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PubMed2003

Diversification in sexual and asexual organisms.

Sexual reproduction has long been proposed as a major factor explaining the existence of species and species diversity. Yet, the importance of sex for diversification remains obscure because of a lack of critical theory, difficulties of applying universal concepts of species and speciation, and above all the scarcity of empirical tests. Here, we use genealogical theory to compare the relative tendency of strictly sexual and asexual organisms to diversify into discrete genotypic and morphological clusters. We conclude that asexuals are expected to display discrete clusters similar to those found in sexual organisms. Whether sexuals or asexuals display stronger clustering depends on a number of factors, but in at least some scenarios asexuals should display a stronger pattern. Confounding factors aside, the only explanation we identify for stronger patterns of diversification in sexuals than asexuals is if the faster rates of adaptive change conferred by sexual reproduction promote greater clustering. Quantitative comparisons of diversification in related sexual and asexual taxa are needed to resolve this issue. The answer should shed light not only on the importance of the different stages leading to diversification, but also on the adaptive consequences of sex, still largely unexplored from a macroevolutionary perspective.

Adaptation, Biological↗
PubMed2002

Sexual selection driving diversification in jumping spiders.

Theory predicts that speciation rates should be accelerated in organisms undergoing sexual selection. In systems involving female choice, sexual selection acts directly on traits that may be important in prezygotic reproductive isolation, potentially fostering rapid divergence of such traits among allopatric populations. Despite the appeal of this concept, it has proven difficult to document. We provide genetic, behavioral, and simulation data illustrating that the striking and possibly recent divergence in traits of male behavior and morphology among populations of the jumping spider Habronattus pugillis can be attributed to sexual selection. We have found evidence for varying degrees of lower female response and offspring viability among some between-population crosses, consistent with the early stages of speciation. We have developed a gene-tree-based method for comparing phenotypic and genetic data sets to infer selection, and have found robust statistical evidence that directional selection has acted on male traits, by confirming that their rate of fixation exceeds that of neutral mitochondrial genes. Because these traits are apparent targets of female choice, the results indicate that sexual selection is driving divergence of phenotypes potentially crucial to the speciation process.

Animals↗
PubMed2002

Adaptive diversification of germination strategies.

Evolution of the germination rate (the proportion of newly produced and dormant seeds that germinates every year) of annual plants is investigated, when the environment is temporally stochastic and spatially heterogeneous. The environment consists of two habitats with synchronous stochastic variation in the annual yield and permanent difference in constant seed survival rates. Density dependence operates within the habitats, which are connected via restricted seed dispersal. We find that instead of a single common evolutionarily stable strategy the coexistence of several germination strategies is possible and that in an initially monomorphic population evolutionary branching may occur. During evolutionary branching the population undergoes disruptive selection and splits into two branches of different lineages that converge to the evolutionarily stable coalition of different germination strategies. It is shown that spatial heterogeneity and restricted dispersal are essential for evolutionary branching. Disruptive selection on the germination rate presents yet another possibility for parapatric speciation.

Adaptation, Physiological↗
PubMed2002

The role of parasites in sympatric and allopatric host diversification.

Exploiters (parasites and predators) are thought to play a significant role in diversification, and ultimately speciation, of their hosts or prey. Exploiters may drive sympatric (within-population) diversification if there are a variety of exploiter-resistance strategies or fitness costs associated with exploiter resistance. Exploiters may also drive allopatric (between-population) diversification by creating different selection pressures and increasing the rate of random divergence. We examined the effect of a virulent viral parasite (phage) on the diversification of the bacterium Pseudomonas fluorescens in spatially structured microcosms. Here we show that in the absence of phages, bacteria rapidly diversified into spatial niche specialists with similar patterns of diversity across replicate populations. In the presence of phages, sympatric diversity was greatly reduced, as a result of phage-imposed reductions in host density decreasing competition for resources. In contrast, allopatric diversity was greatly increased as a result of phage-imposed selection for resistance, which caused populations to follow divergent evolutionary trajectories. These results show that exploiters can drive diversification between populations, but may inhibit diversification within populations by opposing diversifying selection that arises from resource competition.

