Morphological Cladistic Analysis Research Articles

Argasid and ixodid systematics: Implications for soft tick evolution and systematics, with a new argasid species list

The systematics of the genera and subgenera within the soft tick family Argasidae is not adequately resolved. Different classification schemes, reflecting diverse schools of scientific thought that elevated or downgraded groups to genera or subgenera, have been proposed. In the most recent classification scheme, Argas and Ornithodoros are paraphyletic and the placement of various subgenera remains uncertain because molecular data are lacking. Thus, reclassification of the Argasidae is required. This will enable an understanding of soft tick systematics within an evolutionary context. This study addressed that knowledge gap using mitochondrial genome and nuclear (18S and 28S ribosomal RNA) sequence data for representatives of the subgenera Alectorobius, Argas, Chiropterargas, Ogadenus, Ornamentum, Ornithodoros, Navis (subgen. nov.), Pavlovskyella, Persicargas, Proknekalia, Reticulinasus and Secretargas, from the Afrotropical, Nearctic and Palearctic regions. Hard tick species (Ixodidae) and a new representative of Nuttalliella namaqua (Nuttalliellidae), were also sequenced with a total of 83 whole mitochondrial genomes, 18S rRNA and 28S rRNA genes generated. The study confirmed the utility of next-generation sequencing to retrieve systematic markers. Paraphyly of Argas and Ornithodoros was resolved by systematic analysis and a new species list is proposed. This corresponds broadly with the morphological cladistic analysis of Klompen and Oliver (1993). Estimation of divergence times using molecular dating allowed dissection of phylogeographic patterns for argasid evolution. The discovery of cryptic species in the subgenera Chiropterargas, Ogadenus and Ornithodoros, suggests that cryptic speciation is common within the Argasidae. Cryptic speciation has implications for past biological studies of soft ticks. These are discussed in particular for the Ornithodoros (Ornithodoros) moubata and Ornithodoros (Ornithodoros) savignyi groups.

A molecular phylogeny of the cicadas (Hemiptera: Cicadidae) with a review of tribe and subfamily classification.

A molecular phylogeny and a review of family-group classification are presented for 137 species (ca. 125 genera) of the insect family Cicadidae, the true cicadas, plus two species of hairy cicadas (Tettigarctidae) and two outgroup species from Cercopidae. Five genes, two of them mitochondrial, comprise the 4992 base-pair molecular dataset. Maximum-likelihood and Bayesian phylogenetic results are shown, including analyses to address potential base composition bias. Tettigarcta is confirmed as the sister-clade of the Cicadidae and support is found for three subfamilies identified in an earlier morphological cladistic analysis. A set of paraphyletic deep-level clades formed by African genera are together named as Tettigomyiinae n. stat. Taxonomic reassignments of genera and tribes are made where morphological examination confirms incorrect placements suggested by the molecular tree, and 11 new tribes are defined (Arenopsaltriini n. tribe, Durangonini n. tribe, Katoini n. tribe, Lacetasini n. tribe, Macrotristriini n. tribe, Malagasiini n. tribe, Nelcyndanini n. tribe, Pagiphorini n. tribe, Pictilini n. tribe, Psaltodini n. tribe, and Selymbriini n. tribe). Tribe Tacuini n. syn. is synonymized with Cryptotympanini, and Tryellina n. syn. is synonymized with an expanded Tribe Lamotialnini. Tribe Hyantiini n. syn. is synonymized with Fidicinini. Tribe Sinosenini is transferred to Cicadinae from Cicadettinae, Cicadatrini is moved to Cicadettinae from Cicadinae, and Ydiellini and Tettigomyiini are transferred to Tettigomyiinae n. stat from Cicadettinae. While the subfamily Cicadinae, historically defined by the presence of timbal covers, is weakly supported in the molecular tree, high taxonomic rank is not supported for several earlier clades based on unique morphology associated with sound production.

A new lineage of Cretaceous jewel wasps (Chalcidoidea: Diversinitidae).

