Hybrids of the Genus Hesperis

(1) The taxon Hesperis silvestris CRANTZ d̊) var. pachycarpa BORB . Magy. Bot. Lap. 1:376, 1902 is a hybrid arisen by crossing of H. sylvestris with H. matronalis. (2) In the gardens are cultivated, besides H. matronalis L. subsp. matronalis and H. matronalis L. subsp. nivea (Baumg.) KULZC . also the hybrid plants: Hesperis matronalis subsp. matronalis X Hesperis matronalis subsp. nivea.     

Infrageneric Classification of Hesperis L

The genus Hesperis L. is a group of five phyletic lines which I ascribe the degree of the taxonomic value of a subgenus to: subgen. Hesperis, subgen. Mediterranea Borbás, subgen. Cvelevia Dvořák subgen. nov., subgen. Contorta Dvořák in Hedge & Rech., subgen. Diaplictos (Dvořák in Hedge & Rech.) Dvořák. The probable evolutional centre of the genus is in Asia Minor, in southern Transcaucasia and on the territory situated southwards. There is a suggestion to declare the name Hesperis a nom. conservandum.     

Notes on the Species Hesperis microcalyx FOURN

I prove that Hesperis schischkinii TZVEL . Mat. Gerb. Inst., 21 . 146 (1961) is a synonym of the species Hesperis microcalyx FOURN . Bull. Soc. bot. France, 13 , 351 (1866). I specify and complement the diagnosis of the species Hesperis microcalyx.     

Hesperis turkmendaghensis (sect. Hesperis) (Cruciferae/Brassicaceae), a new species from the Central Anatolia region, Turkey

Hesperis turkmendaghensis A.Duran & A.Ocak sp. nov. (Cruciferae) is described and illustrated from Anatolia, Turkey. The species grows under mixed forest, open forest and shady slopes in Türkmen Dağı (B3 Eskişehir) in Central Anatolia. It is closely related to H. matronalis L. ssp. matronalis , an endemic confined to Central Anatolia. Diagnostic morphological characters are discussed. Notes are also presented on its ecology, biogeography and conservation status. In addition, the pollen characteristics and seed coat surface of H. turkmendaghensis and H. matronalis are examined by SEM.   © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 239–247.     

Effects of kin-structured seed dispersal on the genetic structure of the clonal dioecious shrub ilex leucoclada

Nonrandom patterns of gene dispersal have been identified as possible causes of genetic structuring within populations. Attempts to model these patterns have generally focused solely on the effects of isolation by distance, but the processes involved are more complex than such modeling suggests. Here, we extend considerations of gene dispersal processes beyond simple isolation by distance effects by directly evaluating the effects of kin-structured gene dispersal mediated by the group dispersal of related seeds within fruits (i.e., kin-structured seed dispersal) by birds on genetic structure in Ilex leucoclada, a clonal dioecious shrub. To examine the genetic structure patterns, we established two 30x30 m plots (one with immature soils in old-growth forest and one in secondary forest, designated IM and SC, respectively) with different I. leucoclada stem densities. In these two plots 145 and 510 stems were found, representing 78 and 85 genets, respectively, identified by analyzing their genotypes at eight microsatellite loci. The clonal structure was stronger in the SC plot than in the IM plot. Correlograms of coancestry for genets in both plots exhibited significant, positive, high values in the shortest distance class, indicating the presence of strong genetic structure. However, Sp statistics revealed that the pattern of the genetic structure differed between the plots. In addition, to estimate the family structure within fruits, we sampled forty fruits, in total, from 15 randomly selected plants in the area around the IM and SC plots, and found that 80% of the fruits were multiseeded and 42-100% of the multiseeded fruits contained at least one pair of full sibs. Simulations based on these estimates demonstrated that the group dispersal of related seeds produced through correlated mating both within and across fruits, but not unstructured half-sib dispersal, could generate the observed magnitude and trends of genetic structure found in the IM plot. Furthermore, in addition to kin-structured seed dispersal, isolation by distance processes is also likely to promote genetic substructuring in the SC plot. After discussing possible ecological factors that may have contributed to the observed genetic structure, we contrast our results with those predicted by general isolation by distance models, and propose that kin-structured seed dispersal should promote some evolutionary phenomena, and thus should be incorporated, where appropriate, in models of gene dispersal in natural plant populations.     

