Iridoids as systematic markers in dicotyledon

Iridoid evolution is postulated to involve a gradual increase in the state of oxidation. From this, it appears that the iridoid-containing dicotyledons bifurcated at a primitive stage near the Ericales into the Cornales, with an extension to a Dipsacales branch and a Gentianiflorae branch, and into the Lamiiflorae.     

Indole alkaloids as systematic markers of the Apocynaceae

Indole alkaloids can be characterized by skeletal specialization (S), determined upon consideration of their relative position on a biogenetic map and the number of their naturally occurring substitutional derivatives, as well as by oxidation level (O). The mean (S) and (O) for contained alkaloids of a given plant taxon are taken to represent evolutionary advancement parameters, respectively EA_s and EA_o.A correlation of these EA_s/EA_o values for tribes of the Apocynaceae-Plumerioideae reveals a chemical gradient, given by gradually increasing EA_s and EA_o values, to link Carisseae-Alstonieae-Rauvolfieae-Tabernaemontaneae.     

Quinolizidine alkaloids as systematic markers of the Genisteae

A previously reported postulate concerning the evolution of quinolizidine alkaloids and the detailed consideration of the chemical composition led to a revised dendrogram showing proposed phylogenetic relations within the subfamily Papilionoideae in general and the tribe Genisteae in particular.     

Quinolizidine alkaloids as systematic markers of the papilionoideae

The structural characteristics of quinolizidine alkaloids have been quantified on the basis of their biogenetic origins. Such data have been used to determine evolutionary advancement parameters for genera of the Papilionoideae. These analyses indicate a correlation of the structural characters of alkaloids with ecogeography and morphology of the genera, suggesting an adaptive radiation of the taxa from tropical Africa in three major directions along a southern temperate “pre-cytisine” route, a northern temperatre “pre-cytisine-cytisine” route and a tropical “ormosanine” route with a temperate cytisine branch. The data also suggest the division of the Sophoreae into three chemical groups giving rise to Liparieae, Genisteae, Thermopsideae and Bossiaeeae. These concepts are embodied in a tentative phyletic classification of all genera of the Papilionoideae which contain quinolizidine alkaloids.     

Isoflavonoids as systematic markers

A taxonomic procedure, applicable to biogenetic groups (BG) of secondary metabolities, involves initially the determination of the relative probability of occurrence (RPO) with respect to skeleton and substitution for each compound of the BG. The means of the RPO-values of the constituents represent the evolutionary advancement parameters (EAP) of the species. Consideration of the EAPs and of the chemical composition leads to the classification of species along chemical lines. This procedure, which is independent of morphological evidence, applied to isoflavonoids, suggests the sequence of structural changes which accompany the evolution of this BG in nature, and, used as an auxiliary criterion to the conventional morphological classification, provides the basis for understanding of the evolutionary development in the Lotoideae.     

Evidence of regenerative ability in Myxicola infundibulum (Annelida,Sabellida): evolutionary and systematic implications

Members of only a few species of annelids are reported as being incapable of regeneration; of these, Myxicola infundibulum is the only example in the family Sabellidae. Interestingly, its congener Myxicola aesthetica exhibits noteworthy regenerative ability. Unambiguously identifying non‐regenerating species is critical to reconstructing how regenerative abilities evolved within the phylum. However, studies designed specifically to assess the regenerative potential of M. infundibulum have never been performed. In this study, we aimed to confirm the lack of regeneration ability of M. infundibulum, reported previously for Atlantic specimens, or to determine the extent to which regeneration occurs. Our results showed that individuals from the Mediterranean Sea (Adriatic Sea) do undergo regeneration of lost body parts, although to a lesser extent than do other sabellids. Therefore, M. infundibulum should no longer be considered a non‐regenerating species. At present, uncertainties regarding phylogenetic relationships of Sabellidae prevent inferences about the polarity of change in M. infundibulum. Since our findings are counter to those of previous studies which describe Atlantic specimens as non‐regenerating, more extensive analysis is required to ascertain if they could actually belong to a different species than Mediterranean M. infundibulum, accounting for these differences in reported regenerative capacity.     

螨类系统学研究中的分子标记

近年来,分子标记技术在螨类系统学研究中起到越来越重要的作用。文章就几种螨类系统学中用到的分子标记的原理和应用作一回顾,其中包括随机扩增多态性RAPD、限制性内切酶片段长度多态性RFLP、直接扩增片段长度多态性DALP、扩增片段长度多态性AFLP、微卫星DNASSR、核酸序列分析。讨论这几种分子标记在其应用中的优势及其局限性,并对分子标记在螨类系统学研究中的应用作出展望。     

Xanthones as systematic markers

An evolutionary scheme for shikimate-acetate derived xanthones is deduced from their substitution pattern. Increasing distance of a particular xanthone from the primitive precursor is symbolized by increasing numbers. Each xanthone containing plant species is characterized by the average of the numbers attributed to its constituents. Each genus is characterized by the average of the numbers calculated for its species. The method is useful in comparing phyletic order of genera within the Guttiferae.     

