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PubMed1997

An interspecific backcross of Lycopersicon esculentum x L. hirsutum: linkage analysis and a QTL study of sexual compatibility factors and floral traits.

A BC1 population of the self-compatible tomato Lycopersicon esculentum and its wild self-incompatible relative L. hirsutum f. typicum was used for restriction fragment length polymorphism linkage analysis and quantitative trait loci (QTL) mapping of reproductive behavior and floral traits. The self-incompatibility locus, S, on chromosome 1 harbored the only QTL for self-incompatibility indicating that the transition to self-compatibility in the lineage leading to the cultivated tomato was primarily the result of mutations at the S locus. Moreover, the major QTL controlling unilateral incongruity also mapped to the S locus, supporting the hypothesis that self-incompatibility and unilateral incongruity are not independent mechanisms. The mating behavior of near-isogenic lines carrying the L. hirsutum allele for the S locus on chromosome 1 in an otherwise L. esculentum background support these conclusions. The S locus region of chromosome 1 also harbors most major QTL for several floral traits important to pollination biology (e.g., number and size of flowers), suggesting a gene complex controlling both genetic and morphological mechanisms of reproduction control. Similar associations in other flowering plants suggest that such complex may have been conserved since early periods of plant evolution or else reflect a convergent evolutionary process.

Chromosome Mapping↗
PubMed1996

Novel alleles HLA-B*7802 and B*51022: evidence for convergency in the HLA-B5 family.

We have characterized two novel HLA-B alleles, B*7802 and B*51022. The Caucasian-derived variant B*7802 most resembles the African-derived variant B*7801, from which B*7802 differs by two nucleotides. Only one of these modifications, however, is translated: a tyrosine for aspartate substitution occurs at residue 74 in B*7802, while the second nucleotide difference reflects a proximal synonymous substitution in codon 23. A second variant, B*51022, differs synonymously only at codon 23 from B*51021. Comparative analysis of the B5 CREG demonstrates that other pairs of B5 alleles differ synonymously only at codon 23 or synonymously at codon 23 and non-synonymously at a second more distal location. Contrary to the genesis of like pairs of B5 alleles via introduction of coordinate yet distant mutagenic events onto a single B5 progenitor, we postulate that synonymously different B5 progenitor molecules, B5ATT and B5ATC, are evolving in convergence to generate homologous B5 allele pairs differing silently at codon 23. Our finding that B*7802 is a single amino acid away from complete convergence with B*7801 and that B*51022 and B*51021 are in complete convergence is exemplary of such evolution.

Alleles↗
PubMed1990

The multifunctional 6-methylsalicylic acid synthase gene of Penicillium patulum. Its gene structure relative to that of other polyketide synthases.

6-Methylsalicylic acid synthase (MSAS) from Penicillium patulum is a homomultimer of a single, multifunctional protein subunit. The enzyme is induced, at the transcriptional level, during the end of the logarithmic growth phase. After approximately 150-fold purification, a homogeneous enzyme preparation was obtained exhibiting, upon SDS gel electrophoresis, a subunit molecular mass of 188 kDa. By immunological screening of a genomic P. patulum DNA expression library, the MSAS gene together with its flanking sequences was isolated; 7131 base pairs of the cloned genomic DNA were sequenced. Within this sequence the MSAS gene was identified as a 5322-bp-long open reading frame coding for a protein of 1774 amino acids and 190,731 Da molecular mass. Transcriptional initiation and termination sites were determined both by primer extension studies and from cDNA sequences specially prepared for the 5' and 3' portions of the gene. The same cDNA sequences revealed the presence of a 69-bp intron within the N-terminal part of the MSAS gene. The intron contains the canonical GT and AG dinucleotides at its 5'- and 3'-splice junctions. An internal TACTGAC sequence, resembling the TACTAAC consensus element of Saccharomyces cerevisiae introns is suggested to represent the branch point of the lariat splicing intermediate. When compared to other known polyketide synthases, distinct amino acid sequence similarities of limited lengths were observed with some, though not all, of them. A comparatively low degree of similarity was detected to the yeast and Penicillium FAS or to the plant chalcone and resveratrol synthases. In contrast, a significantly higher sequence similarity was found between MSAS and the rat fatty acid synthase, especially at their transacylase, 2-oxoacyl reductase, 2-oxoacyl synthase and acyl carrier protein domains. Besides several dissimilar, interspersed regions probably coding for MSAS- and FAS-specific functions, the sequential order of the similar domains was colinear in both enzymes. The low similarity between the two P. patulum polyketide synthases, MSAS and FAS, possibly supports a convergent rather than a divergent evolution of both multienzyme proteins.

