Phenetic Approach Research Articles

Study on Several Genus of The Solanaceae Family with Phenetic Approach Methods

This study aimed to determine the morphological diversity of several genera from the Solanaceae family through a morphological approach, and the morphological characters that influence their grouping. The sampling activity is located in Lumajang district. The plant parts studied consisted of 30 characters including stature, stems, leaves and flowers which were then analyzed descriptively and phenetically. Based on the results of the descriptive analysis, it was found that there was a diversity of morphological characteristics between several genera of the Solanaceae family, namely the Solanum, Capsicum, Physalis, Datura, Nicotiana, and Petunia genera. Based on the analysis used the phenetic method in the SPSS program, a dendrogram was produced showing two groups, namely the genus Nicotiana and Petunia and the other groups Solanum, Capsicum, Datura, and Physalis. Then it grouped again and separated and finally got the species. Based on the results of PCA (Principal Component Analysis), the characters that influence the grouping of several genera from the Solanaceae family include phyllotaxis characters, leaf margins, leaf width, leaf length, leaf texture, anther color, and flower type. The result implications a morphological character can be used for plant identification.

Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach.

Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes. In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae. In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.

Morphological Characteristics and Taxonomical Positions of Annonaceae in Indonesia

Annonaceae is one of the most important and economically valuable plant families in Malesia region. Taxonomical studies could contribute to further utilization and conservation of the studied taxa. Due to their importance, an update in the morphological characters and taxanomical position of Annonaceae is required. This study aims to characterize the taxonomical position and relationships of 24 species belongs to the family Annonaceae found in the Purwodadi Botanic Gardens. In this work, we reported the taxonomical position and the phenetic clustering of 24 Annonaceae species collected from the Purwodadi Botanic Garden, East Java, Indonesia. The taxonomical study was performed based on morphological and phenetic approach where 81 characters (leaves, stem, and flower) were used in the analysis. A dendogram was produced following the scoring of the character using statistical program PAST ver. 3.0. (Hierarchial Cluster Analysis using Jukes Cantor Similarity approach). The dendogram showed clear separation between members of sub-family Annonoideae and Malmeoideae; however Alphonsea javanica and Sageraea lanceolata were not grouped into their respective tribe or sub-family. Further studies are required to evaluate these taxonomical separations. Overall, from the 24 studied species, we found that they grouped into 2 sub-family (Annonoideae and Malmeoideae), 3 tribes (Annoneae, Miliuseae, and Uvarieae), and 13 genus (Alphonsea, Annona, Desmos, Fissistigma, Miliusa, Mitrephora, Orophea, Polyalthia, Popowia, Pseuduvaria, Sageraea, Stelechocarpus, dan Uvaria).

Median-Joining Networks and Bayesian Phylogenies Often Do Not Tell the Same Story

Inferring phylogenies among intraspecific individuals often yields unresolved relationships (i.e., polytomies). Consequently, methods that compute distance-based abstract networks, like Median-Joining Networks (MJNs), are thought to be more appropriate tools for reconstructing such relationships than traditional trees. Median-Joining Networks visualize all routes of relationships in the form of cycles, if needed, when traditional approaches cannot resolve them. However, the MJN method is a distance-based phenetic approach that does not involve character transformations and makes no reference to ancestor–descendant relationships. Although philosophical and theoretical arguments challenging the implication that MJNs reflect phylogenetic signal in the traditional sense have been presented elsewhere, an empirical comparison with a character-based approach is needed given the increasing popularity of MJN analysis in evolutionary biology. Here, we use the conservative Approximately Unbiased (AU) test to compare 85 cases of branching patterns of cycle-free MJNs and Bayesian Inference (BI) phylogenies using datasets from 55 empirical studies. By rooting the MJN analyses to provide directionality, we report substantial disagreement between computed MJNs and posterior distributions on BI phylogenies. The branching patterns in MJNs and BI phylogenies show significantly different relationships in 37.6% of cases. Among the relationships that do not significantly differ, 96.2% show alternative sets of relationships. Our results indicate that the two methods provide different measures of relatedness in a phylogenetic sense. Finally, our analyses also support previous observations of the statistical hypothesis testing by reconfirming the over-conservativeness of the Shimodaira-Hasegawa test versus the AU test.

