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PubMed2006

Testing dispersal and cryptic diversity in a widely distributed groundwater amphipod (Niphargus rhenorhodanensis).

Theories about colonization and evolution in groundwater have assumed that the fragmented structure of groundwater strongly limits dispersal. The high number of endemic and allopatric species in groundwater supports this hypothesis, but the occurrence of widely distributed groundwater taxa calls into question its universality. These widely distributed taxa might also be sets of cryptic species because extreme conditions of life in groundwater promote cryptic diversity by inducing convergent morphological evolution. Niphargus rhenorhodanensis is a widely distributed and ubiquitous groundwater amphipod which supposedly colonized the Alps after Quaternary glaciations. We tested the dispersal and the cryptic species hypotheses within this species using a phylogeographic approach based on two mitochondrial genes (COI and 16S) and a nuclear gene (28S). Results support the view that poor dispersal is a main evolutionary factor in groundwater. All genes independently supported the existence of numerous cryptic and mostly allopatric units within N. rhenorhodanensis, indicating that its apparently wide distribution range is an artefact generated by cryptic diversity. We reject the hypothesis of a recent and global colonization of the Alps and argue that some N. rhenorhodanensis lineages probably survived glaciations near or within the Alps.

Amphipoda↗
PubMed2002

Why are olfactory systems of different animals so similar?

As we learn more about the neurobiology of olfaction, it is becoming increasingly clear that olfactory systems of animals in disparate phyla possess many striking features in common. Why? Do these features provide clues about the ways the nervous system processes olfactory information? This might be the case if these commonalities are convergent adaptations that serve similar functions, but similar features can be present in disparate animals for other reasons. For example, similar features may be present because of inheritance from a common ancestor (homology), may represent responses to similar constraints, or may be superficial or reflect strategies used by researchers studying the system. In this paper, I examine four examples of features of olfactory systems in members of different phyla: the presence of odorant binding proteins in the fluid overlying olfactory receptor neurons; the use of G protein-coupled receptors as odorant receptors; the use of a two-step pathway in the transduction of odorant signals; and the presence of glomerular neuropils in the first central target of the axons of olfactory receptor cells. I analyze data from nematodes, arthropods, molluscs, and vertebrates to investigate the phylogenetic distribution of these features, and to try to explain the presence of these features in disparate animals. Phylogenetic analyses indicate that these features are not homologous across phyla. Although these features are often interpreted as convergent adaptations, I find that alternative explanations are difficult to dismiss. In many cases, it seems that olfactory system features that are similar across phyla may reflect both responses to similar constraints and adaptations for similar tasks.

Adaptation, Physiological↗
PubMed2004

Identification of cytogenetic subgroups and karyotypic pathways of clonal evolution in follicular lymphomas.

Follicular lymphoma (FL) is characterized by the activation of BCL2 through t(14;18)(q32;q21). Additional acquired mutations are necessary to generate a fully malignant clonal proliferation. Many of these secondary genetic alterations are visible in the clonal karyotype; however, the sequence by which they arise and their influence on clinical behavior have not been determined. The ability to address these issues has been hampered by the lack of computational methods to manipulate complex chromosomal data in a sufficiently large cohort of cases. In the present investigation, we analyzed secondary karyotypic alterations in 336 cases of FL with t(14;18) to identify the most common regions of recurrent chromosomal gain or loss. This revealed 29 recurrent changes present in more than 5% of the tumors. Each tumor karyotype was then assessed for the presence or absence of each of these 29 specific changes. By statistical means, we show that the chromosomal changes arise in an apparent temporal order, with distinct early and late changes. We identify, by principal-components analysis, four possible cytogenetic pathways that characterize the early stages of clonal evolution, which converge to a common route at later stages. We show that FLs with t(14;18) may be classified into cytogenetic subgroups determined by the presence or absence of 6q-, +7, or der(18)t(14;18). Correlation with clinical outcomes in a subset of cases with clinical data revealed del(17p) and +12 to be correlated with an adverse clinical outcome. The clinical implications of these pathways of clonal evolution need to be examined on a prospective basis in a large cohort of FLs.

Chromosome Aberrations↗
PubMed1995

The recurring evolution of lipoprotein(a). Insights from cloning of hedgehog apolipoprotein(a).

