MOLECULAR PHYLOGENETIC ANALYSIS OF rbcL IN THE PRYMNESIOPHYTA1

The nucleotide sequences of rbcL genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) were determined from six species of Prymnesiophyta to clarify their phylogenetic relationships. Molecular phylogenetic trees were constructed using PAUP (Phylogenetic Analysis Using Parsimony). These analyses suggest that the Prymnesiophyta, except for the Pavlovales, area relatively stable monophyletic group. Pleurochrysis carterae, included in the Isochrysidales, is a sister species of a monophyletic group consisting of other members of the Isochrysidales, Gephyrocapsa oceanica and Emiliania huxleyi, members of the Coccosphaerales, Calyptrosphaera sphaeroidea and Umbilicosphaera sibogae var. foliosa, and a member of the Prymnesiales, Chrysochromulina hirta. The nucleotide sequence of rbcL from G. oceanica was identical to that from E. huxleyi within the region examined. Our trees show that G. oceanica and E. huxleyi are more closely related to C. hirta than to U. sibogae, C. sphaeroidea, and P. carterae. These results suggest that orders in the Prymnesiophyceae, including the above-mentioned genera, should be redefined.     

Phylogenetic relationships of the garter snakes based on DNA sequence and allozyme variation

We estimated phylogenetic relationships among 26 species of garter snakes (genus Thamnophis ) using allozyme and mitochondrial cytochrome b gene nucleotide sequence variation. Parsimony analyses of the two data sets give substantially different estimates of phylogeny. Several lines of evidence indicate that much of this conflict is due to error associated with the restricted number of characters in each data set. Such sampling error may be reduced by combining all the characters; we therefore present an estimate of phylogeny based on parsimony analysis of all the data combined. All our analyses support several conclusions in conflict with previous views: a very distant relationship between T.errans and T. elegans , non-monophyly of the elegans group (even excluding T: errans ), and nesting of the form validus (previously considered a member of the genus Nerodia ) within Thamnophis.
The combined analysis gives an almost fully resolved tree. However, bootstrapping indicates only weak support for many clades in this tree. Furthermore, paraphyly of the assemblages of cytochrome b gene lineages within T. elegans and T. radix indicate the potential for discordance between the mitochondrial DNA (mtDNA) and species phylogenies through the sorting of ancestral mtDNA polymorphisms. These problems suggest the need for assaying additional characters, especially ones likely to be independent of those used in the present study.     

Cladistics and the comparative morphology of linyphiid spiders and their relatives (Araneae, Araneoidea, Linyphiidae)

This paper provides the first quantitative cladistic analysis of linyphiid morphology. Classical and novel homology hypotheses for a variety of character systems (male and female genitalia, somatic morphology, spinneret silk spigot morphology, etc.) are critically examined and studied within a phylogenetic context. Critical characters have been illustrated. A sample of linyphiid taxa (nine genera in four subfamilies), five species of Pimoa (Pimoidae), and two other araneoid families (Tetragnathidae and Araneidae, represented by Tetragnatha and Zygiella , respectively) were used to study the implications of the phylogeny of Pimoidae for the systematics of linyphiids. The phylogenetic relationships of these 16 exemplar taxa, as coded for the 47 characters studied, were analysed using numerical cladistic methods. In the preferred cladogram Pimoidae and Linyphiidae are sister groups, Stemonyphantinae are sister group to the remaining linyphiids, and Mynogleninae are sister group to the clade composed of Erigoninae plus Linyphiinae. These results agree with the relationships recently proposed by Wunderlich, except by finding erigonines as the sister group to linyphiines rather than to mynoglenines.     

Two distinct P element subfamilies in the genome of Drosophila bifasciata

The genome of Drosophila bifasciata harbours two distinct subfamilies of P-homologous sequences, designated M-type and O-type elements based on similarities to P element sequences from other species. Both subfamilies have some general features in common: they are of similar length (M-type: 2935 bp, O-type: 2986 bp), are flanked by direct repeats of 8 by (the presumptive target sequence), contain terminal inverted repeats, and have a coding region consisting of four exons. The splice sites are at homologous positions and the exons have the coding capacity for proteins of 753 amino acids (M-type) and 757 amino acids (O-type). It seems likely that both types of element represent functional transposons. The nucleotide divergence of the two P element subfamilies is high (31%). The main structural difference is observed in the terminal inverted repeats. Whereas the termini of M-type elements consist of 31 by inverted repeats, the inverted repeats of the O-type elements are interrupted by non-complementary stretches of DNA, 12 by at the 5 end and 14 by at the 3 end. This peculiarity is shared by all members of the O-type subfamily. Comparison with other P element sequences indicates incongruities between the phylogenies of the species and the P transposons. M-type and O-type elements apparently have no common origin in the D. bifasciata lineage. The M-type sequence seems to be most closely related to the P element from Scaptomyza pallida and thus could be considered as a more recent invader of the D. bifasciata gene pool. The origin of the O-type elements cannot be unequivocally deduced from the present data. The sequence comparison also provides new insights into conserved domains with possible implications for the function of P transposons.     

Structure and function at the root apex - phylogenetic and ontogenetic perspectives on apical cells and quiescent centres

The summit of roots of various plant species may be occupied by a single, rapidly proliferating tetrahedral apical cell (as in ferns), or by a multicellular and slowly proliferating quiescent centre (as in angiosperms), or by intermediate types of cellular organizations. The present paper attempts to deduce the phylogeny of these various types of cellular patterning at the root apex.     

