 9,001 native and alien taxa. We have seedbanked 72% of the native and archaeophyte angiosperm taxa and 78% of threatened taxa. Knowledge of the UKOTs flora varies across territories and we report a UKOTs flora comprising 4,093 native and alien taxa. We have conserved 27% of the native flora and 51% of the threatened vascular plants in Kew's Millennium Seed Bank, UK. We need a better understanding of the conservation status of plants in the wild, and progress toward completion or updating national red lists varies. Site‐based protection of key plant assemblages is outlined, and progress in identifying Important Plant Areas analyzed. Knowledge of the non‐vascular flora, especially seaweeds remains patchy, particularly in many UKOTs. The biggest gaps overall are in fungi, particularly non‐lichenized fungi. Considerable investment is needed to fill these knowledge gaps and instigate effective conservation strategies.

Estimating effective population size (Ne) is essential for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of Ne in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of vegetative (clonal) growth and sexual reproduction are a common group of organisms in which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) may be striking, and it is unclear how this discrepancy relates to Ne. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal vs. sexual reproduction impacted Ne. We sampled and genotyped >1000 ramets at microsatellites and SNPs loci, and estimated contemporary Ne with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower Ne. We considered factors potentially affecting our estimates, including using different molecular markers and sampling strategies, and pseudoreplication in genomic datasets. The magnitude of Ne/Nramets and Ne/Ngenets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that Ne in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction because demographic changes over time strongly influence Ne. This is especially relevant in species of conservation concern, in which population declines may not be detected by only ascertaining the number of genets.

International audience; Intense research efforts over the last two decades have renewed our understand-ing of plant phylogeography and domestication in the Mediterranean basin. Here we aim to investigate the evolutionary history and the origin of domestication of the carob tree (Ceratonia siliqua), which has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to delimit seven carob evolutionary units (CEUs). We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 single nucleotide polymorphisms generated by restriction-site asso-ciated DNA sequencing (RADseq). To address the complex wild vs. cultivated status of sampled trees, we classified 56 sampled populations across the Mediterranean basin as wild, seminatural or cultivated. Nuclear and cytoplasmic loci were identified from RADseq data and separated for analyses. Phylogenetic analyses of these genomic- wide data allowed us to resolve west-to- east expansions from a single long-term refu-gium probably located in the foothills of the High Atlas Mountains near the Atlantic coast. Our findings support multiple origins of domestication with a low impact on the genetic diversity at range-wide level. The carob was mostly domesticated from locally selected wild genotypes and scattered long-distance westward dispersals of domesticated varieties by humans, concomitant with major historical migrations by Romans, Greeks and Arabs. Ex situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in southwest Morocco, south Spain and eastern Mediterranean. Our study highlights the relevance of wild and seminatural habitats in the conservation of genetic resources for cultivated trees

Intense research efforts on phylogeography over the last two decades uncovered major biogeographical trends and renewed our understandings of plant domestication in the Mediterranean. We aim to investigate the evolutionary history and the origin of domestication of the carob tree that has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to identify carob evolutionary units (CEUs) based on genetic diversity structure and geography. We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 SNPs generated by restriction-site associated DNA sequencing (RADseq). The 56 populations sampled across the Mediterranean basin, classified as natural, semi-natural or cultivated, were examined. Although, RADseq data are consistent with previous studies identifying a strong West-to-East genetic structure and considerable admixture in some geographic parts, we reconstructed a new phylogeographic scenario with two migration routes occurring from a single refugium likely located in South-Western Morocco. Our results do not favour the regionally bound or single origin of domestication. Indeed, our findings support a cultivation model of locally selected wild genotypes, albeit punctuated by long-distance westward dispersals of domesticated varieties by humans, concomitant with major cultural waves by Romans and Arabs in the regions of dispersal. Ex-situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in South-Western Morocco, South Spain and Eastern Mediterranean. Our study underscores the relevance of natural and seminatural habitats of Mediterranean forests and their refugia in the conservation efforts of tree crops.