The lipoprotein Lp(a), a major inherited risk factor for atherosclerosis, consists of a low density lipoprotein-like particle containing apolipoprotein B-100 plus the distinguishing component apolipoprotein(a) (apo(a)). Human apo(a) contains highly repeated domains related to plasminogen kringle four plus single kringle five and protease-like domains. Apo(a) is virtually confined to primates, and the gene may have arisen during primate evolution. One exception is the occurrence of an Lp(a)-like particle in the hedgehog. Cloning of the hedgehog apo(a)-like gene shows that it is distinctive in form and evolutionary history from human apo(a), but that it has acquired several common features. It appears that the primate and hedgehog apo(a) genes evolved independently by duplication and modification of different domains of the plasminogen gene, providing a novel type of "convergent" molecular evolution.

Amino Acid Sequence↗
PubMed2002

The role of reelin in the development and evolution of the cerebral cortex.

Reelin is an extracellular matrix protein that is defective in reeler mutant mice and plays a key role in the organization of architectonic patterns, particularly in the cerebral cortex. In mammals, a "reelin signal" is activated when reelin, secreted by Cajal-Retzius neurons, binds to receptors of the lipoprotein receptor family on the surface of cortical plate cells, and triggers Dab1 phosphorylation. As reelin is a key component of cortical development in mammals, comparative embryological studies of reelin expression were carried out during cortical development in non-mammalian amniotes (turtles, squamates, birds and crocodiles) in order to assess the putative role of reelin during cortical evolution. The data show that reelin is present in the cortical marginal zone in all amniotes, and suggest that reelin has been implicated in the evolution of the radial organization of the cortical plate in the synapsid lineage leading from stem amniotes to mammals, as well as in the lineage leading to squamates, thus providing an example of homoplastic evolution (evolutionary convergence). The mechanisms by which reelin instructs radial cortical organization in these two lineages seem different: in the synapsid lineage, a drastic amplification of reelin production occurred in Cajal-Retzius cells, whereas in squamates, in addition to reelin-secreting cells in the marginal zone, a second layer of reelin-producing cells developed in the subcortex. Altogether, our results suggest that the reelin-signaling pathway has played a significant role in shaping the evolution of cortical development.

Animals↗
PubMed1995

The structure and evolution of alpha/beta barrel proteins.

Roughly 10% of all known enzyme structures have an alpha/beta barrel domain. The members of this large family of proteins catalyze very different types of reactions. Such diversity of function has made this family a target for protein engineering. The evolutionary history of this family has been the subject of vigorous debate. In this paper, arguments are made to support the divergence of all members of this family from a common ancestor. Because of the lack of strong sequence homology, the ancestral molecule must be very old. A hypothesis concerning the relationship between chemical mechanism and evolutionary history is discussed. Evidence is presented to suggest that convergent molecular evolution occurs when there is only one energetically reasonable pathway for a chemical reaction.

Amino Acid Sequence↗
PubMed2025

Multiomic Analyses Reveal the Molecular Mechanisms of Arid Adaptation in a Desert Rodent Species.

Organisms living in desert habitats face multiple simultaneous pressures, such as high temperatures and arid, and the population dynamics and community diversity of small rodents are strongly affected by climate extremes. However, the potential mechanisms by which desert rodents adapt to arid remain largely unexplored. Here, we assembled a 3.18 Gb genome, including 25,812 protein-encoding genes, for Orientallactaga sibirica, which is widely distributed across both arid and semihumid environments in Eurasia. Orientallactaga sibirica has longer ears and hind limbs to enhance heat dissipation, which may be related to the positively selected genes, such as Fgf10, Fgf11, Hoxc4, Hoxd1, and Bmp4. The renal transcriptome revealed increased fat and carbohydrate metabolism for metabolic water production in O. sibirica residing in arid habitats. Pathways such as material metabolism, oxidative stress response, osmoregulation, and water and salt reabsorption were enriched in candidate genes, such as Avp, Ang, and Ace, under positive selection in O. sibirica. Moreover, amino acid replacement was observed in the protein sequences of seven candidate genes, including Aldh7a1, Lnpep, Wnk4, C1qc, and Awat2, and these specific amino acid replacements of genes such as Umod and Scnn1a were related to unique osmoregulation, osmotic protection, and water retention compensation mechanisms. Water deprivation under laboratory conditions induced the upregulation of Umod and Aldh7a1 expression, further supporting the results observed in the wild population. These findings demonstrate that the positively selected genes related to limb development and specific amino acid replacements in the genes Umod and Scnn1a for unique osmoregulation in the renal vascular system may contribute to arid adaptation in the desert rodent species O. sibirica. This study provides novel insights into the adaptive evolution of desert small mammals and can serve as a reference for future research on renal damage-related diseases, such as human kidney stones and salt-sensitive hypertension.