Clonality, local population structure and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex.

Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with ~300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. We assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. Four hundred and five samples of the four species, representing 57 populations, were subjected to restriction site-associated DNA sequencing (RADseq). Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Difference in fitness between genets was estimated as the numbers of ramets each genet comprised. Degrees of clonality [numbers of genets/numbers of ramets (samples)] within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but two to eight ramets were dsumbers ansd text etected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets and sexes were not detected. Within S. divinum, however, female gametophytes harboured two to three times the number of microbial taxa as males. These four Sphagnum species all exhibit similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns, where genets abut one another but do not extensively mix because of limited ramet fragmentation, and the guerrilla patterns, where extensive genet fragmentation and dispersal result in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.

NOTES ON TAXONOMY OF ATHYRIUM NIGRIPES (BLUME) T. MOORE COMPLEX, AN INSIGHT FROM MOUNTAINS IN JAVA

Athyrium nigripes is a highly variable species described and recorded mostly from Java and few from surrounding islands. There are different arguments on its delimitation and hence its extent of distribution. We attempted to elucidate disagreement on delimitation of four related species described from Java: Athyrium nigripes, Aspidium costale, At. pulcherrimum and At. nitidulum with phenetic approach. The analysis formed four clusters; cluster I consist of the large sized and include type specimen of At. pulcherrimum and Asp. costale, cluster II for plants with standard form and include type specimen of At. nigripes, cluster III only for serrated plants and cluster IV contain the At. nitidulum form. Since Asp. costale clustered in group I, this species is more closely related to At. pulcherrimum than to At. nigripes nested in group II. Large size and degree of division indicate major clustering within the complex species.

Creating environment for students to make interdisciplinary competences in botany

The authors have developed an innovative botanical course that integrates genetic ideas into the botany curriculum. The process of choosing regional relics was conducted with the aim of illustrating the notions of full and partial dominion. This paper presents a novel phenetic approach for examining population genetic trends via the analysis of discrete alternative characteristics. In order to achieve this purpose, it is recommended to choose plant specimens from the local area that have significant morphological variety. This will allow students to actively participate in the collecting and study process during trips. The educational institution’s curriculum integrates research components and cultivates the growth of mathematical statistical skills for the purpose of conducting quantitative analysis of results. The exploitation of currently available regional objects demonstrates the concept of the law of homologous series in genetic diversity and mutagenesis in plants. One of the recommended papers provides a detailed and concentrated overview of the developmental cycles seen in the primary plant categories. The investigation of hybridization in plants is often undertaken via the examination of this phenomena over a diverse range of plant species, including both widely dispersed wild plants and cultivated varieties. These botanical specimens have the capacity to engage in crossbreeding, leading to the emergence of hybrids that may occur either naturally or by deliberate human intervention.

Varietal Descriptors for the Distinction of Underutilized Varieties of Sechium edule (Jacq) Swartz.

Sechium edule (Jacq.) Sw. (Cucurbitaceae) is a species native to Mexico and Central America. The collection, characterization, and evaluation of accessions maintained in genebanks is essential for the conservation of this species. However, there are no specific varietal descriptors that differ from those used in a phenetic approach and are adapted to international registration guidelines to help distinguish, improve, cluster, and protect intraspecific variants of common use and those obtained by breeding. Therefore, 65 morphological descriptors (qualitative and quantitative) were evaluated in 133 accessions obtained from Mexico, Guatemala, and Costa Rica located in the National Germplasm Bank of S. edule in Mexico. These characteristics were observed to be phenetically stable for five generations under the same agroclimatic conditions. In addition, an analysis of amplified fragment length polymorphism (AFLP) was applied to 133 samples from a set of 245 accessions. According to the multivariate analysis, 26 of the 65 descriptors evaluated (qualitative and quantitative) enabled differentiation of varieties of S. edule. The AFLP analysis showed a high level of polymorphism and genetic distance between cultivated accessions and their corresponding wild ancestor. The variations in S. edule suggest that the morphological characteristics have differentiated from an essentially derived initial edible variety (ancestral original variety), but unlike other cucurbits, there is no evidence of the ancestral edible for Sechium since the seed is unorthodox and there are no relicts.

