Genomic Organization Around the Centromeric End of the HLA Class I Region: Large-Scale Sequence Analysis

We previously sequenced two regions around the centromeric end of HLA class I and the boundary between class I and class III. In this paper we analyze the two regions of about 385 kb and confirm, giving a new line of evidence, that the following two pairs of the genomic segments were duplicated in evolution: (i) a 43-kb genomic segment including the HLA-B gene showing the highest polymorphism among the classical HLA class I loci (class Ia) and a 40-kb segment including the HLA-C locus showing the lowest polymorphism and (ii) a 52-kb segment including the MIC (MHC class I chain related gene) B and a 35-kb segment including MICA. We also found that repetitive elements such as SINEs, LINEs, and LTRs occupy as much as 47% of nucleotides in this 385-kb region. This unusually high content of repetitive elements indicates that repeat-mediated rearrangements have frequently occurred in the evolutionary history of the HLA class Ia region. Analysis of LINE compositions within the two pairs of duplicated segments revealed that (i) LINEs in these regions had been dispersed prior to both the duplication of the HLA-B and -C loci and the duplication of the MICB and MICA loci, and (ii) the divergence of the HLA-B and -C loci occurred prior to the duplication of the MICA and MICB loci. To find novel genes responsible for HLA class I-associated or other diseases, we performed computer analysis applying GenScan and GRAIL to GenBank's dbEST. As a result, at least five as yet uncharacterized genes were newly mapped on the HLA class I centromeric region studied. These novel genes should be analyzed further to determine their relationships to diseases associated with this region. Received: 16 June 1998 / Accepted: 18 August 1998     

Specialist deterrent chemoreceptors enable Pieris caterpillars to discriminate between chemically different deterrents

Pieris butterflies (Lepidoptera: Pieridae) are specialist herbivores of cruciferous plants. They exploit glucosinolates, secondary plant metabolites chemotaxonomically characteristic for this plant family, as token stimuli. In addition to particular glucosinolates, some genera of the Cruciferae contain cardenolides, steroidal allelochemicals that act as potent feeding and oviposition deterrents to several Pieris species. We investigated the sensory mechanisms by which these compounds are perceived in larvae. Pieris caterpillars and many other lepidopterous species are endowed with so-called generalist deterrent receptors, that respond to a broad spectrum of secondary plant substances. In Pieris caterpillars we found a second type of deterrent chemoreceptor in maxillary styloconic taste sensilla. This neuron is very sensitive to cardenolides (threshold 0.1–0.3 M). The generalist deterrent receptor also responds to these substances but its threshold lies at 50–100× higher concentrations. In behavioural preference experiments Pieris brassicae L. caterpillars preferred cardenolide-treated cabbage leaf discs when confronted with a choice between them and a deterrent substance that does not occur in the Brassicaceae. The cardenolides acted as potent deterrents when offered against untreated cabbage leaf discs. This demonstrates that the balance of activity elicited in the two types of deterrent chemoreceptors determines the behavioural decision.     

Covariance and decoupling of floral and vegetative traits in nine Neotropical plants: a re-evaluation of Berg's correlation-pleiades concept

Nearly forty years ago R. L. Berg proposed that plants with specialized pollination ecology evolve genetic and developmental systems that decouple floral morphology from phenotypic variation in vegetative traits. These species evolve separate floral and vegetative trait clusters, or as she termed them, "correlation pleiades." The predictions of this hypothesis have been generally supported, but only a small sample of temperate-zone herb and grass species has been tested. To further evaluate this hypothesis, especially its applicability to plants of other growth forms, we examined the patterns of phenotypic variation and covariation of floral and vegetative traits in nine species of Neotropical plants. We recognized seven specific predictions of Berg's hypothesis. Our results supported some predictions but not others. Species with specialized pollination systems usually had floral traits decoupled (weak correlation; Canna and Eichornia) or buffered (relationship with shallow proportional slope; Calathea and Canna) from variation in vegetative traits. However, the same trend was also observed in three species with unspecialized pollination systems (Echinodorus, Muntingia, and Wedelia). One species with unspecialized pollination (Croton) and one wind-pollinated species (Cyperus) showed no decoupling or buffering, as predicted. While species with specialized pollination usually showed lower coefficients of variation for floral traits than vegetative traits (as predicted), the same was also true of species with unspecialized or wind pollination (unlike our prediction). Species with specialized pollination showed less variation in floral traits than did species with unspecialized or wind pollination, as predicted. However, the same was true of the corresponding vegetative traits, which was unexpected. Also in contrast to our prediction, plants with specialized pollination systems did not exhibit tighter phenotypic integration of floral characters than did species with generalized pollination systems. We conclude that the patterns of morphological integration among floral traits and between floral and vegetative traits tend to be species specific, not easily predicted from pollination ecology, and generally more complicated than R. L. Berg envisaged.     