Animals↗
PubMed1998

Systematics and evolution of lower Central American cichlids inferred from analysis of cytochrome b gene sequences.

Central American cichlids allied to the genus "Cichlasoma" are thought to be of South American ancestry. The group has apparently undergone extensive morphological, ecological, and behavioral differentiation in Central America following colonization. Uncertainties regarding the systematics of the group and the timing of colonization complicate interpretation of the biological history of cichlids in Central America. We determined complete cytochrome b gene sequences for 54 individual cichlids representing 21 species to test hypotheses regarding the time of origin and pattern of diversification of lower Central American cichlids. The data also bear on issues relating to the systematics and taxonomy of heroine cichlids. Our results suggest that cichlids have been in Central America since the middle to late Miocene. Moreover, the data provide evidence of a rapid radiation early in the history of the group. Similar ecomorphological types have evolved multiple times. Inferences of convergent morphological evolution may, in part, explain a lack of concordance between the mitochondrial gene tree and previous inferences of phylogenetic relationships based on observable characteristics. Phylogenetic inferences based on the molecular data provide support for the recognition of "sections" [erected by Regan (1905) and others] as distinct genera and suggest that thorough revision of Central American cichlids is necessary before the extent of biological diversity within the group can be fully appreciated.

Animals↗
PubMed2001

From cofactor to enzymes. The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes.

The pyridoxal-5'-phosphate (vitamin B(6))-dependent enzymes that act on amino acid substrates have multiple evolutionary origins. Thus, the common mechanistic features of B(6) enzymes are not accidental historical traits but reflect evolutionary or chemical necessities. The B(6) enzymes belong to four independent evolutionary lineages of paralogous proteins, of which the alpha family (with aspartate aminotransferase as the prototype enzyme) is by far the largest and most diverse. The considerably smaller beta family (tryptophan synthase beta as the prototype enzyme) is structurally and functionally more homogenous. Both the D-alanine aminotransferase family and the alanine racemase family consist of only a few enzymes. The primordial pyridoxal-5'-phosphate-dependent protein catalysts apparently first diverged into reaction-specific protoenzymes, which then diverged further by specializing for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages, providing examples of convergent enzyme evolution. The functional specialization of most B(6) enzymes seems to have already occurred in the universal ancestor cell before the divergence of eukaryotes, archebacteria, and eubacteria 1500 million years ago. Pyridoxal-5'-phosphate must have emerged very early in biological evolution; conceivably, metal ions and organic cofactors were the first biological catalysts. To simulate particular steps of molecular evolution, both the substrate and reaction specificity of existent B(6) enzymes were changed by substitution of active-site residues, and monoclonal pyridoxal-5'-phosphate-dependent catalytic antibodies were produced with selection criteria that might have been operative in the evolution of protein-assisted pyridoxal catalysis.

Amino Acid Isomerases↗
PubMed1997

Molecular diversity and evolution of blaTEM genes encoding beta-lactamases resistant to clavulanic acid in clinical E. coli.

The molecular diversity of inhibitor-resistant TEM (IRT) enzymes was explored using a strategy which involved DNA amplification by polymerase chain reaction (PCR), analysis of restriction fragment length polymorphism (RFLP), and direct nucleotide sequencing. The study of plasmid-borne genes from 27 strains, resistant to amoxicillin and beta-lactamase-inhibitor combinations, identified mutations resulting in amino acid change at positions 69, 244, 275, and 276 known to be associated with the IRT phenotype and a mutation at nucleotide position 162 in the promoter region. These mutations were found to lie on two different gene sequences, described here as "TEM-1B like" and "TEM-2 like" restriction linkage groups. Further analysis, of nucleotide sequences of promoter and coding regions of the beta-lactamases, confirmed that a given mutation causing IRT phenotype could be associated with two different gene sequence frameworks and two different causal mutations could lie on identical gene sequence framework. These data argue in favor of convergent phenotypic evolution of IRT enzymes under the selective pressure imposed by the intensive clinical use of beta-lactam-beta-lactamase inhibitor combinations.

Amoxicillin↗
PubMed1996

Tobamovirus evolution: gene overlaps, recombination, and taxonomic implications.