Animals↗
PubMed1998

Dynamics of hypervariable region 1 variation in hepatitis C virus infection and correlation with clinical and virological features of liver disease.

Hepatitis C virus (HCV) infection is a dynamic process during which molecular variants are continuously selected as the result of virus adaptation to the host. Understanding the nature of HCV genetic variation is central to current theories of pathogenesis and immune response. We prospectively studied hypervariable region 1 (HVR1) variation in the E2 gene of 36 hepatitis C patients, including 10 asymptomatic carriers, followed up for 1 to 2 years. Sequence changes in single and consecutive serum samples were assessed and correlated with clinical and virological parameters of liver disease. A region of the E1 gene was sequenced for comparison in 3 subjects. HVR1 heterogeneity at single time points widely varied in individual patients, did not increase cumulatively over the follow-up period, and did not correlate with HVR1 evolutionary rates. Conversely, the process of HVR1 sequence diversification, although differed considerably among patients, was stable over time and directly correlated with infections by HCV type 2, lower alanine aminotransferase (ALT) levels, and absence of cirrhosis. HCV carriers showed the highest HVR1 variation rates. Our findings indicate that HVR1 variation has an adaptive significance and is associated with favorable features of liver disease and suggest that prospective, rather than static, observations are required to model the process of HCV variation.

Adult↗
PubMed2003

Cell size as a link between noncoding DNA and metabolic rate scaling.

Accumulation of noncoding DNA and therefore genome size (C-value) may be under strong selection toward increase of body size accompanied by low metabolic costs. C-value directly affects cell size and specific metabolic rate indirectly. Body size can enlarge through increase of cell size and/or cell number, with small cells having higher metabolic rates. We argue that scaling exponents of interspecific allometries of metabolic rates are by-products of evolutionary diversification of C-values within narrow taxonomic groups, which underlines the participation of cell size and cell number in body size optimization. This optimization leads to an inverse relation between slopes of interspecific allometries of metabolic rates and C-value. To test this prediction we extracted literature data on basal metabolic rate (BMR), body mass, and C-value of mammals and birds representing six and eight orders, respectively. Analysis of covariance revealed significant heterogeneity of the allometric slopes of BMR and C-value in both mammals and birds. As we predicted, the correlation between allometric exponents of BMR and C-value was negative and statistically significant among mammalian and avian orders.

Animals↗
PubMed1987

Tumor cell instability, diversification, and progression to the metastatic phenotype: from oncogene to oncofetal expression.

It is proposed that tumor cell instability and the expression of cellular diversification mechanisms ensure that malignant neoplasms contain heterogeneous, phenotypically diverse tumor cell subpopulations. In such potentially unstable cellular mixtures of tumor cell phenotypes, some malignant cells may ultimately evolve with the most favorable properties for their progression to metastatic cells. Rates of cellular phenotypic instability and phenotypic diversification as well as their underlying causes appear to vary greatly among different tumor cells, and they are probably modulated by further genetic and chromosome changes and more frequently by intra- and extracellular epigenetic events that also differ, depending on the nature of the tumor cells and their cellular and microenvironmental interactions. Diversified malignant cells are characterized by quantitative and perhaps a few qualitative differences in gene expression, which may explain their abilities to undergo rapid changes in phenotypic properties. As tumor diversification and selection proceed uniquely in vivo, highly malignant cell subpopulations may eventually become dominant and gradually and independently lose their cellular and microenvironmental responsiveness. Tumor cell diversification mechanisms may be similar or identical to normal developmentally regulated diversification mechanisms that are used during embryonic and postembryonic cell diversification and development.

Animals↗
PubMed2026

The convergent evolution of the pelvic suction cup: A unique key innovation in spiny-finned fishes.