Comparative genomics of the Bifidobacterium breve taxon

Background

Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host’s health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina.

Results

In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol.

Conclusions

Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-170) contains supplementary material, which is available to authorized users.     

A new Erioderma taxon from the Azores

Abstract:The Azorean lichen previously and erroneously referred in the literature toErioderma wrightii , belongs to the complex, widespread species E. leylandii, and is described as subsp.azoricum , possibly representing a relic, ancestral form with a composite chemistry. It is presently only known from Pico where it is under threat owing to the destruction of the forests.     

The concept of the taxon cycle in biogeography

Taxon cycles are sequential phases of expansion and contraction of the ranges of species, associated generally with shifts in ecological distribution. The important contribution of the taxon cycle to biogeographical analysis is its emphasis on evolutionary and ecological interactions among colonizing and resident species, which influence their extinction dynamics and establish patterns of geographical distribution. Taxon cycles were inferred originally from the distribution of species across island archipelagos, where a correlation was noted between gaps in island occupancy and the degree of phenotypic differentiation. This pattern implied that phases of colonization were followed by range contraction, while endemic Antillean species that were undifferentiated between islands suggested secondary expansion and the beginning of a new cycle. This interpretation was met with scepticism, but reconstruction of phylogenetic relationships from gene sequences has now permitted us to characterize taxon cycles in Lesser Antillean birds. The relative timing of phases of the cycle can be deduced from genetic divergence between island populations. We have found that taxon cycles have periods in the order of 10⁶ years and that cycles in different lineages occur independently of each other and independently of Pleistocene climate cycles. Individual island populations may persist for several millions of years on the larger islands of the Lesser Antilles; occasional expansion phases lead to the replacement of island populations that have disappeared, thus reducing the archipelago‐wide rate of extinction to nil. What drives taxon cycles is unknown, but we speculate that they may be caused by co‐evolution with enemy populations, and a probable mechanism would involve infrequent mutations influencing parasite virulence and avian host disease resistance. Taxon cycles undoubtedly occur on continents, but the geographical configuration of island archipelagos reveals more clearly their presence and invites their study.     

Phylogenetic classification and the definition of taxon names

Taxon names should be founded on phylogenetic relationships. and the names defined on the basis of common ancestry. Definitions based on evolutionary relationships relate the names to a phylogeny, and while the inclusiveness of the name may change with changing hypotheses of monophyly, the actual name remains unaltered. The limits of the name arc fixed by pointing to a monophyletic clade, where group membership is determined by the relationship to this clade. and not to subjective decisions of taxon delineations. Since phylogenetic definitions unambiguously connect the name to a specified clade, and not to a type, the conventional type concept becomes superfluous. We furthermore consider the Linnean categories poorly suited to convey the information in evolutionary trees, and suggest that these categories are abandoned.     

Development and polymorphism of simple sequence repeat DNA markers for the evergreen shrub Ilex leucoclada M.

We have developed 13 microsatellite loci from an enrichment library of genomic DNA in the evergreen shrub Ilex leucoclada. One hundred and eighty‐nine out of 432 clones were found to contain microsatellite repeats. Primer pairs were designed for 92 of these clones according to their sequence data. Thirteen of these primer pairs revealed polymorphism among 36 individuals sampled from 12 populations. Three to 27 alleles per locus were detected, and the expected heterozygosity ranged from 0.133 to 0.971. Because these 13 microsatellite markers showed high degrees of genetic variation, they should be useful tools for studying population and ecological genetics of I. leucoclada.     