Jewel wasps (Hymenoptera: Chalcidoidea) are extremely species-rich today, but have a sparse fossil record from the Cretaceous, the period of their early diversification. Three genera and three species, Diversinitus attenboroughi gen. & sp. n., Burminata caputaeria gen. & sp. n. and Glabiala barbata gen. & sp. n. are described in the family Diversinitidae fam. n., from Lower Cretaceous Burmese amber. Placement in Chalcidoidea is supported by the presence of multiporous plate sensilla on the antennal flagellum and a laterally exposed prepectus. The new taxa can be excluded from all extant family level chalcidoid lineages by the presence of multiporous plate sensilla on the first flagellomere in both sexes and lack of any synapomorphies. Accordingly, a new family is proposed for the fossils and its probable phylogenetic position within Chalcidoidea is discussed. Morphological cladistic analyses of the new fossils within the Heraty et al. (2013) dataset did not resolve the phylogenetic placement of Diversinitidae, but indicated its monophyly. Phylogenetically relevant morphological characters of the new fossils are discussed with reference to Cretaceous and extant chalcidoid taxa. Along with mymarid fossils and a few species of uncertain phylogenetic placement, the newly described members of Diversinitidae are among the earliest known chalcidoids and advance our knowledge of their Cretaceous diversity.

Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids.

Background and AimsBee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus.MethodsAt least two accessions of each of the ten species groups previously circumscribed from large-scale cloned nuclear ribosomal internal transcibed spacer (nrITS) sequencing were subjected to restriction site-associated sequencing (RAD-seq). The resulting matrix of 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to construct an unrooted network and a rooted maximum likelihood phylogeny. A parallel morphological cladistic matrix of 43 characters generated both polymorphic and non-polymorphic sets of parsimony trees before being mapped across the RAD-seq topology.Key ResultsRAD-seq data strongly support the monophyly of nine out of ten groups previously circumscribed using nrITS and resolve three major clades; in contrast, supposed microspecies are barely distinguishable. Strong incongruence separated the RAD-seq trees from both the morphological trees and traditional classifications; mapping of the morphological characters across the RAD-seq topology rendered them far more homoplastic.ConclusionsThe comparatively high level of morphological homoplasy reflects extensive convergence, whereas the derived placement of the fusca group is attributed to paedomorphic simplification. The phenotype of the most recent common ancestor of the extant lineages is inferred, but it post-dates the majority of the character-state changes that typify the genus. RAD-seq may represent the high-water mark of the contribution of molecular phylogenetics to understanding evolution within Ophrys; further progress will require large-scale population-level studies that integrate phenotypic and genotypic data in a cogent conceptual framework.

Revision and cladistic analysis of the Southeast Asian leaf-dwelling spider genus Calapnita Simon (Araneae, Pholcidae).

The Southeast Asian pholcid genus Calapnita Simon, 1892 is revised, with descriptions of 17 new species, five of them in the phyllicola group (Borneo: C. lehi, C. kubah, C. bidayuh, C. bankirai; Malay Peninsula, Sumatra, Java: C. anai), 12 in the vermiformis group (Borneo: C. bario, C. bariengi, C. magaseng, C. dayak, C. lawangan, C. loksado; Sulawesi: C. bugis; Philippines: C. bohol, C. dinagat, C. mae, C. nunezae, C. maragusan). New records are listed for six of the eight previously described species. A morphological cladistic analysis supports the monophyly of Calapnita and of its two previously proposed species groups and presents several new phylogenetically informative characters. New data are presented about ultrastructure and natural history (web, egg-sac, egg parasitism).

The phylogeny of Heliconia (Heliconiaceae) and the evolution of floral presentation