Key innovations open ecological opportunities and can redirect evolutionary trajectories. In spiny-finned fishes, the pelvic suction cup-a fused adhesive structure formed from the pelvic fins and supported by a modified girdle-appears to be one such trait. Using a novel 960-species phylogeny spanning 940 exons and 67 newly sequenced snailfish genomes, we show that the suction cup evolved independently three times across lineages separated by over 100 million years. By enabling adhesion in high-energy habitats such as tide pools and waterfalls, the suction cup set the stage for body depression and accompanying shifts in scales, teeth, and clade-specific ecofunctional profiles. Comparative analyses reveal convergence in a distinctive region of morphospace and body-shape evolution accelerated two- to fivefold. Diversification analyses uncover heterogeneous but elevated rates, with a clear burst in rock-climbing gobies associated with suction cup evolution. By opening novel habitats and fostering phenotypic novelty, the suction cup emerges as a key innovation that reshaped spiny-finned fish evolution.

Animals↗
PubMed2006

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock.

Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.

Animals↗
PubMed2002

Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals.

The fully sequenced chloroplast genomes of maize (subfamily Panicoideae), rice (subfamily Bambusoideae), and wheat (subfamily Pooideae) provide the unique opportunity to investigate the evolution of chloroplast genes and genomes in the grass family (Poaceae) by whole-genome comparison. Analyses of nucleotide sequence variations in 106 cereal chloroplast genes with tobacco sequences as the outgroup suggested that (1) most of the genic regions of the chloroplast genomes of maize, rice, and wheat have evolved at similar rates; (2) RNA genes have highly conservative evolutionary rates relative to the other genes; (3) photosynthetic genes have been under strong purifying selection; (4) between the three cereals, 14 genes which account for about 28% of the genic region have evolved with heterogeneous nucleotide substitution rates; and (5) rice genes tend to have evolved more slowly than the others at loci where rate heterogeneity exists. Although the mechanism that underlies chloroplast gene diversification is complex, our analyses identified variation in nonsynonymous substitution rates as a genetic force that generates heterogeneity, which is evidence of selection in chloroplast gene diversification at the intrafamilial level. Phylogenetic trees constructed with the variable nucleotide sites of the chloroplast genes place maize basal to the rice-wheat clade, revealing a close relationship between the Bambusoideae and Pooideae.

Chloroplasts↗
PubMed2003

Why do species exist? Insights from sexuals and asexuals.

Why does life diversify into the more or less discrete entities we recognise as species? Two main explanations have been proposed: i) species are a consequence of adaptation to different ecological niches, ii) species are a consequence of sexual reproduction and reproductive isolation. Phylogenetic studies of case-study groups can provide insights into the relative importance of divergent selection and isolation for speciation, but it can be difficult to infer causes of speciation unambiguously. The example of North American tiger beetles from the genus Cicindela is discussed. An alternative approach is to compare diversification between related sexual and asexual taxa to infer the relative importance of the two explanations. We outline expected patterns of diversification in sexual and asexual lineages under different scenarios using coalescent theory. Whether sexuals or asexuals diversify to a greater extent depends on the balance among various stages of diversification, particularly on the effects of sexual reproduction on rates of adaptive evolution. Rotifers offer a unique system to test these ideas, allowing comparison of patterns of genetic and functional morphological diversification in sexual (bdelloid) and asexual (monogonont) clades.

Journal Article↗
PubMed2007

Diversity and diversification of light chains in myeloma: the specter of amyloidogenesis by proxy.

BACKGROUND/AIMS: Primary amyloidosis and the cancer, multiple myeloma, are characterized by the overproduction of free antibody light chains. Approximately 10% of myeloma patients develop amyloidosis; primary amyloidosis may be thought of as the pathological analog of monoclonal gammopathy of undetermined significance. The kidney is a common site of accumulation of amyloid fibrils and is also the target of other light chain pathologies. Understanding the structural origin of these pathologies is complicated by the extreme primary structure heterogeneity of light chains. METHODS: Patterns of light chain germline gene usage in myeloma patients were compared to those found in other immune system disorders: lymphoma, leukemia, systemic lupus erythematosus and rheumatoid arthritis. RESULTS: Significant differences in apparent gene usage are found in the various diseases; several germline gene products have not been documented in myeloma patients to date. CONCLUSION: The plasma cell dyscrasias including myeloma, lymphoma, leukemia, and monoclonal gammopathy of undetermined significance are usually monoclonal diseases; however, the light chains produced are not homogeneous. Thus, the pathological risk for the patient may change during the course of the illness. Mutation rates in light chains observed during clonal diversification parallel mutations occurring in all genes in the malignant cells and could be a clinically useful biomarker.