Species: the concept, category and taxon

The term species by itself is vague because it refers to the species concept, the species category and the species taxon, all of which are distinct although related to one another. The species concept is not primarily a part of systematics, but has always been an integral part of basic biological theory, It is based on evolutionary theory and applies only to sexually reproducing organisms. The species concept and the phyletic lineage concept are quite distinct although they are related to one another. The important aspect of the species concept is lack of gene flow between different species, and hence the defining criterion of the species is genetic isolation. The species concept is often considered as non‐dimensional, both in time and space. Species possess three different major properties, namely genetic isolation, reproductive isolation and ecological isolation; these properties evolve at different times and under the effect of different causes during the speciation process. Speciation requires an external isolating barrier during the initial allopatric phase in which genetic isolation evolves and must reach 100% efficiency. The subsequent sympatric phase of speciation occurs after the disappearance of the external isolating barrier when members of the two newly evolved species can interact with one another and exert mutual selective demands on one another. Much of the reproductive and ecological isolation evolves during this secondary sympatric phase. The species category is a rank in the taxonomic hierarchy and serves as the basis on which the diversity of organisms is described; it is not the same as the species concept. The species category applied to all organisms, sexually and asexually reproducing. The species taxon is the practical application of the species category in systematics with the recognition of species taxa requiring many arbitrary decisions. No single set of rules exist by which the species category can be applied to all organisms. Recognition of species taxa in asexually reproducing organisms is based on amount of variation and gaps in the variation of phenotypic features associated with ecological attributes of these organisms as compared with similar attributes in sympatric species taxa of sexually reproducing organisms. Species taxa are multidimensional in that they exist over space–time and often have fuzzy borders. Because recognition of species taxa, including those in sexually reproducing organisms, depends on many arbitrary decisions especially when dealing with broad geographical and temporal ranges, species taxa cannot be used as the foundation for developing and testing theoretical concepts in evolutionary theory which can only be done with the non‐dimensional species concept.     

Rethinking taxon sampling in the light of environmental sequencing

Environmental DNA sequencing efforts of substrates such as soil, wood, and seawater have been found to present very different views of the underlying biological communities compared with efforts based on morphological examination and culture studies. The taxonomic affiliation of many of these environmental sequences cannot be settled with certainty due to the lack of proximate reference sequences in the corpus of public sequence data, and they are typically submitted to the international sequence databases without much indication of their relatedness. The scientific community has proved reluctant to include such unnamed sequences in phylogenetic analyses and taxonomic studies, but the present study shows such a position to be not only largely unwarranted but also potentially unsound. The sequences of 48 published fungal alignments of the nuclear ribosomal internal transcribed spacer region were subjected to similarity searches in the sequence databases to recover environmental sequences with a clear bearing on the respective ingroup. An average of 20 environmental sequences were added to each alignment, and upon rerunning the phylogenetic analyses of each study we found that topological rearrangements involving the original ingroup sequences were observed for no less than 29 (60%) of the studies. In nearly 20% of these cases, the rearrangements were large enough to question or even overthrow at least one conclusion presented in the original studies. The basal branching order was similarly subject to changes in 16% of the applicable studies. Environmental sequences are thus not only relevant in ecological research but form a requisite source of information also in systematics and taxonomy.
© The Willi Hennig Society 2010.     

Molecular phylogeny of the homoptera: a paraphyletic taxon

Homoptera and Heteroptera comprise a large insect assemblage, the Hemiptera. Many of the plant sap-sucking Homoptera possess unusual and complex life histories and depend on maternally inherited, intracellular bacteria to supplement their nutritionally deficient diets. Presumably in connection with their diet and lifestyles, the morphology of many Homoptera has become greatly reduced, leading to major controversies regarding the phylogenetic affiliations of homopteran superfamilies. The most fundamental question concerns whether the Homoptera as a whole are monophyletic. Recent studies based on morphology have argued that the Homoptera Sternorrhyncha (Aphidoidea, Coccoidea, Psylloidea, Aleyrodoidea) is a sister group to a group comprising the Homoptera Auchenorrhyncha (Fulgoroidea, Cicadoidea, Cercopoidea, Cicadelloidea) and the Heteroptera, making the Homoptera paraphyletic. We sequenced the 5 580-680 base pairs of small-subunit (18S) ribosomal DNA from a selection of Homoptera, Hemiptera, and their putative outgroups, the Thysanoptera and Psocoptera, to apply molecular characters to the problem of Homoptera phylogeny. Parsimony, distance, maximum-likelihood, and bootstrap methods were used to construct trees from sequence data and assess support for the topologies produced. Molecular data corroborate current views of relationships within the Sternorrhyncha and Auchenorrhyncha based on morphology and strongly support the hypothesis of homopteran paraphyly as stated above. In addition, it was found that Homoptera Sternorrhyncha have extra, GC-rich sequence concentrated in a variable region of the 18S rDNA, which indicates that some unique evolutionary processes are occurring in this lineage.Correspondence to: C.D. von Dohlen