A Phenetic Approach to Selected Variants of Arabic and Aramaic Scripts

This paper aims to introduce the phenetic method for processing paleographical datasets and evaluating their similarity relationships. The presented numerical taxonomic method was applied for selected varieties of the Arabic and Aramaic scripts. The phenetic model was evaluated by hierarchical clustering and—after applying multidimensional scaling—a centroid-based clustering method. The hierarchical clustering results were presented as dendrograms (phenograms), while the centroid-based results were given in 2- and 3-dimensional Cartesian coordinate systems. The obtained results demonstrate that the numerical taxonomy's phenetic approach is useful in describing the distances between different writing systems. The long-term goal of the research is to apply machine learning tools to clarify the relationships between the large number of Aramaic and Arabic script variants. This study belongs to the field of pattern evolution, in which machine learning methods of biological evolution are used to model evolving patterns (such as writing systems) over time.

DNA Barcode for the Parthenogenetic Surinam Cockroach Pycnoscelus surinamensis (Linnaeus, 1758) (Blattodea: Blaberidae) from India

DNA Barcoding is one of the emerging tools in molecular identification of faunal diversity, specifically insect fauna. The Surinam cockroach, Pycnoscelus surinamensis is the only known roach to be obligatorily parthenogenetic, with reported haplotypes. P. surinamensis is well established in Indomalayan, tropical and subtropical regions and substantially documented from India with a phenetic approach. Herewith we report the first set of mt DNA barcode from a vouchered collection for the species from southern Western Ghats India. Discussions are made on the identity of two sequences each of Blatteria species and Pycnoscelus species reported from USA.

Integrando análisis morfométricos y filogenéticos: de la sistemática fenética a la morfometría filogenética

Antecedentes y Objetivos: Se han acumulado métodos cuantitativos para el uso de mediciones lineales y coordenadas Cartesianas de puntos en análisis de la variación morfométrica. A diferencia de revisiones previas, aquí se enfatizan las bases teóricas de los espacios matemáticos y del morfoespacio de un carácter taxonómico. El objetivo de esta revisión es suministrar elementos conceptuales para una comprensión básica de los métodos morfométricos y estadísticos útiles en la sistemática bajo un enfoque filogenético. Métodos: Los datos morfométricos se están aplicando en estudios de biología comparativa, usando las filogenias como referencia. En contraste, las aplicaciones de la morfometría en sistemática han sido con el objetivo de agrupar y distinguir grupos taxonómicos fenéticamente con la similitud total. Bajo un enfoque filogenético, los datos morfométricos también se pueden usar para el estudio de la variación de caracteres taxonómicos, la identidad de los estados y la inferencia de filogenias. Los grupos taxonómicos debieran ser propuestos a partir de grupos monofiléticos descubiertos con métodos filogenéticos. Resultados clave: Se presentan las bases de la teoría de la morfometría, geometría vectorial, el espacio de Kendall, la distancia Procrustes, proyección de espacios tangenciales y construcción de hipercubos del morfoespacio. Se revisan conceptos estadísticos útiles para la aplicación de los Análisis de Componentes Principales y los Análisis de Variables Canónicas en sistemática. Particularmente se dan recomendaciones y ejemplos sobre el uso de mediciones lineales y coordenadas de puntos en análisis morfométricos para la identificación de especies, la variación de caracteres taxonómicos y en la inferencia de filogenias y clasificación. Conclusiones: El amplio acervo actual de métodos brinda la oportunidad de integrar los datos morfométricos para descubrir homología táxica y homología transformacional. Esto implica un cambio epistemológico necesario para transitar de aplicaciones bajo una sistemática fenética, a la integración de los análisis morfométricos como parte de la investigación filogenética.