Amino Acid Sequence↗
PubMed2000

Timing transantarctic disjunctions in the Atherospermataceae (Laurales): evidence from coding and noncoding chloroplast sequences.

Previous studies of the small Southern Hemisphere family Atherospermataceae have drawn contradictory conclusions regarding the number of transantarctic disjunctions and role of transoceanic dispersal in its evolution. Clarification of intergeneric relationships is critical to resolving (1) whether the two Chilean species, Laurelia sempervirens and Laureliopsis philippiana, are related to different Austral-Pacific species, implying two transantarctic disjunctions as suggested by morphology; (2) where the group is likely to have originated; and (3) whether observed disjunctions reflect the breakup of Gondwana. We analyzed chloroplast DNA sequences from six regions (the rbcL gene, the rpl16 intron, and the trnL-trnF, trnT-trnL, psbA-trnH, and atpB-rbcL spacer regions; for all six regions, 4,372 bp) for all genera and most species of Atherospermataceae, using parsimony and maximum likelihood (ML). The family's sister group, the Chilean endemic Gomortega nitida (Gomortegaceae), was used to root the tree. Parsimony and ML yielded identical single best trees that contain three well-supported clades (> or = 75% bootstrap): Daphnandra and Doryphora from south-eastern Australia; Atherosperma and Nemuaron from Australia-Tasmania and New Caledonia, respectively; and Laurelia novac-zelandiac and Laureliopsis philippiana from New Zealand and Chile, respectively. The second Chilean species, Laurelia sempervirens, is sister to this last clade. Likelihood ratio testing did not reject the molecular clock assumption for the rbcL data, which can therefore be used for divergence time estimates. The atherosperm fossil record, which goes back to the Upper Cretaceous, includes pollen, wood, and leaf fossils from Europe, Africa, South America, Antarctica, New Zealand, and Tasmania. Calibration of rbcL substitution rates with the fossils suggests an initial diversification of the family at 100-140 million years ago (MYA), probably in West Gondwana, early entry into Antarctica, and long-distance dispersal to New Zealand and New Caledonia at 50-30 MYA by the ancestors of L. novae-zelandiae and Nemuaron.

Antarctic Regions↗
PubMed2006

Different levels of alternative splicing among eukaryotes.

Alternative splicing increases transcriptome and proteome diversification. Previous analyses aiming at comparing the rate of alternative splicing between different organisms provided contradicting results. These contradicting results were attributed to the fact that both analyses were dependent on the expressed sequence tag (EST) coverage, which varies greatly between the tested organisms. In this study we compare the level of alternative splicing among eight different organisms. By employing an EST independent approach we reveal that the percentage of genes and exons undergoing alternative splicing is higher in vertebrates compared with invertebrates. We also find that alternative exons of the skipping type are flanked by longer introns compared to constitutive ones, whereas alternative 5' and 3' splice sites events are generally not. In addition, although the regulation of alternative splicing and sizes of introns and exons have changed during metazoan evolution, intron retention remained the rarest type of alternative splicing, whereas exon skipping is more prevalent and exhibits a slight increase, from invertebrates to vertebrates. The difference in the level of alternative splicing suggests that alternative splicing may contribute greatly to the mammal higher level of phenotypic complexity, and that accumulation of introns confers an evolutionary advantage as it allows increasing the number of alternative splicing forms.

Algorithms↗
PubMed1975

Stage-specific switches in histone synthesis during embryogenesis of the sea urchin.

Histones H2A and H2B of the sea urchin embryo have been resolved by new methods into components that are synthesized at different stages of development. One form of H2A and one form of H2B are synthesized only during the period from fertilization to the blastula stage. Subsequently, two other types of H2A and H2B molecules are synthesized. In addition, a histonelike protein was detected which is synthesized only from fertilization until the 16-cell stage when the synthesis of still another H2A-like protein begins. None of the late-appearing forms are derived from histone polypeptide chains synthesized earlier in development. Since the early components do not disappear after their synthesis stops, these modulations of histone synthesis lead to an increase in histone multiplicity, concomitant with the beginning of cell diversification and a decrease in cell division rate.