Acyltransferases↗
PubMed1994

Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution.

The neotropical Heliconius butterflies are famous examples of Müllerian mimicry, due to the diverse array of shared, brightly colored wing patterns that advertise the butterflies' unpalatability. The parallel geographical variation in these patterns within several widespread species has been invoked to support the controversial Pleistocene refugium hypothesis of tropical diversification. However, in no Heliconius species have either evolutionary rates or relationships among geographical races been explicitly examined. I present a phylogenetic hypothesis based on mitochondrial DNA sequences for 14 divergent races of Heliconius erato, which reveals that similar wing patterns have evolved rapidly and convergently within the species. There is a basal split between groups of races from east and west of the Andes, reflecting a vicariant separation at the base of the Pleistocene. Within each of these clades, sequence divergence is very low, and some haplotypes are shared between allopatric races with radically different wing patterns. The topology implies a simultaneous radiation of races in these two areas within the last 200,000 years. Ages for the clades are estimated by comparing sequence divergence to a plot of mitochondrial divergence in several arthropod taxa with independently dated divergence times. This plot is linear and suggests that mitochondrial DNA in arthropods evolves in a clocklike manner, at least initially, when sequence divergence is low.

Animals↗
PubMed2004

Fractal characterization of bpn weights evolution.

Training methodology of the Back Propagation Network (BPN) is well documented. One aspect of BPN that requires investigation is whether or not the BPN would get trained for a given training data set and architecture. In this paper the behavior of the BPN is analyzed during its training phase considering convergent and divergent training data sets. Evolution of the weights during the training phase was monitored for the purpose of analysis. The evolution of weights was plotted as return map and was characterized by means of fractal dimension. This fractal dimensional analysis of the weight evolution trajectories is used to provide a new insight to understand the behavior of BPN and dynamics in the evolution of weights.

Algorithms↗
PubMed2025

Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera.

The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel the evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes or contigs. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of "dispensable" chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g. plastome contraction) and specific (e.g. host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.

Genome, Mitochondrial↗
PubMedDate not supplied

On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?

This paper presents and discusses evidence suggesting how the diversity of domain folds in existence today might have evolved from peptide ancestors. We apply a structure similarity detection method to detect instances where localized regions of different protein folds contain highly similar sequences and structures. Results of performing an all-on-all comparison of known structures are described and compared with other recently published findings. The numerous instances of local sequence and structure similarities within different protein folds, together with evidence from proteins containing sequence and structure repeats, argues in favor of the evolution of modern single polypeptide domains from ancient short peptide ancestors (antecedent domain segments (ADSs)). In this model, ancient protein structures were formed by self-assembling aggregates of short polypeptides. Subsequently, and perhaps concomitantly with the evolution of higher fidelity DNA replication and repair systems, single polypeptide domains arose from the fusion of ADSs genes. Thus modern protein domains may have a polyphyletic origin.

Amino Acid Motifs↗
PubMed2003

The Cambrian "explosion" of metazoans and molecular biology: would Darwin be satisfied?

The origins of metazoan bodyplans and the extent to which they are coincident with the Cambrian "explosion" are both areas of continuing debate. The fossil record has a unique advantage in terms of historical perspective, but remains highly contentious on account of the often controversial interpretations of particular groups (e.g. halkieriids, vetulicolians) and the heavy reliance on "windows" of exceptional preservation (e.g. Chengjiang, Burgess Shale). Molecular and developmental biology offer other unique insights, but may be problematic in terms of conflicting phylogenetic signals and questions revolving around gene co-option, evolution of developmental systems and even convergence. Such topics, far from frustrating the enterprise, actually widen our understanding of the nature of the evolutionary process with the exciting promise of the discovery of more general principles.

Animals↗
PubMed2005

Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny.