The genus Comus: Non-flavonoid glucosides as taxonomic markers

Previous proposals for subdivision of the genus Cornus are reviewed. Twenty-seven authenticated Cornus species have been studied for their content of non-flavonoid glucosides. Two distinct groups of taxa can be distinguished on this basis: one, containing a hydroxycyclohexadienone glucoside, along with salidroside, its reduced counterpart, and the second, characterized by containing various iridoid glucosides. The two types of glucosides are apparently mutually exclusive.     

Benzyltetrahydroisoquinoline-derived alkaloids as systematic markers

Basic unsubstituted skeleta within biogenetic groups can be codified according to their position along biosynthetic pathways aligned in order of probability of occurrence. Correlation of the codified structural type with the taxa in which they are found is effected through frequency indices associated with the relative number of derivatives of the skeleton in the taxon and the relative number of subunits of the taxon which contain derivatives thereof. The benzyltetrahydroisoquinolines, a biogenetically related group of compounds, serves as example of the applicability of the method, which is part of an integrated system of expression of biochemical data in biological systematics.     

Genetic markers, genealogies and biogeographic patterns in the cladocera

Cladoceran crustaceans are an important component of zooplankton in a wide range of freshwater habitats. Although the ecological characteristics of several cladoceran species have been well studied, biogeographical studies have been hampered by problematic taxonomic affiliations. However, recently developed molecular techniques, provide a powerful tool to subject aquatic taxa to comparative analyses. Here we highlight recent molecular approaches in aquatic ecology by presenting a simple method of DNA preparation and PCR amplification of the mitochondrial DNA (16S rDNA) in species from nine different families within the cladocera. On a broad taxonomic scale, sequence analysis of this mtDNA fragment has been used to produce the first molecular based phylogeny of the cladocera. This analysis clustered the cladoceran families in a fashion similar to that suggested by previous systematic classifications. In a more detailed analysis of the family Daphniidae, nuclear randomly amplified polymorphic DNA (RAPD), mitochondrial restriction fragment length polymorphism (RFLP) and morphological analyses were combined to identify species and interspecific hybrids within the Daphnia galeata species complex across 50 lakes in 13 European countries and one lake in Africa. The study revealed interspecific hybridization and backcrossing between some taxa (D. cucullata and D. galeata) to be widespread, and species and hybrids to frequently occur in sympatry. Genetic, as well as morphological information, suggests the occurrence of D. hyalina outside the Holarctic.     

Metazoa-level USCOs as markers in species delimitation and classification

Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.     

The Species Concept as a Cognitive Tool for Biological Anthropology

Taxonomy is caught between the search for the “perfect” theory and an elusive biological variability. The lack of major advances in issues related to how “species” and other taxonomic categories are defined suggests that perhaps we should avoid excessively rigid formalism in this regard. The risk is a separation between elegant but useless theories and confusing applications of the taxonomic tools. Communication is one of the main functions of taxonomy, and stability one of the main parameters that taxonomy users should be sensitive to. An excess of stability may generate anachronistic consequences while continuous revisions may make the tool of taxonomy scarcely practical. The current tendency pushes toward more and more fragmentation of biologically valid taxa. While taxonomy specialists enjoy such challenges, many taxonomy users feel a bit nervous and discouraged when trying to use a tool that is constantly changing. Debates over taxonomy would seem particularly unrewarding for fields with limited samples and scarce biological diversity, such as palaeoanthropology. In this context, where the information available is rarely sufficient to supply consistent taxonomical evidence, there are frequently excessive efforts to create debate on species separations. The risk is that we maintain the debate on a purely theoretical level, or else we distrust a reliable use of taxonomy. A compromise (and recommended) choice between these two extremes would be to rely on shared and reasonable interpretations of homogeneous evolutionary units, without diving into fine‐grained issues that will remain, however, unresolved. Taxonomy should be a tool, not the goal, of the evolutionary biologist. Our mind needs discrete and recognizable objects to structure our perception of reality. There is no reason to expect that nature works the same way. Am. J. Primatol. 75:10‐15, 2013. © 2012 Wiley Periodicals, Inc.     