Tobamoviruses, mostly isolated from solanaceous plants, may represent ancient virus lineages that have codiverged with their hosts. Recently completed nucleotide sequences of six nonsolanaceous tobamoviruses allowed assessment of the codivergence hypothesis and support a third subgroup within tobamoviruses. The genomic sequences of 12 tobamoviruses and the partial sequences of 11 others have been analyzed. Comparisons of the predicted protein sequences revealed three clusters of tobamoviruses, corresponding to those infecting solanaceous species (subgroup 1), those infecting cucurbits and legumes (subgroup 2), and those infecting crucifers. The orchid-infecting odontoglossum ringspot tobamovirus was associated with subgroup 1 genomes by its coat and movement protein sequences, but with the crucifer-pathogenic tobamoviruses by the remainder of its genome, suggesting that it is the progeny of a recombinant. For four of five genomic regions, subgroup 1 and 3 genomes were equidistant from a subgroup 2 genome chosen for comparison, suggesting uniform rates of evolution. A phylogenetic tree of plant families based on the tobamoviruses they harbor was congruent with that based on rubisco sequences but had a different root, suggesting that codivergence was tempered by rare events of viruses of one family colonizing another family. The proposed subgroup 3 viruses probably have an origin of virion assembly in the movement protein gene, a large (25-codon) overlap of movement and coat protein open reading frames, and a comparably shorter genome. Codon-position-dependent base compositions and codon prevalences suggested that the coat protein frame of the overlap region was ancestral. Bootstrapped parsimony analysis of the nucleotides in the overlap region and of the sequences translated from the -1 frame (the subgroup 3 movement protein frame) of this region produced trees inconsistent with those deduced from other regions. The results are consistent with a model in which a no or short overlap organization was ancestral. Despite encoding of subgroup 2 and 3 movement protein C-termini by nonhomologous nucleotides, weak similarities between their amino acid sequences suggested convergent sequence evolution.

Amino Acid Sequence↗
PubMed2003

Divergent evolution during an experimental adaptive radiation.

How repeatable a process is evolution? Comparative studies of multicellular eukaryotes and experimental studies with unicellular prokaryotes document the repeated evolution of adaptive phenotypes during similar adaptive radiations, suggesting that the outcome of adaptive radiation is broadly reproducible. The goal of this study was to test this hypothesis by using phenotypic traits to infer the genetic basis of adaptation to simple carbon-limited environments in an extensive adaptive radiation. We used a clone of the bacterium Pseudomonas fluorescens to found two sets of experimental lines. The first set of lines was allowed to adapt to one of 23 novel environments for 1100 generations while the second set of lines was allowed to accumulate mutations by drift for 2000 generations. All lines were then assayed in the 95 environments provided by Biolog microplates to determine the phenotypic consequences of selection and drift. Replicate selection lines propagated in a common environment evolved similar adaptive components of their phenotype but showed extensive variation in non-adaptive phenotypic traits. This variation in non-adaptive phenotypic traits primarily resulted from the ascendance of different beneficial mutations in different lines. We argue that these results reconcile experimental and comparative approaches to studying adaptation by demonstrating that the convergent phenotypic evolution that occurs during adaptive radiation may be associated with radically different sets of beneficial mutations.

Adaptation, Biological↗
PubMed1986

[Spatial binocular adaptation in microtropia and orthotropia. Definition and method of measurement].

For a long time the problem of the functional recovery in convergent strabismus has been a hardly debated topic. For some authors, it is very rare; for others, on the other hand, the result is frequently achieved. Such disparities seem to be chiefly related to the tests used. The authors have selected 10 binocular tests and they carried out this scale in a prospective study in 100 cases of esotropias having normal moving performances following a medico-surgical management and in 20 normal cases. statistical correlations reveal that there is a very large disparity of "good answers" according to the tests; but there is no redundancy at all between them. Consequently for a relevant check up every single one is necessary. The total of "good scores" and differential values of ten tests allow to know the true state of binocular spatial adaptation. The statistical analysis shows that in secondary microtropias and orthotropias there is almost always an actual binocular spatial adaptation. Its level may be high, medium or low. The high margin is clearly different from the binocular scores in normal cases. Two events are very uncommon: a full recovery of binocular vision and the opposite condition of its complete suppression. The results of such a method give a clear explanation of conflicting opinions about the binocular evolution of convergent squints following medical and surgical management.

Adolescent↗
PubMed1999

Ancient gene duplication and differential gene flow in plastid lineages: the GroEL/Cpn60 example.