We present a well-resolved, highly inclusive phylogeny for monocots, based on ndhF sequence variation, and use it to test a priori hypotheses that net venation and vertebrate-dispersed fleshy fruits should undergo concerted convergence, representing independent but often concurrent adaptations to shaded conditions. Our data demonstrate that net venation arose at least 26 times and was lost eight times over the past 90 million years; fleshy fruits arose at least 21 times and disappeared 11 times. Both traits show a highly significant pattern of concerted convergence (p<10(-9)), arising 16 times and disappearing four times in tandem. This phenomenon appears driven by even stronger tendencies for both traits to evolve in shade and be lost in open habitats (p<10(-13)-10(-29)). These patterns are among the strongest ever demonstrated for evolutionary convergence in individual traits and the predictability of evolution, and the strongest evidence yet uncovered for concerted convergence. The rate of adaptive shifts per taxon has declined exponentially over the past 90 million years, as expected when large-scale radiations fill adaptive zones.

Base Sequence↗
PubMed2000

Epidermal sensory organs of moles, shrew moles, and desmans: a study of the family talpidae with comments on the function and evolution of Eimer's organ.

The epidermal sensory organs of members of the family Talpidae (moles, shrew-moles, and desmans) were investigated and compared to determine the range of sensory specializations and better understand how they evolved. Small domed mechanosensory organs called 'Eimer's organs' were present on the rhinarium of nearly all species of talpids, but not among the sister group of shrews (Soricidae) or other insectivore families. This suggests that the common ancestor to the talpids possessed Eimer's organs. Two species of moles from the driest habitats did not exhibit Eimer's organs - suggesting that their sensory organs degenerated in response to harsh, abrasive soil conditions. The semi-aquatic desmans uniquely possessed tiny sensory hairs interspersed with their Eimer's organs; these may act to sense water currents. Some species exhibited a subdivided, star-like, rhinarium - resembling an early embryonic stage of the star-nosed mole and providing clues to the evolution of the star. A single genera (Uropsilus) that branched off early in the evolution of the talpids had Eimer's organ-like structures but lacked some typical components. These findings fill a major gap in our knowledge of talpid sensory biology and suggest (1) how Eimer's organs evolved, (2) how the unusual appendages of the star-nosed mole evolved, (3) that the evolution of Eimer's organ is convergent with the mechanosensory push-rod of monotremes. The results also demonstrate the features that distinguish Eimer's organ from similar configurations of sensory receptors in other mammalian skin surfaces. Finally, a mechanism for Eimer's organ function in detecting object and prey specific surface features is proposed.

Animals↗
PubMed2006

Accurate evolution of orbiting binary black holes.

We present a detailed analysis of binary black hole evolutions in the last orbit and demonstrate consistent and convergent results for the trajectories of the individual bodies. The gauge choice can significantly affect the overall accuracy of the evolution. It is possible to reconcile certain gauge-dependent discrepancies by examining the convergence limit. We illustrate these results using an initial data set recently evolved by Brügmann et al. [Phys. Rev. Lett. 92, 211101 (2004)10.1103/PhysRevLett.92.211101]. For our highest resolution and most accurate gauge, we estimate the duration of this data set's last orbit to be approximately 59MADM.

Journal Article↗
PubMed1997

Continuous stability and evolutionary convergence.

A stochastic process of long-term evolution due to mutation and selection is defined over an asexually reproducing population, with selection according to a population game with a one-dimensional continuity of pure strategies. Limiting the analysis to mutations of small effect, it is shown that long-term dynamic stability in such a process is equivalent to continuous stability in the relevant population game. In the case of a one-dimensional strategy set (but not necessarily if the strategy set is multi-dimensional), this result is virtually independent of the distribution of mutations.

Animals↗
PubMed1995

Enzymes: chemistry and biochemistry.

Basic principles underlying enzyme action are considered. Catalytic antibodies (abzymes), catalytic RNA (ribozymes), and non-biological counterparts of enzyme-catalyzed reactions are mentioned. Enzyme evolution is considered in terms of divergence, convergence, and lateral gene transfer.

Amino Acid Sequence↗
PubMed2004

Convergence of forelimb and hindlimb Natural Pendular Period in baboons (Papio cynocephalus) and its implication for the evolution of primate quadrupedalism.