Heliconia (Heliconiaceae, order Zingiberales) is among the showiest plants of the Neotropical rainforest and represent a spectacular co-evolutionary radiation with hummingbirds. Despite the attractiveness and ecological importance of many Heliconia, the genus has been the subject of limited molecular phylogenetic studies. We sample seven markers from the plastid and nuclear genomes for 202 samples of Heliconia. This represents ca. 75% of accepted species and includes coverage of all taxonomic subgenera and sections. We date this phylogeny using fossils associated with other families in the Zingiberales; in particular we review and evaluate the Eocene fossil Ensete oregonense. We use this dated phylogenetic framework to evaluate the evolution of two components of flower orientation that are hypothesized to be important for modulating pollinator discrimination and pollen placement: resupination and erect versus pendant inflorescence habit. Our phylogenetic results suggest that the monophyletic Melanesian subgenus Heliconiopsis and a small clade of Ecuadorian species are together the sister group to the rest of Heliconia. Extant diversity of Heliconia originated in the Late Eocene (39Ma) with rapid diversification through the Early Miocene, making it the oldest known clade of hummingbird-pollinated plants. Most described subgenera and sections are not monophyletic, though closely related groups of species, often defined by shared geography, mirror earlier morphological cladistic analyses. Evaluation of changes in resupination and inflorescence habit suggests that these characters are more homoplasious than expected, and this largely explains the non-monophyly of previously circumscribed subgenera, which were based on these characters. We also find strong evidence for the correlated evolution of resupination and inflorescence habit. The correlated model suggests that the most recent common ancestor of all extant Heliconia had resupinate flowers and erect inflorescences. Finally, we note our nearly complete species sampling and dated phylogeny allow for an assessment of taxonomic history in terms of phylogenetic diversity. We find approximately half of the currently recognized species, corresponding to half of the phylogenetic diversity, have been described since 1975, highlighting the continued importance of basic taxonomic research and conservation initiatives to preserve both described and undiscovered species of Heliconia.

A Link No Longer Missing: New Evidence for the Cetotheriid Affinities of Caperea.

The origins of the enigmatic pygmy right whale Caperea marginata, the only living member of its subfamily (Neobalaeninae), are an outstanding mystery of cetacean evolution. Its strikingly disparate morphology sets Caperea apart from all other whales, and has turned it into a wildcard taxon that holds the key to understanding modern baleen whale diversity. Morphological cladistics generally ally this species with right whales, whereas molecular analyses consistently cluster it with rorquals and grey whales (Balaenopteroidea). A recent study potentially resolved this conflict by proposing that Caperea belongs with the otherwise extinct Cetotheriidae, but has been strongly criticised on morphological grounds. Evidence from the neobalaenine fossil record could potentially give direct insights into morphological transitions, but is currently limited to just a single species: the Late Miocene Miocaperea pulchra, from Peru. We show that Miocaperea has a highly unusual morphology of the auditory region, resulting from a–presumably feeding-related–strengthening of the articulation of the hyoid apparatus with the skull. This distinctive arrangement is otherwise only found in the extinct Cetotheriidae, which makes Miocaperea a “missing link” that demonstrates the origin of pygmy right whales from cetotheriids, and confirms the latter’s resurrection from the dead.

Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification

The explosive, long fuse, and short fuse models represent competing hypotheses for the timing of placental mammal diversification. Support for the explosive model, which posits both interordinal and intraordinal diversification after the KPg mass extinction, derives from morphological cladistic studies that place Cretaceous eutherians outside of crown Placentalia. By contrast, most molecular studies favor the long fuse model wherein interordinal cladogenesis occurred in the Cretaceous followed by intraordinal cladogenesis after the KPg boundary. Phillips (2016) proposed a soft explosive model that allows for the emergence of a few lineages (Xenarthra, Afrotheria, Euarchontoglires, Laurasiatheria) in the Cretaceous, but otherwise agrees with the explosive model in positing the majority of interordinal diversification after the KPg mass extinction. Phillips (2016) argues that rate transference errors associated with large body size and long lifespan have inflated previous estimates of interordinal divergence times, and further suggests that most interordinal divergences are positioned after the KPg boundary when rate transference errors are avoided through the elimination of calibrations in large-bodied and/or long lifespan clades. Here, we show that rate transference errors can also occur in the opposite direction and drag forward estimated divergence dates when calibrations in large-bodied/long lifespan clades are omitted. This dragging forward effect results in the occurrence of more than half a billion years of ‘zombie lineages’ on Phillips’ preferred timetree. By contrast with ghost lineages, which are a logical byproduct of an incomplete fossil record, zombie lineages occur when estimated divergence dates are younger than the minimum age of the oldest crown fossils. We also present the results of new timetree analyses that address the rate transference problem highlighted by Phillips (2016) by deleting taxa that exceed thresholds for body size and lifespan. These analyses recover all interordinal divergence times in the Cretaceous and are consistent with the long fuse model of placental diversification. Finally, we outline potential problems with morphological cladistic analyses of higher-level relationships among placental mammals that may account for the perceived discrepancies between molecular and paleontological estimates of placental divergence times.

The impact of fossil data on annelid phylogeny inferred from discrete morphological characters.