ON THE LATIN SOURCE OF THE ITALIAN VERSION OF ALHACEN'S DE ASPECTIBUS (VAT. LAT. 4595)

AbstractA comparison of the manuscripts has shown that De li aspecti, the Italian version of Alhacen's De aspectibus, Vat. lat. 4595 (I), was copied from London, British Library, Royal 12.G.vii (L). The discovery of long omissions in L, not reproduced in I, disproves this conclusion. The error has two reasons: a sampling too small, the confusion between phenetic and cladistic approaches.

Genetic Variation and Phylogenetic Relationship among four Parrotfishes (genus Scarus) in Hurghada, Red Sea Coast, Egypt Based on RAPD Markers

Random amplified polymorphic DNA (RAPD) fingerprints were obtained for 4 Parrotfishes (genus Scarus) namely, Scarus collana Ruppell 1835; Scarus frenatus Lacepede 1802; Scarus (Chlorurus) sordidus Forsskal 1775 andScarus niger Forsskal 1775 using RAPD-PCR typing technique. A total of 111 bands (ranging from 200 to 2000 base pair) were produced, 13 monomorphic (common) and 98 polymorphic (88.29% level of polymorphism). The Scarus frenatus recorded highest band frequencies among studied species. Under phenetic approaches clustering using unweighted pair group method average (UPGMA) based on Nei-72 genetic distance, principal coordinate analysis (PCOA), and neighbour joining (NJ) based on pairwise mean character differences, the studied scarids formed two groups as sister taxa and most likely to have the most common ancestor. There is a close genetic relatedness among group members [Scarus collana/Scarus niger and Scarus frenatus/Scarus sordidus]. According to parsimony (Cladistic) analysis, RAPD markers obtained are reliable and phylogenetically instructive. The four parrotfishes are related, but S. frenatus, S. sordidus, and S. niger have a close evolutionary relationships. Splitting of Scarus collana as basal group suggested a common ancestor having unique features (synapomorphies) be inherited in the studied parrotfishes. This study’s results possibly provide useful information about the genetic variation and phylogenetic relationships among parrotfishes.

Vertebrate endemism in south-eastern Africa numerically redefines a biodiversity hotspot.

We use numerical methods to explore patterns of vertebrate endemism in south-eastern Africa, refining the boundaries of the intuitively-defined Maputaland-Pondoland-Albany biodiversity hotspot, also proposing a zoogeographic regionalisation. An incidence matrix of 300 vertebrate species endemic to south-eastern Africa sensu lato in 37 operational geographic units were used in (a) phenetic cluster analysis (PCA) using the algorithm of unweighted pair-group method with arithmetic averages (phenetic approach), and (b) parsimony analysis of endemicity (PAE; parsimony approach), in order to numerically evaluate the bioregional delimitations. The analyses provide a valid biogeographical entity 37% larger than the Maputaland-Pondoland-Albany hotspot, but substantially (131%) higher in vertebrate endemicity viz. the Greater Maputaland-Pondoland-Albany (GMPA) region of vertebrate endemism. South-east Africa is recognised as a dominion in the global zoogeographical area hierarchy, with subordinate units including the GMPA province. Various spatially-based measures of endemism were mapped for vertebrate species restricted to the dominion, i.e. endemic to south-eastern Africa sensu stricto. Areas and centres of endemism detected respectively from PAE and PCA, within the south-east Africa dominion also support the refined boundary of the GMPA region of endemism, which provides a better spatial conservation priority compared to the Maputaland-Pondoland-Albany hotspot. Reptiles and amphibians are found to be the main drivers of the overall pattern of endemism, while the pattern in freshwater fish is the most distinctive. Our analyses also indicate a good congruence of the centres of endemism across different terrestrial vertebrate taxa.