Cryptomonads, small biflagellate algae, contain four different genomes. In addition to the nucleus, mitochondrion, and chloroplast is a fourth DNA-containing organelle the nucleomorph. Nucleomorphs result from the successive reduction of the nucleus of an engulfed phototrophic eukaryotic endosymbiont by a secondary eukaryotic host cell. By sequencing the chloroplast genome and the nucleomorph chromosomes, we identified a groEL homologue in the genome of the chloroplast and a related cpn60 in one of the nucleomorph chromosomes. The nucleomorph-encoded Cpn60 and the chloroplast-encoded GroEL correspond in each case to one of the two divergent GroEL homologues in the cyanobacterium Synechocystis sp. PCC6803. The coexistence of divergent groEL/cpn60 genes in different genomes in one cell offers insights into gene transfer from evolving chloroplasts to cell nuclei and convergent gene evolution in chlorophyll a/b versus chlorophyll a/c/phycobilin eukaryotic lineages.

Amino Acid Sequence↗
PubMed2001

Distal-less expression in embryos of Limulus polyphemus (Chelicerata, Xiphosura) and Lepisma saccharina (Insecta, Zygentoma) suggests a role in the development of mechanoreceptors, chemoreceptors, and the CNS.

The homeobox gene Distal-less (Dll) is well known for its participation in the development of arthropod limbs and their derivatives. Dll activity has been described for all groups of arthropods, but also for molluscs, echinoderms and vertebrates. Generally, Dll participates in the establishment of the proximo-distal-axis and differentiation along this axis. During our investigation of the expression pattern in the silverfish Lepisma saccharina and the horseshoe crab Limulus polyphemus, we found several expressions in late stages which cannot be explained with the "normal" limb-specific function. The antenna, cerci and terminal filament of the silverfish show a striped expression; single cells on the labrum, mandibles, maxillary palps and anal valves are also strongly stained by the Dll antibody. In addition to cell groups in the developing ganglia of the CNS, in the coxal endites and several nerve cells in femur and the trochanter of the prosomal limbs, the whole prosomal shield of Limulus polyphemus is surrounded by Dll-positive cell clusters. Furthermore, the lateral processes of the opisthosoma and the edges of the opisthosomal appendages are Dll positive. To get an indication of the cell fate of these regions, we examined hatched larvae and juvenile stages of both species with the SEM. We found a striking correlation of these Dll-positive areas and different sense organs, especially mechanoreceptors. Since many sense organs in arthropods are situated on the limbs, interpretation of the Dll expression in limbs is problematical. This has critical implications for comparative analysis of Dll expression patterns between arthropods and for the claim of homology between limb-like structures. Furthermore, we discuss the possibility of convergent appendage evolution in various bilaterian groups based on the improvement of spatial sensory resolution.

Animals↗
PubMed1990

Phosphorylation of rat liver inorganic pyrophosphatase by ATP in the absence and in the presence of protein kinase.

Cytoplasmic inorganic pyrophosphatase of rat liver can be phosphorylated by cAMP-dependent protein kinase on a serine residue with a concomitant increase in enzymic activity. Phosphorylation is also observed in the absence of protein kinase, but in this case much higher concentrations of ATP are required and the stability characteristics of the phosphoenzyme resemble those of an acyl phosphate. Kinase-free phosphorylation of the animal inorganic pyrophosphatase, unlike that of microbial pyrophosphatases, does not activate the enzyme. Pyrophosphatase may thus provide a new example of an enzyme whose evolution involves convergence of regulatory phosphorylation mechanisms.

Adenosine Triphosphate↗
PubMed2006

Molecular and morphological incongruence in European species of Isothecium (Bryophyta).

During the identification of Moroccan samples a plant belonging to Isothecium with characteristics of I. alopecuroides (Dubois) Isov. and, to a smaller degree, I. algarvicum W.E. Nicholson and Dixon was found. Problems with attributing the plant to any of the European Isothecium species and the known large morphological variation in I. alopecuroides suggested that molecular studies were needed to evaluate patterns of relationships in this complex. We investigated one nuclear and one chloroplast marker from 66 samples (gametophytes) of Isothecium alopecuroides and from 18 samples of other Isothecium species. Parsimony and likelihood (via Bayesian analysis) were used as optimality criteria to compute phylogenetic trees. Bootstrapping and posterior probabilities were used, not only to quantify support, but also to evaluate competing phylogenetic alternatives in consensus networks. Finally, split decomposition and neighbour net analysis were used to compute distance based split networks, in order to avoid systematic error. The observed discrepancy among morphological and molecular data suggests that none of the European species Isothecium alopecuroides, I. holtii and I. myosuroides are monophyletic as defined by traditional morphological characters. Convergent morphological evolution cannot explain the discrepancy in this particular case; instead exchange of genetic material among Isothecium species is considered a potential explanation for the molecular diversity within morphospecies.

Base Sequence↗