As a result of their plastic body plan, the relationships of the annelid worms and even the taxonomic makeup of the phylum have long been contentious. Morphological cladistic analyses have typically recovered a monophyletic Polychaeta, with the simple-bodied forms assigned to an early-diverging clade or grade. This is in stark contrast to molecular trees, in which polychaetes are paraphyletic and include clitellates, echiurans and sipunculans. Cambrian stem group annelid body fossils are complex-bodied polychaetes that possess well-developed parapodia and paired head appendages (palps), suggesting that the root of annelids is misplaced in morphological trees. We present a reinvestigation of the morphology of key fossil taxa and include them in a comprehensive phylogenetic analysis of annelids. Analyses using probabilistic methods and both equal- and implied-weights parsimony recover paraphyletic polychaetes and support the conclusion that echiurans and clitellates are derived polychaetes. Morphological trees including fossils depict two main clades of crown-group annelids that are similar, but not identical, to Errantia and Sedentaria, the fundamental groupings in transcriptomic analyses. Removing fossils yields trees that are often less resolved and/or root the tree in greater conflict with molecular topologies. While there are many topological similarities between the analyses herein and recent phylogenomic hypotheses, differences include the exclusion of Sipuncula from Annelida and the taxa forming the deepest crown-group divergences.

A New Extinct Inioid (Cetacea, Odontoceti) from the Upper Miocene Senhata Formation, Chiba, Central Japan: The First Record of Inioidea from the North Pacific Ocean

Abstract. Inioidea, which consists of Iniidae and Pontoporiidae, includes only four extant species, all of which occur in South America. Inioids were, however, more diversified and widely distributed in the past, starting from the late middle Miocene, as recorded from the eastern Pacific, North and South Atlantic, North Sea and the riverine systems of South America. In this paper, the author describes a new extinct inioid, Awadelphis hirayamai gen. et sp. nov. (WU SILS G 408), from the uppermost Miocene Senhata Formation (6.3–5.7 Ma) of Chiba, central Japan. Morphological cladistic analysis supports placement of this new taxon within the Inioidea. The new species is characterized by a right premaxillary eminence with a pronounced overhang on the right maxilla and a short zygomatic process of the squamosal. This is the first fossil record of an inioid not only from Japan but also from the North Pacific. The discovery of this new taxon considerably extends the paleobiogeographic range of inioids, and indica...

The phylogeny, evolutionary developmental biology, and paleobiology of the Deuterostomia: 25 years of new techniques, new discoveries, and new ideas

Over the past 25 years, new techniques, new discoveries, and new ideas have profoundly impacted our understanding of deuterostome interrelationships and, ultimately, deuterostome evolution. During the late 1980s and early 1990s morphological cladistic analyses made predictions about both taxonomic history and homology, predictions that would be tested independent of the morphological characters themselves with the advent of molecular systematics, the rise of evolutionary developmental biology, and continued exploration of the fossil record. Thanks to these three areas of inquiry, we have gone from scenarios where animals like mobile enteropneust hemichordates and chordates were derived from sessile filter-feeding animals like modern lophophorates, echinoderms, and pterobranch hemichordates, to a new perspective where hemichordates are recognized as the nearest living relative of the echinoderms, and that vagile gill-bearing animals like Cambrian vetulicolians are seen—at least by some—as close to the deuterostome last common ancestor, with both sessility and filter-feeding convergent features of deuterostomes (e.g., echinoderm) and non-deuterostomes (e.g., lophophorates) alike. Although much of the backbone of the new deuterostome phylogeny is supported by multiple independent data sets, as are statements of homology of several different morphological characters, in particular the homology of gill slits across Deuterostomia, nonetheless, the next quarter century of study on this remarkable group of animals promises to be as equally illuminating and exciting as the past quarter century.

The word is not enough: on morphemes, characters and ontological concepts.