Phylogeny of mitochondrial DNA clones in tassel-eared squirrels Sciurus aberti

The tassel-eared squirrel, Sciurus aberti , includes six subspecies which occupy restrictive and apparently identical habitats in Ponderosa pine forests in the south-western United States and Mexico; the strict habitat requirement of this species is based on dietary requirements which are only fulfilled in these forests. To examine evolutionary relationships among certain subspecies of S. aberti , we obtained estimates of nucleotide diversity within subspecies as well as nucleotide divergence between subspecies using mitochondrial DNA (mtDNA) analysis. Restriction site polymorphisms were identified in samples of the four US subspecies: S. a. aberti (Abert), S. a. kaibabensis (Kaibab), S. a. ferreus (Ferreus), and S. a. chuscensis (Chuska) Fourteen mtDNA clones were resolved that were, with one exception, uniquely subspecific. Dendrograms constructed by neighbour-joining and maximum parsimony methods revealed two major assemblages: (1) an Abert/Kaibab group; and (2) a Ferreus/Chuska group. The Abert vs. Ferreus clones exhibited the greatest net nucleotide divergence, with a lineage separation estimate approximating 572 000 years ago assuming a nucleotide substitution rate of 7.15 × 10^-9/year/site. Five out of ten Chuska squirrels shared a clone with one Abert sample; the relative sizes of these two populations and their respective ranges as well as their close proximity support the proposal for relatively recent intermixing of Abert and Chuska populations resulting in what appears to be Abert → Chuska migration. Nucleotide diversity within subspecies ranked as Kaibab < Ferreus < Abert < Chuska; the relatively high diversity for the Chuska sample is based on the apparent introgression of Abert mtDNA. The relative diversity exhibited by Kaibab, Ferreus and Aberti samples corresponds to the range size of the respective subspecies.     

Reproduction in the North Atlantic oceanic ichthyofauna and the relationship between fecundity and species' sizes

Synopsis The pelagic (589 spp.) and demersal (505 spp.) oceanic ichthyofaunas of the North Atlantic Basin have very different compositions at ordinal and family level. Yet the pattern of relationships between species' maximum size and maximum fecundity from data available (10% of the pelagic, 19% of the demersal species) was similar. A positive relationship between fecundity and weight was confirmed among most teleosts, but was not followed by the elasmobranchs represented. Species' reproductive styles are reviewed in ordinal groupings within a framework of the overall body size/fecundity distribution. Species size (maximum weight) spectra were synthesized for both pelagic and demersal assemblages to assess the allocation of potential reproductive effort throughout the North Atlantic oceanic ichthyofauna. The only available examples of species size spectra and biomass spectra from the pelagic and demersal ichthyofauna in this ocean basin imply geographic and bathymetric variation in overall reproductive effort among fishes whose fecundity is size dependent. Further implications concerning reproductive effort are discussed in the light of food availability.     

Phylogeny ofRubiaceae-Rubieae inferred from the sequence of a cpDNA intergene region

A phylogenetic analysis of 25 species, representing eight genera of theRubieae tribe (Rubiaceae), has been made using the DNA sequence of the chloroplastatp B-rbc L intergene region. Six tropical genera from other tribes ofRubiaceae have been used as outgroups. Whatever the method of analysis (distance, parsimony or maximum likelihood), five groups are clearly separated and described as informal clades. Their relative relationships are not clearly resolved by the parsimony analysis, resulting in eight equally parsimonious trees, 327 steps long, with a consistency index (CI) of 0.749 (excluding uninformative sites). TheRubieae tribe appears monophyletic from the data available. Some new and partly unexpected phylogenetic relationships are suggested. The genusRubia forms a separate clade and appears to be the relatively advanced sister group of the remaining taxa. TheSherardia clade also includes the generaCrucianella andPhuopsis. Galium sect.Aparinoides appears closely attached to theAsperula sect.Glabella clade. The remaining taxa ofGalium are paraphyletic:Galium sect.Platygalium (in theCruciata clade) is linked to the advanced generaCruciata andValantia; the more apomorphic groups ofGalium form theGalium sect.Galium clade, including the perennial sectionsGalium, Leiogalium, andLeptogalium as well as the annual (and possibly polyphyletic) sect.Kolgyda.     

cpDNA intergene sequences corroborate restriction site data for reconstructingRubiaceae phylogeny

Representatives of seven genera from five tribes ofRubiaceae have been compared in respect to a non-coding intergene cpDNA region of about 1000 bp, situated between the atpB and the rbcL genes. The resulting most parsimonious PAUP cladogram corresponds very well with one based on total cpDNA restriction site data obtained byBremer & Jansen (1991). The two different molecular analyses thus corroborate each other and contribute to an improved systematic arrangement of the large family, e.g., in respect to placing the tribeHedyotideae clearly into the subfamilyRubioideae, closer toRubieae than toPsychotrieae.     

Restriction fragment length polymorphisms of the phytohemagglutinin genes inPhaseolus andVigna (Leguminosae)

Restriction fragment length polymorphisms at the phytohemagglutinin (PHA) locus were determined among 21 genotypes ofPhaseolus vulgaris, P. coccineus, P. acutifolius, P. lunatus, and threeVigna species, using five restriction enzymes and one double digestion, in order to provide molecular evidence for their genetic relatedness. The dissimilarity between genotypes was estimated from binary RFLP data. The dissimilarity was high among species (from 0.75 to 0.95), and of variable extent among genotypes of the same species (0.33–0.89). InP. vulgaris, two different DNA hybridization patterns were found, giving further evidence for two major gene pools in that species. The restriction patterns ofP. vulgaris var.aborigineus, the putative ancestral form ofP. vulgaris, exhibit clear homology toP. vulgaris genotypes. An undefined landrace from Taiwan could be identified as aP. vulgaris genotype. RFLP-based trees for the phytohemagglutinin genes of the species studied were computed with several distance matrix and parsimony methods.