Phylogeny of the core Malvales: evidence from ndhF sequence data

The monophyly of the group comprising the core malvalean families, Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae, was recently confirmed by molecular studies, but the internal structure of this clade is poorly understood. In this study, we examined sequences of the chloroplast ndhF gene (aligned length 2226 bp) from 70 exemplars representing 35 of the 39 putative tribes of core Malvales. The monophyly of one traditional family, the Malvaceae, was supported in the trees resulting from these data, but the other three families, as traditionally circumscribed, are nonmonophyletic. In addition, the following relationships were well supported: (1) a clade, /Malvatheca, consisting of traditional Malvaceae and Bombacaceae (except some members of tribe Durioneae), plus Fremontodendron and Chiranthodendron, which are usually treated as Sterculiaceae; (2) a clade, /Malvadendrina, supported by a unique 21-bp (base pair) deletion and consisting of /Malvatheca, plus five additional subclades, including representatives of Sterculiaceae and Tiliaceae, and Durionieae; (3) a clade, /Byttneriina, with genera traditionally assigned to several tribes of Tiliaceae, plus exemplars of tribes Byttnerieae, Hermannieae, and Lasiopetaleae of Sterculiaceae. The most striking departures from traditional classifications are the following: Durio and relatives appear to be more closely related to Helicteres and Reevesia (Sterculiaceae) than to Bombacaceae; several genera traditionally considered as Bombacaceae (Camptostemon, Matisia, Phragmotheca, and Quararibea) or Sterculiaceae (Chiranthodendron and Fremontodendron) appear as sister lineages to the traditional Malvaceae; the traditional tribe Helictereae (Sterculiaceae) is polyphyletic; and Sterculiaceae and Tiliaceae, as traditionally circumscribed, represent polyphyletic groups that cannot sensibly be maintained with their traditional limits for purposes of classification. We discuss morphological characters and conclude that there has been extensive homoplasy in characters previously used to delineate major taxonomic groups in core Malvales. The topologies here also suggest that /Malvatheca do not have as a synapormophy monothecate anthers, as has been previously supposed but, instead, may be united by dithecate, transversely septate (polysporangiate) anthers, as found in basal members of both /Bombacoideae and /Malvoideae. Thus, “monothecate” anthers may have been derived at least twice, independently, within the /Bombacoideae (core Bombacaceae) and /Malvoideae (traditional Malvaceae).     

The Amino Acid Sequence of Ribitol Dehydrogenase-F, a Mutant Enzyme with Improved Xylitol Dehydrogenase Activity

A mutant ribitol dehydrogenase (RDH-F) was purified from Klebsiella aerogenes strain F which evolved from the wild-type strain A under selective pressure to improve growth on xylitol, a poor substrate used as sole carbon source. The ratio of activities on xylitol (500 mM) and ribitol (50 mM) was 0.154 for RDH-F compared to 0.033 for the wild-type (RDH-A) enzyme. The complete amino acid sequence of RDH-F showed the mutations. Q60 for E60 and V215 for L215 in the single polypeptide chain of 249 amino acid residues. Structural modeling based on homologies with two other microbial dehydrogenases suggests that E60 Q60 is a neutral mutation, since it lies in a region far from the catalytic site and should not cause structural perturbations. In contrast, L215 V215 lies in variable region II and would shift a loop that interacts with the NADH cofactor. Another improved ribitol dehydrogenase, RDH-D, contains an A196 P196 mutation that would disrupt a surface -helix in region II. Hence conformational changes in this region appear to be responsible for the improved xylitol specificity.     

Alternative Ways to Become a Juvenile or a Definitive Phenotype (and on Some Persisting Linguistic Offenses)

Lack of knowledge of early and juvenile development often makes it difficult to decide when a fish becomes a juvenile or, for that matter, a definitive phenotype. According to the established life-history model, a fish develops naturally in a saltatory manner, its entire life consisting of a sequence of stabilized self-organizing steps, separated by distinct less stabilized thresholds. Changes are usually introduced during thresholds. In principle, there are two ways to reach the juvenile period: by indirect or by direct development. Indirectly developing fishes have a distinct larva period that ends in a cataclysmic or mild remodeling process, called metamorphosis, from which the fishes emerge as juveniles. During metamorphosis, most temporary organs and structures of the embryos and larvae are replaced by definitive organs and structures that are also possessed by the adults. In contrast, directly developing fishes have no larvae. Their embryos develop directly into juveniles and do not need major remodeling. Consequently, the beginning of their juvenile period is morphologically and functionally less distinct than in indirect development. The life-history model helps to find criteria that identify the natural boundaries between the different periods in the life of a fish, among them, the beginning of the juvenile period. Looking at it from a different angle, when ontogeny progresses from small eggs with little yolk, larvae are required as the necessary providers of additional nutrients (feeding entities similar to amphibian tadpoles or butterfly caterpillars) in order to accumulate materials for the metamorphosis into the definitive phenotypes. Directly developing fishes start with large demersal eggs provided with an adequate volume of high density yolk and so require no or little external nutrients to develop into the definitive phenotype. These large eggs are released and develop in concentrated clutches. It therefore becomes possible and highly effective to guard them in nests or bear them in external pouches, gill chambers or the buccal cavity. Viviparity is the next natural step. Now the maternal investment into large yolks can be supplemented or replaced by direct food supply to the developing embryos like, for example, the secretion of uterine histotrophe or nutrient transfer via placental analogues. When the young of guarders and bearers start exogenous feeding, they are much larger or better developed than larvae of nonguarders and the larva period in the former is reduced to a vestige or eliminated entirely. In the latter case, the juvenile period begins with the first exogenous feeding. Such precocial fishes are more specialized and able to survive better in competitive environments. In contrast, altricial forms retain or revert to a life-history style with indirect development and high fecundity when dispersal is advantageous or essential. Fishes become juveniles when the definitive phenotype is formed in most structures, either indirectly from a larva via metamorphosis or directly from the embryo.     