The field of morphology has recently seen the arrival of computer-aided ontologies, tools which permit the semantic organization of defined concepts and which therefore promise to be extremely useful in computer-mediated approaches involving morphological data, for example in cladistics. The theoretical relationship between ontologies and cladistics, however, has hardly been explored. Here we examine the ontological status of the main terms in morphological cladistics, i.e. morpheme, character, character state and ontological concept. Morphemes are units of the descriptional perspective, whereas character states are units of the evolutionary perspective and refer to identical stages of transformation. Both morphemes and character states represent things, i.e. real entities. However, character state and morpheme denote different perspectives on these entities (description vs. evolution). Characters (transformation series; Hennig's ideographic character concept) and ontological concepts are both classes, but not of the same nature. Ontological concepts which are used to classify morphemes are constructs, i.e. totally man-made classes that serve only as a way of classifying real entities for human recognition. Characters, however, are classes that encompass all character states of common descent and which therefore have objective, human-independent properties. Characters, then, are natural kinds, classes which exhibit a natural identity in the same way as monophyla do, for example, which also have common descent as an objective property. Against this background, ontology-based morphology can be a valuable addition to phylogenetic systematics. Formalized, machine-parsable descriptions permit the generalization of morphemes in large datasets and can facilitate the recognition of identical character states. However, the expertise of the researcher is indispensable, and full automation of the transfer from the descriptive level to the evolutionary level thus appears impossible.

Morphological cladistic analysis resolves the generic limits of the Neotropical potter wasp genera Minixi Giordani Soika and Pachyminixi Giordani Soika (Hymenoptera : Vespidae : Eumeninae)

The generic classification of Neotropical Eumeninae has been termed chaotic, and synonymisation of taxa has become constant in recent years. Recognition of some generic limits are problematic due to features showing a great deal of variation, such as the length of the first metasomal tergum. This applies to the Neotropical Alphamenes van der Vecht, Minixi Giordani Soika and Pachyminixi Giordani Soika. Minixi has already been demonstrated to be paraphyletic in regards to Pachyminixi. These taxa are the focus of the present study, which used morphological data to infer the phylogenetic relationships among their constituent species. A total of 14 taxa and 34 characters were subjected to cladistic analysis under implied weighting. A single most-parsimonious cladogram was obtained, recovering Pachyminixi as monophyletic. Minixi, however, was paraphyletic relative to Pachyminixi and they are thus synonymised, with the former name having priority. A new species from Mexico, Minixi mariachii, sp. nov., is described. Minixi joergenseni bicingulatus (Zavattari, 1912) is synonymised under M. joergenseni (Schrottky, 1909), comb. nov. Additional new combinations are: Minixi arechavaletae (Brèthes, 1903), comb. nov., M. bifasciatum (von Schulthess, 1904), comb. nov., M. brethesi (Bertoni, 1927), comb. nov., M. sumichrasti (de Saussure, 1875), comb. nov., and M. uruguyense (de Saussure, 1855), comb. nov. Illustrations and a new key to species of Minixi are provided. The present study enhances our knowledge on Neotropical potter wasp systematics, providing one further step into a natural classification for a group whose taxonomy has suffered from irrational splitting of genera in the past century.

A hairy case: The evolution of filtering carnivorous Drusinae (Limnephilidae, Trichoptera)

The caddisfly subfamily Drusinae BANKS comprises roughly 100 species inhabiting mountain ranges in Europe, Asia Minor and the Caucasus. A 3-gene phylogeny of the subfamily previously identified three major clades that were corroborated by larval morphology and feeding ecologies: scraping grazers, omnivorous shredders and filtering carnivores. Larvae of filtering carnivores exhibit unique head capsule complexities, unknown from other caddisfly larvae. Here we assess the species-level relationships within filtering carnivores, hypothesizing that head capsule complexity is derived from simple shapes observed in the other feeding groups. We summarize the current systematics and taxonomy of the group, clarify the systematic position of Cryptothrix nebulicola, and present a larval key to filtering carnivorous Drusinae.We infer relationships of all known filtering carnivorous Drusinae and 34 additional Drusinae species using Bayesian species tree analysis and concatenated Bayesian phylogenetic analysis of 3805bp of sequence data from six gene regions (mtCOI5-P, mtCOI3-P, 16S mrDNA, CADH, WG, 28S nrDNA), morphological cladistics from 308 characters, and a total evidence analysis.All analyses support monophyly of the three feeding ecology groups but fail to fully resolve internal relationships. Within filtering carnivores, variation in head setation and frontoclypeus structure may be associated with progressive niche adaptation, with less complex species recovered at a basal position. We propose that diversification of complex setation and frontoclypeus shape represents a recent evolutionary development, hypothetically enforcing speciation and niche specificity within filtering carnivorous Drusinae.

Phylogeny and New Classification of Hydrothermal Vent and Seep Shrimps of the Family Alvinocarididae (Decapoda).