The patterns of muscle mass distribution along the lengths of limbs may have important effects on the mechanics and energetics of quadrupedalism. Specifically, Myers and Steudel (J. Morphol. 234 (1997) 183) have shown that fore- and hindlimb Natural Pendular Periods (NPPs) may affect quadrupedal kinematics and must converge to reduce locomotor energetic costs. This study quantifies patterns of limb mass distribution in a live sample of Papio cynocephalus using limb inertial properties (mass, center of mass, mass moment of inertia, and radius of gyration). These inertial properties are calculated using a geometric modeling technique similar to that of Crompton et al. (Am. J. phys. Anthrop. 99 (1996) 547). The inertial properties in Papio are compared to those of Canis from Myers and Steudel (J. Morphol. 234 (1997) 183). The Papio sample has convergent fore- and hindlimb NPPs. Additionally, these limb NPPs are relatively large compared to those of Canis due to the relatively distally distributed limb mass in the Papio sample (relatively large limb masses, relatively distal centers of mass and radii of gyration, and relatively large limb mass moments of inertia). This relatively distal limb mass appears related to the grasping abilities of their hands and feet. Causal links are explored between limb shape adaptations for grasping hands and feet and the kinematics of primate quadrupedalism. In particular, if primates in general follow Papio's limb mass distribution pattern, then relatively large limb NPPs may lead to the relatively low stride frequencies already documented for primates. The kinematics of primate quadrupedalism appears to have been strongly influenced by both selection for grasping hands and feet and selection for reduced locomotor energetic costs.

Animals↗
PubMed2005

A multidimensional approach for detecting species patterns in Malagasy vertebrates.

The biodiversity of Madagascar is extraordinarily distinctive, diverse, and endangered. It is therefore urgent that steps be taken to document, describe, interpret, and protect this exceptional biota. As a collaborative group of field and laboratory biologists, we employ a suite of methodological and analytical tools to investigate the vertebrate portion of Madagascar's fauna. Given that species are the fundamental unit of evolution, where micro- and macroevolutionary forces converge to generate biological diversity, a thorough understanding of species distribution and abundance is critical for understanding the evolutionary, ecological, and biogeographic forces that have shaped Malagasy vertebrate diversity. We illustrate the means by which we apply Mayr's "three basic tasks" of the systematist [Mayr, E. (1942) Systematics and the Origin of Species from the Viewpoint of a Zoologist (Harvard Univ. Press, Cambridge, MA)] to identify, classify, and study the organisms that together constitute Madagascar's vertebrate community. Using field inventory methods, specimen-based studies, and morphological and molecular analyses, we formulate hypotheses of species identity that then serve as the foundation for subsequent studies of biology and history. Our experience, as well as that of other investigators, has shown that much of the vertebrate species diversity in Madagascar is "cryptic" for both biological and practical reasons. Beyond issues of cryptic biological diversity, the resolution of species identity in Madagascar has been hampered because of a lack of vouchered comparative material at the population level. Through our activities, we are attempting to remedy these limitations while simultaneously enhancing research capacity in Madagascar.

Animals↗
PubMed1993

The 12-transmembrane helix transporters.

From the hydropathic profiles of their amino acid sequences many transport proteins are conceived to comprise 12-transmembrane alpha-helices. In only a few examples, however, is there genetical and/or biochemical evidence to support the 12-helix structure or illuminate the molecular mechanism of the transport process. A number of these transport proteins occur in evolutionarily related families, and sometimes superfamilies, indicating divergent evolution of the 12-helix structure. Other individual members or families of transport proteins are sufficiently different in amino acid sequence for their evolution to have taken place by convergence from independent ancestral origins.

Amino Acid Sequence↗
PubMed2000

Diffusion-reorganized aggregates: attractors in diffusion processes?

A process based on particle evaporation, diffusion, and redeposition is applied iteratively to a two-dimensional object of arbitrary shape. The evolution spontaneously transforms the object morphology, converging to branched structures. Independently of initial geometry, the structures found after a long time present fractal geometry with a fractal dimension around 1.75. The final morphology, which constantly evolves in time, can be considered as the dynamic attractor of this evaporation-diffusion-redeposition operator. The ensemble of these fractal shapes can be considered to be the dynamical equilibrium geometry of a diffusion-controlled self-transformation process.

Journal Article↗