ACTIN GENE DUPLICATION AND THE EVOLUTION OF MORPHOLOGICAL COMPLEXITY IN LAND PLANTS

Actin is a highly conserved cytoskeletal protein that is a key component of cells. Genes encoding actin occur in single copies in most green algae, in 2–3 copies in bryophytes, and in increasingly more complex gene families in ferns and seed plants. We use the well-resolved phylogenetic frameworks of the Streptophyta as a guide to reconstruct the patterns of actin gene duplication in early diverging land plants. Our working hypothesis is that the origin of novel tissues in the bryophytes (e.g. multicellular sporophyte) may be reflected in the functional diversification of duplicate actin genes in these taxa. Actin is used as a model cytoskeletal protein with the assumption that its evolutionary history represents those of other cytoskeletal elements and the coevolved binding proteins. Here we provide a phylogenetic perspective on the origin of green algal and land plant actin genes and use this information to speculate on the role of plant actin in early plant evolution.     

The braincases of mosasaurs and Varanus, and the relationships of snakes

The braincase structure of the mosasaur Platecarpus is described in detail and compared to that of Varanus and snakes. The braincase of mosasaurs and Varanus is found to be closely similar in most respects other than the consequences of obliteration of the metakinetic axis in mosasaurs. Neither Varanus, nor mosasaurs, approach snakes in braincase structure. The hypothesis of a sister-group relationship of snakes and mosasauroids is discussed in the light of how hypotheses of homology, or synapomorphy, can be established on an empirical, i.e. testable and potentially falsifiable basis. The establishment of homology qua synapomorphy is recognized as a procedure involving at least two levels of generalization. The most basic level is the conjecture of similarity of constituent elements of two or more organisms. Such conjectures of similarity maintain their testability, and falsifiability, only if established by reference to topographical equivalence, or equivalence of connectivity.     

Population structure, gene flow and evolutionary relationships in four species of the genera Tomocerus and Pogonognathellus (Collembola, Tomoceridae)

Genetic diversity and gene flow at 10 allozyme loci were investigated in 13 natural populations of four species of the collembolan genera Tomocerus and Pogonognathellus. Levels of observed heterozygosity were found to vary from 0.033 in P. longicornis to 0.120 in T. vulgaris. Average Nei's genetic distances (D) ranged from D = 0.222 between populations of P. ftavescens to D = 0.647 between populations of T. vulgaris. Genetic distances between species were always 1.000 and the highest value (D = 4.321) was between P. longicomis and one population of T. vulgaris. Values of F_sr were very high in all species (from 0.567 to 0.696) and levels of gene flow (Nm) derived from F_ST and the private allele method were low (Nm <1). Gene flow was significandy higher only in two subsets of populations of T. vulgaris. The Plio-Pleistocenic geological rearrangements and the effect of stochastic events, such as genetic drift, are invoked to explain the different levels of genetic divergence between and within species. Distance- and character-based approaches were used to reconstruct evolutionary relationships between and within species. While the monophyly of all species was confirmed, the results did not univocally support the monophyly of the two genera, leaving the question of their generic or subgeneric status unresolved.     

Fine-scale geographical structure, intra-individual polymorphism and recombination in nuclear ribosomal internal transcribed spacers in Armeria (Plumbaginaceae)

BACKGROUND AND AIMS: Isolation and drift are the main causes for geographic structure of molecular variation. In contrast, the one found in a previous survey in Armeria (Plumbaginaceae) for nuclear ribosomal ITS multicopy regions was species-independent and has been hypothesized to be due to extensive gene-flow and biased concerted evolution. Since this was inferred from a genus-level phylogenetic analysis, the aim of this study was to check for the occurrence of such structure and the validity of the proposed model at a local scale, in a southern Spanish massif (Sierra Nevada), as well as to examine the evolutionary implications at the organism level. METHODS: In addition to 117 sequences of direct PCR products from genomic DNA, 50 sequences of PCR products from cloned DNA were obtained to analyse cases of intragenomic polymorphisms for the ITS regions. KEY RESULTS: Sequence data confirm the occurrence of a species-independent structure at a local scale and reveal insights through the analysis of contact areas between different ITS copies (ribotypes). A comparison between cloned and direct sequences (a) confirms that, within these contact areas, ITS copies co-occur both in different individuals and within single genomes; and (b) reveals recombination between different copies. CONCLUSIONS: This study supports the utility of direct sequences for detecting intra-individual polymorphism and for partially inferring the ITS copies involved, given previous knowledge of the variability. The main evolutionary implication at the organism level is that gene-flow and concerted evolution shape the geographic structure of ITS variation.