The paper addresses the phylogeny and classification of the hydrothermal vent shrimp family Alvinocarididae. Two morphological cladistic analyses were carried out, which use all 31 recognized species of Alvinocarididae as terminal taxa. As outgroups, two species were included, both representing major caridean clades: Acanthephyra purpurea (Acanthephyridae) and Alpheus echiurophilus (Alpheidae). For additional support of the clades we utilised available data on mitochondrial Cytochrome c Oxidase I gene (CO1) and 16S ribosomal markers. Both morphological and molecular methods resulted in similar tree topologies and nearly identical clades. We consider these clades as evolutionary units and thus erect two new subfamilies: Rimicaridinae (Alvinocaridinides, Manuscaris, Opaepele, Shinkaicaris, Rimicaris), Alvinocaridinae (Alvinocaris), whilst recognising Mirocaridinae (with genera Mirocaris and Nautilocaris) at subfamily level. One genus, Keldyshicaris could not be assigned to any subfamily and is thus left as incertae sedis. The monophyly of Alvinocardinae was supported by morphological data, but not supported by molecular data (two analyses); the monophyly of all subfamilies was supported both by morphological and molecular data. Chorocaris is herein synonymized with Rimicaris, whilst Opaepele vavilovi is herein transferred to a new genus Keldyshicaris. Morphological trends within Alvinocarididae are discussed and short biogeographical remarks are given. We provide emended diagnoses for all subfamilies and genera along with keys to all recognized species.

Molecular phylogenetics, diversification, and systematics of Tibicen Latreille 1825 and allied cicadas of the tribe Cryptotympanini, with three new genera and emphasis on species from the USA and Canada(Hemiptera: Auchenorrhyncha: Cicadidae).

North America has a diverse cicada fauna with multiple genera from all three Cicadidae subfamilies, yet molecular phylogenetic analyses have been completed only for the well-studied periodical cicadas (Magicicada Davis). The genus Tibicen Latreille, a large group of charismatic species, is in need of such work because morphological patterns suggest multiple groups with complicated relationships to other genera in the tribe Cryptotympanini. In this paper we present a molecular phylogenetic analysis, based on mitochondrial and nuclear DNA, of 35 of the 38 extant USA species and subspecies of the genus Tibicen together with their North American tribal allies (Cornuplura Davis, Cacama Davis), selected Tibicen species from Eurasia, and representatives of other Eurasian and Pacific cryptotympanine genera. This tree shows that Tibicen contains several well-supported clades, one predominating in eastern and central North America and related to Cryptotympana Stål and Raiateana Boulard, another in western North America related to Cacama and Cornuplura, and at least two clades in Eurasia. We also present a morphological cladistic analysis of Tibicen and its close allies based on 27 characters. Character states identified in the cladistic analysis define three new genera, two for North American taxa (Hadoa gen. n. and Neotibicen gen. n.) including several Mexican species, and one for Asian species (Subsolanus gen. n.). Using relaxed molecular clocks and literature-derived mtDNA rate estimates, we estimate the timeframe of diversification of Tibicen clades and find that intergeneric divergence has occurred since the late Eocene, with most extant species within the former Tibicen originating after the mid-Miocene. We review patterns of ecology, behavior, and geography among Tibicen clades in light of the phylogenetic results and note that the study of these insects is still in its early stages. Some Mexican species formerly placed in Tibicen are here transferred to Diceroprocta, following refinement of the definition of that genus.

Morphological cladistic analysis of eight popular Olive (Olea europaea L.) cultivars grown in Saudi Arabia using Numerical Taxonomic System for personal computer to detect phyletic relationship and their proximate fruit composition

Varietal identification of olives is an intrinsic and empirical exercise owing to the large number of synonyms and homonyms, intensive exchange of genotypes, presence of varietal clones and lack of proper certification in nurseries. A comparative study of morphological characters of eight olive cultivars grown in Saudi Arabia was carried out and analyzed using NTSYSpc (Numerical Taxonomy System for personal computer) system segregated smaller fruits in one clade and the rest in two clades. Koroneiki, a Greek cultivar with a small sized fruit shared arm with Spanish variety Arbosana. Morphologic analysis using NTSYSpc revealed that biometrics of leaves, fruits and seeds are reliable morphologic characters to distinguish between varieties, except for a few morphologically very similar olive cultivars. The proximate analysis showed significant variations in the protein, fiber, crude fat, ash and moisture content of different cultivars. The study also showed that neither the size of fruit nor the fruit pulp thickness is a limiting factor determining crude fat content of olives.