Caffeic acid as a taxonomic marker in dicotyledons

Caffeic acid is plotted in the Dahlgren diagram and its distribution is compared to that of proanthocyanidins, the condensed tannins. The two chemicals derived from the same basic substance by a shift in the later steps in the pathway. Caffeic acid derivatives may be seen as more advanced constituents than proanthocyanidins.
Caffeic acid may function as a biosynthetical sink for surplus cinnamic acid in a system where the end-product, proanthocyanidins, has lost importance, and where lignin is not formed. Consequently, this may apply to all groups where a shift from woody to herbaceous habit has occurred, i.e. Asteridae, Araliiflorae and Ranuncu-liflorae. This is used as an argument in the presentation of a theory that evolution in dicotyledons was dichotomous. One main Magnoliiflorean-Caryophylliflorean group terminates in Ranunculiflorae and Caryophylliflorae with caffeic acid and ferulic acid, respectively. The other group, comprising most other dicotyledons, terminates in the Asteridae, also with caffeic acid.
There is much evidence pointing towards a similar protective effect of caffeic acid as has long been known for the condensed tannins. The advantages of caffeic acid as compared to condensed tannins is the shorter biosynthetic pathway, the less carbon bound in the molecule, and the possibility of re-entering the substance into the primary metabolism.     

Flavonoids as taxonomic markers in old world Lupinus species

In a leaf survey of 54 specimens of 11 Old World Lupinus species three classes of flavonoids were detected: flavones (in 82%), flavonols (in 36%) and flavone C-glycosides (in 55%). The rough-seeded species were clearly distinguished from the smooth-seeded taxa by the presence of a novel 2′-hydroxyflavone, luteolin and flavone C-glycosides as major leaf constituents and by the absence of flavonols. Within the smooth-seeded species, there are three flavonoid patterns: (a) flavonols only, L. albus; (b) flavones and flavonols, L. luteus, L. hispanicus and L. angustifolius; and (c) flavones only, L. micranthus. L. angustifolius further differed in uniquely producing diosmetin as a major leaf constituent. These divisions coincide exactly with previous groupings based on alkaloidal and morphological data. Amongst the 12 samples of L. angustifolius three chemical races were distinguished and a number of diosmetin glucoside malate esters detected. The flower flavonoid aglycone patterns of the nine Old World species surveyed differed markedly from the corresponding leaf profiles by the presence of flavones: luteolin and apigenin in eight and chrysoeriol in seven species as major constituents, while flavone C-glycosides were found only in trace amount in three species. In a leaf flavonoid survey of 13 representative New World Lupinus taxa, glycoflavones were major leaf components, a variety of methylated flavones were identified and flavonols were absent. The presence of the novel 2′-hydroxyflavone in five New World species may indicate some evolutionary link with the rough seeded taxa of the Old World.     

Seed-coat anatomy in Fumariaceae-Fumarioideae

Seed-coat anatomy is described in 122 species of Fumarioideae, which represent all the genera, subgenera, and most sections. Nine seed-coat types were recognized: (I) Dicentra subg. Hedycapnos , (II) Dicentra subg. Chrysocapnos , (III) Dicentra subg. Macranthos , (IV) Dicentra subg. Dicentra , (V) Corydalis p.p. , (VI) rest of Corydaleae, Cysticapnos, Pseudofumaria and Ceratocapnos , (VII) Discocapnos and Sarcocapnos p. p. , (VIII) Sarcocapnos p. p., Platycapnos and Trigonocapnos , and (IX) Fumariinae. Variable characters are polarized based on the comparison with Fumariaceae Hypecooideae, Papaveraceae and Pteridophyllaceae. It is assumed that endotestal seed-coat type (I) is most primitive, that exotestal seed coat types (II—VIII) are derived therefrom, and that the reduction of the mechanical layer, including the origin of thin seed-coat type (IX) occurred repeatedly in combination with indehiscent, hard-walled fruits. Dicentra subg. Hedycapnos (with type I) possesses a combination of primitive testal characters unique within the subfamily, suggesting it represents a sister group to the rest of the subfamily. Each of the other subgenera (with II, III or IV) is also characterized by a unique combination of seed-coat characters, which are found in the outgroups but not in the other genera. Seed-coat characters support the monophyly of Fumarioideae exclusive of Dicentra subg. Hedycapnos , Fumarioideae exclusive of Dicentra , of Dicentra subg. Dicentra , of Corydalis p.p. , and of Fumariinae.     