Flower colour constitutes a pivotal evolutionary force in speciation. The MediterraneanLysimachia arvensisandL. monelliare morphologically variable species having both blue or red flowered plants. Previous studies suggested thatL. arvensisplants differing in colour are diverging lineages, but this variation has not been considered in a phylogenetic context. We reconstruct the phylogenetic signal and the ancestral states of flower colour of MediterraneanLysimachiaspecies by using nuclear (ITS) and three plastid markers. Blue and red specimens are nested in two independent clades in the ITS tree, thus supporting thatL. arvensisandL. monelliare polyphyletic, whereas low phylogenetic resolution was found in plastid markers. Blue-floweredL. arvensisis reconstructed sister toL. talaveraein a monophyletic clade sister to the remainingLysimachia. Red-floweredL. arvensisis reconstructed sister to red-floweredL. monelliin a monophyletic clade sister to blue-floweredL. monelliandL. foemina. Our results suggest that colour lineages inL. arvensisandL. monelliconstitute different species, but flower colour did not promote the separation of these lineages. We propose a new name for blue-floweredL. arvensis(L. loeflingii) and a new combination for red-floweredL. monelli(L. collina).

Enabling food security requires access to a broad range of genetic resources to facilitate crop breeding. This need is increased in a climate change scenario, which will require the production of novel crops adapted to new conditions. However, many major crops have reduced genetic diversity due to the genetic bottlenecks that they have experienced during their domestication and subsequent breeding. Crop wild relatives (CWRs) remain underexploited in plant breeding programmes, mostly because of the lack of knowledge of their cross-compatibility with crops. In this study, we use a combination of phylogenetic distance metrics, cytogenetic compatibility data (e.g. chromosome number and ploidy) and information about breeding systems to predict interspecific cross-compatibility between crop and wild species and hence identify crop wild phylorelatives (CWPs) (i.e. CWRs that can breed with the crop). We illustrate this concept using cultivated asparagus as a model by integrating previous cross-compatibility knowledge and CWR classifications into a phylogenetic framework reconstructed using available sequence data. Our approach aims to reinforce the use of the gene pool classification system of CWRs of Harlan and De Wet, since CWPs are estimated to belong to the secondary gene pool and non-CWPs to the tertiary gene pool. Identifying CWPs unlocks novel uses of genetic resources, although such data are available for less than half of the known CWRs (43.4% with sequence data and 32.5% with known ploidy). The need to conserve plants that provide or enhance provisioning ecosystem services, including CWRs, is clear if we are to rise to the global challenge of ensuring food security for all. However, basic knowledge about their conservation status is still lacking, with only c. 20% of CWRs assigned an IUCN red list assessment, 23% of which are Data Deficient (DD). Using the CWP classification presented here to define CWRs will contribute towards helping to prioritize CWRs for IUCN assessments and, where prioritised, conservation.

Premise: The genetic structure of hybrid zones provides insight into the potential for gene flow to occur between plant taxa. Four closely related European orchid species (Orchis anthropophora, O. militaris, O. purpurea, and O. simia) hybridize when they co-occur. We aimed to characterize patterns of hybridization in O. militaris–O. purpurea, O. purpurea–O. simia, and O. anthropophora–O. simia hybrid zones using molecular and morphological data. Methods: We used 11 newly isolated nuclear microsatellites to genotype 695 individuals collected from seven hybrid zones and six allopatric parental populations in France. Geometric morphometric analysis was conducted using 15 labellum landmarks to capture the main aspects of petal shape. Results: Backcrossing was asymmetric toward O. militaris in multiple O. militaris–O. purpurea hybrid zones. Hybrids in O. purpurea–O. simia and O. anthropophora–O. simia hybrid zones were largely limited to F1 and F2 generations, but further admixture had occurred. These patterns were reflected in labellum geometric morphometric data, which correlated strongly with nuclear microsatellite data in all three species combinations. Conclusions: The coexistence of parental and admixed individuals in these Orchis hybrid zones implies they are likely to be tension zones being maintained by a balance between gene flow into the hybrid zone and selection acting against admixed individuals. The pattern of admixture in the three species combinations suggests intrinsic selection acting on the hybrids is weaker in more closely related taxa. This work was supported by NERC, the Bentham-Moxon Trust, the Systematics Research Fund, the Botanical Research Fund, and the OSU-OREME.