Bichir microRNA repertoire suggests a ray-finned fish affinity of Polypteriforme

The phylogenetic position of Polypteriforme (bichirs) remains elusive, despite extensive research both on morphological and molecular datasets. Unfortunately morphological cladistic analyses and molecular phylogenetic analyses had reached conflicting conclusions, as Polypteriformes were either grouped with lobe-finned fishes (Sarcopterygii) or ray-finned fishes (Actinopterygii), or even classified as their own group, the Brachiopterygii. In this study, we applied a third independent source of datasets, the presence versus absence of microRNAs, to re-investigate the phylogenetic relationship of bichirs. Through deep sequencing of small RNA library, we showed that bichirs should be grouped into ray-finned fishes rather than lobe-finned fishes. Phylogenetic analysis confirmed that bichirs were placed as the most basal member of the ray-finned fishes. Bichirs shared five unique microRNA families with teleostei, which were not found in any other species investigated to date. Bichirs have also retained three of five microRNAs that were previously deemed to be lost exclusively in teleostei. Furthermore, we report more than one hundred novel microRNAs that are unique to bichir. The identification of microRNAs in bichir provides overwhelming evidence for their affinity of ray-finned fishes. The sarcopterygian-like characteristics such as lobed fins, paired ventral lungs, and external gills in juveniles should not be considered as derived traits shared with those of sarcopterygians.

Morphological characters are compatible with mitogenomic data in resolving the phylogeny of nymphalid butterflies (lepidoptera: papilionoidea: nymphalidae).

Nymphalidae is the largest family of butterflies with their phylogenetic relationships not adequately approached to date. The mitochondrial genomes (mitogenomes) of 11 new nymphalid species were reported and a comparative mitogenomic analysis was conducted together with other 22 available nymphalid mitogenomes. A phylogenetic analysis of the 33 species from all 13 currently recognized nymphalid subfamilies was done based on the mitogenomic data set with three Lycaenidae species as the outgroups. The mitogenome comparison showed that the eleven new mitogenomes were similar with those of other butterflies in gene content and order. The reconstructed phylogenetic trees reveal that the nymphalids are made up of five major clades (the nymphaline, heliconiine, satyrine, danaine and libytheine clades), with sister relationship between subfamilies Cyrestinae and Biblidinae, and most likely between subfamilies Morphinae and Satyrinae. This whole mitogenome-based phylogeny is generally congruent with those of former studies based on nuclear-gene and mitogenomic analyses, but differs considerably from the result of morphological cladistic analysis, such as the basal position of Libytheinae in morpho-phylogeny is not confirmed in molecular studies. However, we found that the mitogenomic phylogeny established herein is compatible with selected morphological characters (including developmental and adult morpho-characters).

Revision of <I>Heuchera</I> Section <I>Rhodoheuchera</I> Subsections <I>Hemsleyanae</I> and <I>Rosendahliae</I> Subsectio Nova (Saxifragaceae)

A revision of a closely allied and poorly studied group of Mexican Heuchera species is presented. This work has necessitated several taxonomic and nomenclatural actions, namely: the recognition of the name H. longipetala as referring to the Mexican plant usually known as H. hemsleyana; the reduction of the latter to synonymy; the description of two new species, H. rosendahlii and H. wellsiae, having such divergent morphology as to warrant a new subsection, subsection Rosendahliae; the transfer of H. mexicana to subsect. Hemsleyanae; the description of a new variety for H. mexicana (H. mexicana var. potosiensis) and for H. longipetala (H. longipetala var. nudicaulis); the reduction of H. orizabensis to a variety of H. longipetala (H. longipetala var. orizabensis) and of H. amoena to a synonym of H. mexicana; and the lectotypification of the names H. orizabensis and H. hemsleyana. Provided are descriptions, notes on habitat and phenology, range maps, line drawings, and full specimen citations for all taxa treated, as well as a taxonomic key for all known species of Heuchera in Mexico, new chromosome counts for two taxa, and a morphological cladistic analysis of section Rhodoheuchera.