Transformation from manufacturing process taxonomy to repair process taxonomy: a phenetic approach

The need of taxonomy is vital for knowledge sharing. This need has been portrayed by through-life engineering services/systems. This paper addresses this issue by repair process taxonomy development. Framework for repair process taxonomy was developed followed by its implementation. The importance of repair process taxonomy has been highlighted.

Phenotypic identification and numerical taxonomy of pigmented bacteria isolated from marine and freshwater aquatic at Yogyakarta, Indonesia

<p class="Abstract"><span class="fontstyle01">Numerical phenetic analysis was used to compare phenotypic data obtained from 6 isolates of pigmented bacteria strains taken from marine and river aquatic. Each strain was tested for 120 characters, analysed using the simple matching (SSM) and Jaccard (SJ) similarity indices with unweighted pair-group method with arithmetic mean (UPGMA) clustering method. All of the strains classified into two clusters, cluster A as marine pigmented bacteria and cluster B as river pigmented bacteria. Differences were observed between the dendrograms derived from the SSM and SJ. Presence of bacteriochlorophyll–a (Bchl–a), carotenoids, as well as other biochemical tests of three marine pigmented strains were in match with key characters of the genera<i> </i></span><span class="fontstyle01" style="font-style: italic;">Roseobacter, Roseateles</span><span class="fontstyle01" style="">, and </span><span class="fontstyle01" style="font-style: italic;">Erythrobacter</span><span class="fontstyle01">. Three of river pigmented strains were identified as </span><span class="fontstyle01" style="font-style: italic;">Xanthobacter</span><span class="fontstyle01" style="font-style: italic;">, </span><span class="fontstyle01" style="font-style: italic;">Flavobacterium</span><span class="fontstyle01" style=""><i>, </i>and </span><span class="fontstyle01" style="font-style: italic;">Pseudomonas</span><span class="fontstyle01"><i>.</i> It was proved that the marine and river pigmented bacteria isolates showed a relative phenotypically distance. It was clearly seen that the phenetic approach was a necessary tool to delimitate and identify the pigmented bacteria from different habitats.</span><o:p></o:p></p>

Morphological affinities of Homo naledi with other Plio-Pleistocene hominins: a phenetic approach.

Recent fossil material found in Dinaledi Chamber, South Africa, was initially described as a new species of genus Homo, namely Homo naledi. The original study of this new material has pointed to a close proximity with Homo erectus. More recent investigations have, to some extent, confirmed this assignment. Here we present a phenetic analysis based on dentocranial metric variables through Principal Components Analysis and Cluster Analysis based on these fossils and other Plio-Pleistocene hominins. Our results concur that the Dinaledi fossil hominins pertain to genus Homo. However, in our case, their nearest neighbors are Homo habilis and Australopithecus sediba. We suggest that Homo naledi is in fact a South African version of Homo habilis, and not a new species. This can also be applied to Australopithecus sediba.

Cephalic and limb anatomy of a new Isoxyid from the Burgess Shale and the role of "stem bivalved arthropods" in the disparity of the frontalmost appendage.