[Background and Aims] Extant plant groups with a long fossil history are key elements in understanding vascular plant evolution. Horsetails (Equisetum, Equisetaceae) have a nearly continuous fossil record dating back to the Carboniferous, but their phylogenetic and biogeographic patterns are still poorly understood. We use here the most extensive phylogenetic analysis to date as a framework to evaluate their age, biogeography and genome size evolution. [Methods] DNA sequences of four plastid loci were used to estimate divergence times and investigate the biogeographic history of all extant species of Equisetum. Flow cytometry was used to study genome size evolution against the framework of phylogenetic relationships in Equisetum. [Key Results] On a well-supported phylogenetic tree including all extant Equisetum species, a molecular clock calibrated with multiple fossils places the node at which the outgroup and Equisetum diverged at 343 Mya (Early Carboniferous), with the first major split among extant species occurring 170 Mya (Middle Jurassic). These dates are older than those reported in some other recent molecular clock studies but are largely in agreement with a timeline established by fossil appearance in the geological record. Representatives of evergreen subgenus Hippochaete have much larger genome sizes than those of deciduous subgenus Equisetum, despite their shared conserved chromosome number. Subgenus Paramochaete has an intermediate genome size and maintains the same number of chromosomes. [Conclusions] The first divergences among extant members of the genus coincided with the break-up of Pangaea and the resulting more humid, warmer climate. Subsequent tectonic activity most likely involved vicariance events that led to species divergences combined with some more recent, long-distance dispersal events. We hypothesize that differences in genome size between subgenera may be related to the number of sperm flagellae., INTRODUCTION MATERIALS AND METHODS Taxonomic sampling and DNA sequencing Phylogenetic analyses Divergence time estimates using fossil calibrations Ancestral range reconstruction analyses Genome size estimation using flow cytometry RESULTS Phylogenetic analyses Molecular clock analysis using fossil calibrations Ancestral range reconstruction analyses Genome size analysis of Equisetum DISCUSSION Origin, age and diversification of Equisetum Biogeography of Equisetum Genome size diversity and evolution in Equisetum Conclusions SUPPLEMENTARY DATA ACKNOWLEDGEMENTS LITERATURE CITED Supplementary data

International audience; Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or “drip” tips filled with extracellular bacteria of the species Orrella dioscoreae.1 This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and underground tubers, which also contain a small population of O. dioscoreae.2,3 Despite apparent vertical transmission, the genome of O. dioscoreae does not show any of the hallmarks of genome erosion often found in hereditary symbionts (e.g., small genome size and accumulation of pseudogenes).4, 5, 6 We investigated here the range and distribution of leaf symbiosis between D. sansibarensis and O. dioscoreae using preserved leaf samples from herbarium collections that were originally collected from various locations in Africa. We recovered DNA from the extracellular symbiont in all samples, showing that the symbiosis is widespread throughout continental Africa and Madagascar. Despite the degraded nature of this DNA, we constructed 17 symbiont genomes using de novo methods without relying on a reference. Phylogenetic and genomic analyses revealed that horizontal transmission of symbionts and horizontal gene transfer have shaped the evolution of the symbiont. These mechanisms could help explain lack of signs of reductive genome evolution despite an obligate host-associated lifestyle. Furthermore, phylogenetic analysis of D. sansibarensis based on plastid genomes revealed a strong geographical clustering of samples and provided evidence that the symbiosis originated at least 13 mya, earlier than previously estimated.3