Age Factors↗
PubMed2004

Analysis of mutational lineage trees from sites of primary and secondary Ig gene diversification in rabbits and chickens.

Lineage trees of mutated rearranged Ig V region sequences in B lymphocyte clones often serve to qualitatively illustrate claims concerning the dynamics of affinity maturation. In this study, we use a novel method for analyzing lineage tree shapes, using terms from graph theory to quantify the differences between primary and secondary diversification in rabbits and chickens. In these species, Ig gene diversification starts with rearrangement of a single (in chicken) or a few (in rabbit) V(H) genes. Somatic hypermutation and gene conversion contribute to primary diversification in appendix of young rabbits or in bursa of Fabricius of embryonic and young chickens and to secondary diversification during immune responses in germinal centers (GCs). We find that, at least in rabbits, primary diversification appears to occur at a constant rate in the appendix, and the type of Ag-specific selection seen in splenic GCs is absent. This supports the view that a primary repertoire is being generated within the expanding clonally related B cells in appendix of young rabbits and emphasizes the important role that gut-associated lymphoid tissues may play in early development of mammalian immune repertoires. Additionally, the data indicate a higher rate of hypermutation in rabbit and chicken GCs, such that the balance between hypermutation and selection tends more toward mutation and less toward selection in rabbit and chicken compared with murine GCs.

Algorithms↗
PubMed1992

Transfection of activated c-H-rasEJ/pSV2neo or pSV2neo genes into rat mammary cells: rapid stimulation of clonal diversification of spontaneous metastatic and cell-surface properties.

We examined whether the conversion of benign rat mammary cells to metastatic cells by transfection of c-H-rasEJ/pSV2neo or control pSV2neo genes results in rapid stimulation of diversification of cellular phenotypes. Transfection of c-H-rasEJ into twice-cloned, stable (greater than 1 year) rat mammary MTC.4 cells, followed quickly by cell cloning, revealed differences in transfected oncogene copy numbers and expression of p21rasEJ. No correlation between c-H-rasEJ copy numbers or the cellular amounts of p21rasEJ or total p21ras and spontaneous metastatic potentials was found. By subcloning transfected cells as soon as possible after gene transfer, we found some rearrangements and amplifications of c-H-rasEJ and heterogeneous spontaneous metastatic potentials. In addition, the expression of the mammary tumor metastasis-associated cell-surface glycoprotein gp580 on untransfected and transfected MTC.4 cells indicated that the cell populations of higher metastatic potential were also more diverse in their cell-to-cell antigen expression than untransfected or non-metastatic, transfected MTC.4 cells. In contrast, the expression of a putative metastasis-suppressor gene, nm23, was unchanged after transfection and subcloning. Control pSV2neo transfections or calcium phosphate treatment alone also resulted in the generation of cellular heterogeneity, although at an apparently lower frequency than c-H-rasEJ transfections, suggesting that transfection of activated, dominantly acting oncogenes, or in some cases control genes, can result in destabilization of transfected cells, rapid diversification and generation of heterogeneity in growth rate, spontaneous metastatic potential and antigen expression.

Animals↗
PubMed2002

Different genomic evolutionary rates in the various reptile lineages.

Although Reptiles occupy a strategic position among terrestrial vertebrates, studies of the composition and evolution of their genome are scarce. The cytogenetic analysis of nearly 1400 species evidenced different karyotypical evolutionary rates and different G-banding structures in turtles and crocodiles on the one hand and squamates on the other. A similar dichotomy was also identified through the study of the quantitative and compositional characteristics of the genome. The different evolutionary rates of chromosome morphology and genome size and composition and the diversification of coding and non-coding sequences bear an interesting relationship to the number of extant species and the extinction rates of the reptilian orders and suborders studied, suggesting a large role for such different evolutionary rates in the phylogenesis of this class. The different molecular and structural organisation of chromosomes could be an important, though by no means the sole, factor affecting the genome's evolutionary rate.

Alligators and Crocodiles↗