Phylogenetic utility of the first two introns of the S7 ribosomal protein gene in African electric fishes (Mormyroidea: Teleostei) and congruence with other molecular markers

A series of recent molecular systematic studies of the African electric fishes (Mormyroidea) have challenged many aspects of their traditional taxonomy and precladistic hypotheses of their phylogeny. However, poor resolution of some interrelationships within the subfamily Mormyrinae in these studies highlights the need for additional data and analyses. Here we evaluate the phylogenetic information content of nucleotide sequences from the first two introns of the low‐copy nuclear S7 ribosomal protein gene in 40 mormyroid species. Alignment of S7 sequences from 38 taxa within the subfamily Mormyrinae is non‐problematic, but these are difficult to align with sequences of Petrocephalus bovei (Petrocephalinae) and Gymnarchus niloticus (Gymnarchidae), which we exclude from our analysis. There are no significant differences in base frequencies among these sequences and base compositional bias is low. Maximum parsimony (MP) analysis on the S7 dataset, designating Myomyrus macrops as the outgroup, generates a phylogenetic hypothesis for these taxa with a low level of homoplasy (RI = 0.87). We examine agreement between the S7 data with previously published mitochondrial (12S/16S, cytochrome b) and nuclear (rag 2) datasets for the same taxa by means of incongruence length difference tests and partitioned Bremer support (decay) analysis. While we find significant agreement between the S7 dataset and the others, MP analysis of the S7 data alone and in combination with the other datasets indicates two novel relationships within the Mormyrinae: (1) Mormyrus is the sister group to Brienomyrus brachyistius and Isichthys henryi, and (2) Hippopotamyrus pictus is the sister group of a clade, previously recovered, containing Marcusenius senegalensis. S7 data provide additional support for a number of clades recovered in the earlier molecular studies, some of which conflict with current mormyrid taxonomy. Inferred indels and a single inversion in the S7 fragment provide supplemental character support for many of these relationships. These phylogenetic results strengthen recent hypotheses concerning the evolution of electric organ structure in these fishes. The evolutionary characteristics of this nuclear marker and its phylogenetic utility in this group suggests that it could be widely useful for systematic studies at the subfamilial level in teleost fishes. © 2003 The Linnean Society of London. Biological Journal of the Linnean Society, 2003, 78 , 273–292.     

Flavonoids and the evolution of the angiosperms

Data on the distribution of flavonoids in the angiosperms are summarized and patterns of occurence are shown to be related to plant evolution. Different flavonoid types are regarded as primitive or advanced characters on the basis of biosynthetic complexity and on correlated frequencies of occurrence with morphological and anatomical features. The evolutionary significance of distribution patterns of proanthocyanidins, glycosylflavones, biflavonoids, 6- and 8-hydroxyflavonoids and anthocyanins is discussed in turn. The importance of these various distribution patterns is considered in relation to an ecological function for these flavonoids.     

Brood chambers constructed from spines in fossil and Recent cheilostome bryozoans

Most cheilostome bryozoans brood their larvae in skeletal structures called ovicells which, in evolutionary terms, were derived from spines. Ovicells in the great majority of fossil and Recent cheilostomes, however, have lost all or most traces of their spinose origin. Here we review the occurrence of spinose (including costate) brood chambers in cheilostomes, investigating in detail 32 species belonging to ten genera among five families (Calloporidae, Monoporellidae, Macroporidae, Cribrilinidae and Tendridae). Spinose ovicells are moderately common in the Upper Cretaceous, where they are recorded in 28 species, and also occur in one Palaeocene, seven Eocene‐Miocene and 11 Recent species. The most primitive cheilostome ovicells occur in mid‐Cretaceous calloporids in which a group of mural spines belonging to the distal zooid were apparently bent towards the maternal zooid to form a cage‐like structure for reception of the embryo. The bases of these spines were initially aligned in a distally concave row that later became straight, distally convex and finally horseshoe‐shaped, affording progressively better protection for the developing embryo. We suggest that primitive monoporellids inherited from calloporid ancestors a distally concave arrangement of ovicell spine bases, while cribrilinids inherited a horseshoe‐shaped arrangement. Important trends that can be recognized in early ovicell evolution include: (1) loss of basal spine articulation; (2) spine flattening; (3) closure of the gaps between spines; (4) reduction in spine number (through loss or fusion), and (5) development of a concave ovicell floor. The conventional ‘unipartite’ ovicells found in the majority of cheilostomes may have originated either by spine fusion, as seems likely in some cribrilinids, or through a progressive loss of spines via an intermediate stage, seen in some calloporids and in two monoporellids, where the ovicell comprises a large pair of flattened spines. The spinose ovicells of some monoporellids and macroporids subsequently evolved investments of hypostegal coelom that allowed secretion of a surface layer of cryptocystal calcification. Acanthostegous brood chambers characteristic of Tendridae apparently provide an example of independent evolution of spinose brooding structures. © 2005 The Natural History Museum, London, Zoological Journal of the Linnean Society, 2005, 144 , 317?361.