Global biodiversity hotspots are areas containing high levels of species richness, endemism and threat. Similarly, regions of agriculturally relevant diversity have been identified where many domesticated plants and animals originated, and co-occurred with their wild ancestors and relatives. The agro-biodiversity in these regions has, likewise, often been considered threatened. Biodiversity and agro-biodiversity hotspots partly overlap, but their geographic intricacies have rarely been investigated together. Here we review the history of these two concepts and explore their geographic relationship by analysing global distribution and human use data for all plants, and for major crops and associated wild relatives. We highlight a geographic continuum between agro-biodiversity hotspots that contain high richness in species that are intensively used and well known by humanity (i.e., major crops and most viewed species on Wikipedia) and biodiversity hotspots encompassing species that are less heavily used and documented (i.e., crop wild relatives and species lacking information on Wikipedia). Our contribution highlights the key considerations needed for further developing a unifying concept of agro-biodiversity hotspots that encompasses multiple facets of diversity (including genetic and phylogenetic) and the linkage with overall biodiversity. This integration will ultimately enhance our understanding of the geography of human-plant interactions and help guide the preservation of nature and its contributions to people.

Oceanic islands constitute natural laboratories to study plant speciation and biogeographic patterns of island endemics. Juan Fernandez is a southern Pacific archipelago consisting of three small oceanic islands located 600–700 km west of the Chilean coastline. Exposed to current cold seasonal oceanic climate, these 5.8–1 Ma old islands harbor a remarkable endemic flora. All known Fernandezian endemic grass species belong to two genera, Megalachne and Podophorus, of uncertain taxonomic adscription. Classical and modern classifications have placed them either in Bromeae (Bromus), Duthieinae, Aveneae/Poeae, or Loliinae (fine-leaved Festuca); however, none of them have clarified their evolutionary relationships with respect to their closest Festuca relatives. Megalachne includes four species, which are endemic to Masatierra (Robinson Crusoe island) (M. berteroniana and M. robinsoniana) and to Masafuera (Alejandro Selkirk island) (M. masafuerana and M. dantonii). The monotypic Podophorus bromoides is a rare endemic species to Masatierra which is only known from its type locality and is currently considered extinct. We have used museomic approaches to uncover the challenging evolutionary history of these endemic grasses and to infer the divergence and dispersal patterns from their ancestors. Genome skimming data were produced from herbarium samples of M. berteroniana and M. masafuerana, and the 164 years old type specimen of P. bromoides, as well as for a collection of 33 species representing the main broad- and fine-leaved Loliinae lineages. Paired-end reads were successfully mapped to plastomes and nuclear ribosomal cistrons of reference Festuca species and used to reconstruct phylogenetic trees. Filtered ITS and trnTLF sequences from these genomes were further combined with our large Loliinae data sets for accurate biogeographic reconstruction. Nuclear and plastome data recovered a strongly supported fine-leaved Fernandezian clade where Podophorus was resolved as sister to Megalachne. Bayesian divergence dating and dispersal-extinction-cladogenesis range evolution analyses estimated the split of the Fernandezian clade from its ancestral southern American Pampas-Ventanian Loliinae lineage in the Miocene-Pliocene transition, following a long distance dispersal from the continent to the uplifted volcanic palaeo-island of Santa Clara-Masatierra. Consecutive Pliocene-Pleistocene splits and a Masatierra-to-Masafuera dispersal paved the way for in situ speciation of Podophorus and Megalachne taxa.

Bearberry (Arctostaphylos uva-ursi) is a medicinal plant traditionally employed for the treatment of urinary tract infections due to high contents of arbutin (hydroquinone &beta, D-glucoside), which is now mainly used as a natural skin-whitening agent in cosmetics. Bearberry has also been proposed as a natural antioxidant additive due to the high contents of phenolic compounds in leaves. We studied the variation on phenolic compounds in 42 wild populations of bearberry, aiming to elucidate if intrinsic biological, climatic, and/or geographic factors affect phenolic contents across its natural distribution in the Iberian Peninsula. Bearberry leaves were collected during autumn over a three-year period (2014&ndash, 2016) in populations across a latitude and altitude gradient. Methanolic extracts showed a wide range of variation in total phenols content, and different phenolic profiles regarding arbutin (levels of this major constituent varied from 87 to 232 mg/g dr wt), but also catechin and myricetin contents, which were affected by geographic and climatic factors. Moderate levels of variation on genome size&mdash, assessed by flow cytometry&mdash, and on two plastid DNA regions were also detected among populations. Genetic and cytogenetic differentiation of populations was weakly but significantly associated to phytochemical diversity. Elite bearberry genotypes with higher antioxidant capacity were subsequently identified.