We herein describe Surusicaris elegans gen. et sp. nov. (in Isoxyidae, amended), a middle (Series 3, Stage 5) Cambrian bivalved arthropod from the new Burgess Shale deposit of Marble Canyon (Kootenay National Park, British Columbia). Surusicaris exhibits 12 simple, partly undivided biramous trunk limbs with long tripartite caeca, which may illustrate a plesiomorphic “fused” condition of exopod and endopod. We construe also that the head is made of five somites (= four segments), including two eyes, one pair of anomalocaridid-like frontalmost appendages, and three pairs of poorly sclerotized uniramous limbs. This fossil may therefore be a candidate for illustrating the origin of the plesiomorphic head condition in euarthropods, and questions the significance of the “two-segmented head” in, e.g., fuxianhuiids. The frontalmost appendage in isoxyids is intriguingly disparate, bearing similarities with both dinocaridids and euarthropods. In order to evaluate the relative importance of bivalved arthropods, such as Surusicaris, in the hypothetical structuro-functional transition between the dinocaridid frontal appendage and the pre-oral—arguably deutocerebral—appendage of euarthropods, we chose a phenetic approach and computed morphospace occupancy for the frontalmost appendages of 36 stem and crown taxa. Results show different levels of evolutionary decoupling between frontalmost appendage disparity and body plans. Variance is greatest in dinocaridids and “stem bivalved” arthropods, but these groups do not occupy the morphospace homogeneously. Rather, the diversity of frontalmost appendages in “stem bivalved” arthropods, distinct in its absence of clear clustering, is found to link the morphologies of “short great appendages,” chelicerae and antennules. This find fits the hypothesis of an increase in disparity of the deutocerebral appendage prior to its diversification in euarthropods, and possibly corresponds to its original time of development. The analysis of this pattern, however, is sensitive to the—still unclear—extent of polyphyly of the “stem bivalved” taxa.

Extent of the genetic diversity in Lebanese olive (Olea europaea L.) trees: a mixture of an ancient germplasm with recently introduced varieties

The olive tree was primary domesticated in the North-East Levant at least six millennia ago. Nowadays monumental trees are surviving across the Mediterranean Basin. These ancient, traditional varieties testify for the long cultivation of the crop but this germplasm remains incompletely characterized. Here, we investigated the genetic diversity among Lebanese cultivated olives in comparison to accessions from the whole Mediterranean Basin. Seventy-three olive trees including six monumentals were sampled in four main Lebanese areas, and characterized with 12 nuclear microsatellites and 39 plastid DNA markers. These genetic profiles were combined to those previously obtained in the world collection of Marrakech (WOGB) and analyzed with a phenetic approach, a multivariate analysis, and a Bayesian clustering method. Three main genetic clusters were identified in the Mediterranean cultivated olive tree as previously shown. The majority of Lebanese olive trees were assigned to the Eastern Mediterranean gene pool. A few genotypes were however assigned to the Central Mediterranean cluster. Plastid DNA markers revealed the presence of four haplotypes belonging to lineages E1 (72 olive trees) and E2 (one plant). Haplotype E1.1 that originated in the Eastern Mediterranean was found in 68 individuals (93 %). Within the common variety “Baladi”, several nuclear microsatellite profiles were identified including closely related olive trees that may correspond to molecular variants due to somatic variation. The six monumentals were remarkably positioned close to the Cypriot accessions and showed three different profiles, one of which matched to the most common profile of the widespread traditional variety “Baladi”. Our findings suggest that the Lebanese olive trees were locally selected during the beginning stages of olive growing and served as basic plant material for the current traditional varieties derived by both sexual and clonal propagation. Recent variety introductions from westernmost regions were also evidenced, but only in modern orchards from the Bekaa district.

Automated DNA‐based plant identification for large‐scale biodiversity assessment

Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable, markers can be problematic across divergent taxa. We advocate the combination of phylogenetic and phenetic methods for taxonomic assignment of DNA-barcode sequences against incomplete reference databases such as GenBank, and we developed a pipeline to implement this approach on large-scale plant diversity projects. The pipeline workflow includes several steps: database construction and curation, query sequence clustering, sequence retrieval, distance calculation, multiple alignment and phylogenetic inference. We describe the strategies used to establish these steps and the optimization of parameters to fit the selected psbA-trnH marker. We tested the pipeline using infertile plant samples and herbivore diet sequences from the highly threatened Nicaraguan seasonally dry forest and exploiting a valuable purpose-built resource: a partial local reference database of plant psbA-trnH. The selected methodology proved efficient and reliable for high-throughput taxonomic assignment, and our results corroborate the advantage of applying 'strict' tree-based criteria to avoid false positives. The pipeline tools are distributed as the scripts suite 'BAGpipe' (pipeline for Biodiversity Assessment using GenBank data), which can be readily adjusted to the purposes of other projects and applied to sequence-based identification for any marker or taxon.