This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting typical quadripartite arrangement (LSC, SSC and two IRs). Variation detected in the LSC/IR and SSC/IR junctions is explained by the loss of ndhF and ycf1 length variation. For the two genera of epiphytic clade in Spiranthinae, almost whole sets of the ndh-gene family were missing. Eight mutation hotspots were identified based on nucleotide diversity, sequence variability and parsimony-informative sites. Three of them (rps16-trnQ, trnT-trnL, rpl32-trnL) seem to be universal hotspots in the family, and the other five (trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, and rps15-ycf1) are described for the first time as orchid molecular hotspots. These regions have much more variation than all those used previously in phylogenetics of the group and offer useful plastid markers for phylogenetic, barcoding and population genetic studies. The use of whole plastomes or exclusive no-gap matrices also positioned with high support the holomycotrophic Rhizanthella among Orchidoideae plastomes in model-based analyses, showing the utility of plastomes for phylogenetic placement of this unusual genus.

The reduced cost of high‐throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per‐sample cost, which can be inflated when using off‐the‐shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per‐sample costs in high‐throughput targeted sequencing projects. We review the minimal equipment and consumable requirements for targeted sequencing while comparing several alternatives to reduce bulk costs in DNA extraction, library preparation, target enrichment, and sequencing. We consider how each of the workflow alterations may be affected by DNA quality (e.g., fresh vs. herbarium tissue), genome size, and the phylogenetic scale of the project. We provide a cost calculator for researchers considering targeted sequencing to use when designing projects, and identify challenges for future development of low‐cost sequencing in non‐model plant systems.

Premise We developed a target enrichment panel for phylogenomic studies of Dioscorea, an economically important genus with incompletely resolved relationships. Methods Our bait panel comprises 260 low- to single-copy nuclear genes targeted to work in Dioscorea, assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent-based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species. Results The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm-wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives. Discussion Our customized panel reliably retrieves targeted loci from Dioscorea, is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.

Subtribe Angraecinae (Orchidaceae: Vandeae) are mainly distributed in Africa, but with two genera, Campylocentrum and Dendrophylax, restricted to the Neotropics. As a widespread Neotropical genus, Campylocentrum constitutes an appropriate model for revealing biogeographical patterns in this area and investigating routes of colonization and dispersal. In this study, we reconstructed phylogenetic relationships of the genus with Bayesian inference and maximum parsimony analyses of combined nuclear (ITS rDNA and Xdh) and plastid (matK exon, rpl32-trnL spacer, trnL intron, trnL-trnF spacer and ycf1 exon) DNA datasets, aimed at establishing a new infrageneric classification for this taxonomically complex genus. Based on the most comprehensive phylogenetic tree, we investigated the biogeographical history of Campylocentrum by estimating divergence times, inferred using fossil and secondary calibrations applying a relaxed-clock model approach, and reconstructing ancestral areas of distribution under a time-stratified likelihood model. The phylogenetic analyses provided strong support for the majority of the clades. Campylocentrum is monophyletic, and we recognize five sections based upon strongly supported clades. We conclude that the African angraecoid ancestor of Campylocentrum and Dendrophylax dispersed to the Antilles. Campylocentrum is estimated to be a relatively young genus (late Miocene, c. 8.2 Mya) and its most recent common ancestor had a disjunct distribution in the Antilles and Parana dominion. During the Pliocene, the five sections diverged and expanded their distributions in the Neotropics, and in the Pleistocene diversification was experienced by some of the terminal clades. We hypothesize that the evolutionary history of Campylocentrum was strongly influenced by orogenic events during the Pliocene and climatic fluctuations during the Pleistocene Universidad de Costa Rica/[814-B5-A87]/UCR/Costa Rica National Science Foundation/[DEB-0946618]/NSF/Estados Unidos UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL)