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PubMed2005

Origin and rapid diversification of a tropical moss.

Molecular sequences rarely evolve at a constant rate. Yet, even in instances where a clock can be assumed or approximated for a particular set of sequences, fossils or clear patterns of vicariance are rarely available to calibrate the clock. Thus, obtaining absolute timing for diversification of natural lineages can prove difficult. Unfortunately, without absolute time we cannot develop a complete understanding of important evolutionary processes, including adaptive radiations and key innovations. In the present study, the coding sequence of the nuclear gene, glyceraldehyde 3-phosphate dehydrogenase (gpd), extracted from the paleotropical moss, Mitthyridium, was found to exhibit clocklike behavior and used to reconstruct the history of 80 distinct molecular lineages that cover the full geographic range of Mitthyridium. Two separate clades endemic to two geographically distinct oceanic archipelagos were revealed by this phylogenetic analysis. This allowed the use of island age (as derived from potassium-argon dating) as a maximum age of origin of each monophyletic group, providing two independent time anchors for the clock found in gpd, the final piece needed to study absolute time. Based on results from both maximum age calibrations, which separately yielded highly consistent estimates, the ancestor of this moss group arose approximately 8 million years ago, and then diversified at the rapid rate of 0.56 +/- 0.004 new lineages per million years. Such a rate is on par with the highest diversification rates reported in the literature including rapidly radiating insular groups like the Hawaiian silversword alliance, a classic example of an adaptive radiation. Using independent sources of data, it was found that neither the age nor diversification estimates were affected by the use of molecular lineages rather than species as the operational taxonomic units. Identifying the cause for this rapid diversification requires further testing, but it appears to be related to a general shift in reproductive strategy from sexual to asexual, which may be a key innovation for this young group.

Asia, Southeastern↗
PubMed2003

Molecular clocks and explosive radiations.

Molecular data are ideal for exploring evolutionary history because of its universality, stochasticity, and abundance. These features provide a means of exploring the evolutionary history of all organisms (including those that do not tend to leave fossils), potentially within a statistical framework that allows testing of evolutionary hypotheses. However, the discrepancy between molecular and paleontological dates for three key "explosive" radiations inferred from the fossil record--the Cambrian explosion of animal phyla and the post-KT radiations of modern orders of mammals and birds--have led to a reexamination of the assumptions on which molecular dates are based. Could variation in the rate of molecular evolution, perhaps associated with "explosive" radiations, cause overestimation of diversification dates? Here I examine four hypothetical causes of fast molecular rates in explosive radiations--body size, morphological rate, speciation rate, and ecological diversification--using available empirical evidence on patterns of variation in rate of molecular evolution.

Animals↗
PubMed2003

Inferring the rate and time-scale of dengue virus evolution.

Dengue is often referred to as an emerging disease because of the rapid increases in incidence and prevalence that have been observed in recent decades. To understand the rate at which genetic diversification occurs in dengue virus and to infer the time-scale of its evolution, we employed a maximum likelihood method that uses information about times of virus sampling to estimate the rate of molecular evolution in a large number of viral envelope (E) gene sequences and to place bounds around the dates of appearance of all serotypes and specific genotypes. Our analysis reveals that dengue virus generally evolves according to a molecular clock, although some serotype-specific and genotype-specific rate differences were observed, and that its origin is more recent than previously suggested, with the virus appearing approximately 1,000 years ago. Furthermore, we estimate that the zoonotic transfer of dengue from sylvatic (monkey) to sustained human transmission occurred between 125 and 320 years ago, that the current global genetic diversity in the four serotypes of dengue virus only appeared during the past century, and that the recent rise in genetic diversity can be loosely correlated both to human activities such as population growth, urbanization, and mass transport and to the emergence of dengue hemorrhagic fever as a major disease problem.

Animals↗
PubMed2006

Confounding asymmetries in evolutionary diversification and character change.

Studies of character evolution often assume that a phylogeny's shape is determined independently of the characters, which then evolve as mere passengers along the tree's branches. However, if the characters help shape the tree, but this is not considered, biased inferences can result. Simulations of asymmetrical speciation (i.e., one character state conferring a higher rate of speciation than another) result in data that are interpreted to show a higher rate of change toward the diversification-enhancing state, even though the rates to and from this state were in fact equal. Conversely, simulations of asymmetrical character change yield data that could be misinterpreted as showing asymmetrical rates of speciation. Studies of biased diversification and biased character change need to be unified by joint models and estimation methods, although how successfully the two processes can be teased apart remains to be seen.

Biological Evolution↗
PubMed1998

Multigene tracking of hepatitis C virus quasispecies after liver transplantation: correlation of genetic diversification in the envelope region with asymptomatic or mild disease patterns.

To investigate the role of hepatitis C virus (HCV) quasispecies mutation in the pathogenesis of HCV infection, we analyzed changes in the genetic diversity of HCV genomes in 22 patients before and after liver transplantation by using heteroduplex mobility assay (HMA) technology. All patients were infected with HCV genotype 1 and developed high-titer posttransplant viremia. Each patient was classified according to the severity of posttransplant hepatitis, as assessed by standard biochemical and histological criteria. HCV quasispecies were characterized by HMA analysis of eight separate subgenomic regions of HCV, which collectively comprise 44% of the entire genome. The glycoprotein genes E1 and E2, as well as the nonstructural protein genes NS2 and NS3, had the greatest genetic divergence after liver transplantation (the change in the heteroduplex mobility ratio [HMR] ranged from 2.5 to 7.0%). In contrast, genes encoding the core, NS4, and NS5b proteins had the least amount of genetic divergence after liver transplantation (range, 0.3 to 1.2%). The E1/E2 region showed the greatest change in genetic diversity after liver transplantation, and the change in HMRs was 2.5- to 3.3-fold greater in patients with asymptomatic or moderate disease than in those with severe disease. The E1-5' region of HCV quasispecies isolated from patients in the asymptomatic group had a significantly greater degree of diversification after liver transplantation than the same regions of HCV quasispecies isolated from patients in the severe disease group (P = 0.05). While changes in the genetic diversity of some nonstructural genes were also greater in asymptomatic patients or in patients with mild disease than in patients with severe disease, the results were not significant. Data from this cohort demonstrate that greater rates of HCV quasispecies diversification are associated with mild or moderate liver disease activity in this immunosuppressed population.

Base Sequence↗
PubMed2001

The pace of modern life II: from rates of contemporary microevolution to pattern and process.

We compiled a database of microevolution on contemporary time scales in nature (47 source articles; 30 animal species), comprising 2649 evolutionary rates in darwins (proportional change per million years) and 2151 evolutionary rates in haldanes (standard deviations per generation). Here we demonstrate how quantitative rate measures can provide general insights into patterns and processes of evolution. The frequency distribution of evolutionary rates was approximately log-normal, with many slow rates and few fast rates. Net selection intensities estimated from haldanes were on average lower than selection intensities commonly measured directly in natural populations. This difference suggests that natural selection could easily accomplish observed microevolution but that the intensities of selection typically measured in nature are rarely maintained for long (otherwise observed evolutionary rates would be higher). Traits closely associated with fitness (life history traits) appear to evolve at least as fast as traits less closely tied to fitness (morphology). The magnitude of evolutionary difference increased with the length of the time interval, particularly when maximum rates from a given study were considered. This pattern suggests a general underlying tendency toward increasing evolutionary diversification with time. However, evolutionary rates also tended to decrease with time, perhaps because longer time intervals average increasingly disparate rates over time, or because evolution slows when populations approach new optima or as genetic variation is depleted. In combination, our results suggest that macroevolutionary transitions may ultimately arise through microevolution occasionally 'writ large' but are perhaps temporally characterized by microevolution 'writ in fits and starts'.

Animals↗
PubMed1987

A comparative study of diversification events: the early Paleozoic versus the Mesozoic.

We compare two major long-term diversifications of marine animal families that began during periods of low diversity but produced strikingly different numbers of phyla, classes, and orders. The first is the early-Paleozoic diversification (late Vendian-Ordovician; 182 MY duration) and the other the Mesozoic phase of the post-Paleozoic diversification (183 MY duration). The earlier diversification was associated with a great burst of morphological invention producing many phyla, classes, and orders and displaying high per taxon rates of family origination. The later diversification lacked novel morphologies recognized as phyla and classes, produced fewer orders, and displayed lower per taxon rates of family appearances. The chief difference between the diversifications appears to be that the earlier one proceeded from relatively narrow portions of adaptive space, whereas the latter proceeded from species widely scattered among adaptive zones and representing a variety of body plans. This difference is believed to explain the major differences in the products of these great radiations. Our data support those models that hold that evolutionary opportunity is a major factor in the outcome of evolutionary processes.

Adaptation, Biological↗
PubMed1997

The structure of human lupus anti-DNA antibodies.

B-cell hyperactivity and production of pathogenic autoantibodies are the main immunological events in the pathogenesis of the human autoimmune disease systemic lupus erythematosus. One approach to studying the pathogenesis of this disease and to understanding how the autoantibody response is initiated and sustained has been to analyze the variable genes expressed by antibodies that have the hallmarks of the disease-causing subset of pathogenic autoantibodies. Such studies have provided important clues. Quantitation of this repertoire revealed the presence of a specific expansion of IgG clonotypes that impart reactivity with disease-related autoantigens. The sequences of the genes encoding autoantibodies derived from these patients and expressing nephritogenic idiotopes (present in immune complexes and renal eluates of subjects with active disease) show features of molecular diversification with a high rate of replacement/silent mutations and clustering of the mutations in the hypervariable regions. These characteristics imply that a pure polyclonal B-cell activation process cannot be the only mechanism responsible for autoantibody production. More likely, an antigen drive plays a role in generation of pathogenic autoantibodies. Based on additional studies of their light chain variable region genes, we have offered a novel genetically based model whereby B cells secreting pathogenic lupus autoantibodies are blocked in their capacity to turn off their autoreactivity and to acquire a new specificity, a mechanism called receptor editing. Studies of the molecular events involved in this mechanism and of the clonal fates of B cells in vivo will be important for future research.

Amino Acids↗
PubMed2002

Phylogenetic analysis of Brassiceae based on the nucleotide sequences of the S-locus related gene, SLR1.

Nucleotide sequences of orthologs of the S-locus related gene, SLR1, in 20 species of Brassicaceae were determined and compared with the previously reported SLR1 sequences of six species. Identities of deduced amino-acid sequences with Brassica oleracea SLR1 ranged from 66.0% to 97.6%, and those with B. oleracea SRK and SLR2 were less than 62% and 55%, respectively. In multiple alignment of deduced amino-acid sequences, the 180-190th amino-acid residues from the initial methionine were highly variable, this variable region corresponding to hypervariable region I of SLG and SRK. A phylogenetic tree based on the deduced amino-acid sequences showed a close relationship of SLR1 orthologs of species in the Brassicinae and Raphaninae. Brassica nigra SLR1 was found to belong to the same clade as Sinapis arvensis and Diplotaxis siifolia, while the sequences of the other Brassica species belonged to another clade together with B. oleracea and Brassica rapa. The phylogenetic tree was similar to previously reported trees constructed using the data of electrophoretic band patterns of chloroplast DNA, though minor differences were found. Based on synonymous substitution rates in SLR1, the diversification time of SLR1 orthologs between species in the Brassicinae was estimated. The evolution and function of SLR1 and the phylogenetic relationship of Brassiceae plants are discussed.

Journal Article↗
PubMed1994

Proterozoic and early Cambrian protists: evidence for accelerating evolutionary tempo.

In rocks of late Paleoproterozoic and Mesoproterozoic age (ca. 1700-1000 million years ago), probable eukaryotic microfossils are widespread and well preserved, but assemblage and global diversities are low and turnover is slow. Near the Mesoproterozoic-Neoproterozoic boundary (1000 million years ago), red, green, and chromophytic algae diversified; molecular phylogenies suggest that this was part of a broader radiation of "higher" eukaryotic phyla. Observed diversity levels for protistan microfossils increased significantly at this time, as did turnover rates. Coincident with the Cambrian radiation of marine invertebrates, protistan microfossils again doubled in diversity and rates of turnover increased by an order of magnitude. Evidently, the Cambrian diversification of animals strongly influenced evolutionary rates, within clades already present in marine communities, implying an important role for ecology in fueling a Cambrian explosion that extends across kingdoms.

Biological Evolution↗
PubMed2002

Signatures of random and selective mass extinctions in phylogenetic tree balance.

Current models of diversification with evolving speciation rates have trouble mimicking the extreme imbalance seen in estimated phylogenies. However, these models have not incorporated extinction. Here, we report on a simple simulation model that includes heritable and evolving speciation rates coupled with mass extinctions, Random (but not selective) mass extinctions, coupled with evolving among-lineage variation in speciation rates, increase imbalance of postrecovery clades. Thus, random mass extinctions are plausible contributors to the imbalance of modern clades. Paleontological evidence suggests that mass extinctions are often random with respect to ecological and morphological traits, consistent with our simulations. In contrast, evidence that the current anthropogenic mass extinction is phylogenetically selective suggests that the current extinction episode may be qualitatively different from past ones in the way it reshapes future biotas.

Biological Evolution↗
PubMed2001

B cell tolerance to self in systemic autoimmunity.

After a century of research and despite intensive scrutiny, the origin of autoantibody production remains an enigma. Recently, the essential role of B cells in promoting systemic autoimmunity in mice seems more important than previously thought: self-reactive B cells can be subject to positive selection and a deficiency in serum IgM predisposes to the development of IgG antibodies to autoantigens. Studies of the B cell repertoire expressed in systemic autoimmune diseases have provided important clues. In human lupus, quantitation of this repertoire reveals the presence of an expansion of IgG clonotypes that impart reactivity with disease-related autoantigens. The nucleotide sequences of autoantibodies derived from these patients and expressing nephritogenic idiotopes (present in immune complexes and renal eluates of subjects with active disease) show features of diversification with a high rate of replacement/silent mutations and clustering of the mutations in the hypervariable regions, suggesting than an antigen-driven process plays a role in the generation of pathogenic autoantibodies. Currently, the contributions of apoptosis and of cell receptor signaling to this triggering are being appreciated. Pursuing these and related issues will have an important impact on autoimmune research.

Animals↗
PubMed1993

Calibrating rates of early Cambrian evolution.

An explosive episode of biological diversification occurred near the beginning of the Cambrian period. Evolutionary rates in the Cambrian have been difficult to quantify accurately because of a lack of high-precision ages. Currently, uranium-lead zircon geochronology is the most powerful method for dating rocks of Cambrian age. Uranium-lead zircon data from lower Cambrian rocks located in northeast Siberia indicate that the Cambrian period began at approximately 544 million years ago and that its oldest (Manykaian) stage lasted no less than 10 million years. Other data indicate that the Tommotian and Atdabanian stages together lasted only 5 to 10 million years. The resulting compression of Early Cambrian time accentuates the rapidity of both the faunal diversification and subsequent Cambrian turnover.

Biological Evolution↗
PubMed1986

Temporal scaling of molecular evolution in primates and other mammals.

Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constancy. Temporal scaling provides a test of rates, where scaling coefficients of 1.0 (isochrony) represent stochastic rate constancy. The fossil record of primates and other mammals is now known in sufficient detail to provide several independent divergence times for major taxonomic groups. Molecular difference should scale negatively or isochronically (scaling coefficients less than 1.0) with divergence time: where two or more divergence times are available, molecular difference appears to scale positively (scaling coefficient greater than 1.0). A minimum of four divergence times are required for adequate statistical power in testing the linear model: scaling is significantly nonlinear and positive in six of 11 published investigations meeting this criterion. All groups studied show some slowdown in rates of molecular change over Cenozoic time. The break from constant or increasing rates during the Mesozoic to decreasing rates during the Cenozoic appears to coincide with extraordinary diversification of placental mammals at the beginning of this era. High rates of selectively neutral molecular change may be concentrated in such discrete events of evolutionary diversification.

Amino Acid Sequence↗
PubMed2003

Endemic diversification of the monophyletic cottoid fish species flock in Lake Baikal explored with mtDNA sequencing.

In the ancient Lake Baikal in East Siberia, cottoid fishes have diversified into an endemic flock of 33 species. From an ancestral shallow-water, benthic life-style, Baikalian cottoids have shifted to deep-water life in environments even below 1500 m, and also colonized the pelagic habitat. We examined phylogenetic relationships among 22 Baikalian and 10 extra-Baikalian cottoid taxa using a total of 2822 bp of mitochondrial DNA sequence, from complete sequences of ATPase 8 and 6 and cytochrome b genes and the control region. Unlike in earlier studies, we found strong support for a monophyly of the whole endemic Baikalian cottoid diversity. The Baikalian clade, currently assigned to three families and 12 genera, appears to be nested within the Holarctic freshwater genus Cottus. In the molecular phylogeny, all but one of the current Baikalian genera formed well-supported monophyletic groups. However, the topology was inconsistent with the present morphology-based familial subdivision; particularly in positioning the genus Batrachocottus of Cottidae within Abyssocottidae. The branching order of the Baikalian genera could not be resolved completely, however; short basal branches indicate rapid diversification early in the history of the species flock. Using synonymous divergence rates from other fish species for calibration, the diversification of the Baikalian cottoids seems to have started in the Pliocene or early Pleistocene.

Animals↗
PubMed2004

Two viral strains and a possible novel recombinant are responsible for the explosive injecting drug use-associated HIV type 1 epidemic in Estonia.

HIV-1 infection has been rare in Estonia. In 2000, an explosive epidemic among injecting drug users was detected in the Eastern border region, resulting in 3603 newly reported cases by the end of 2003. The molecular epidemiology of the outbreak was studied to establish whether the Estonian epidemic is linked to the epidemics in Eastern Europe. Over 200 newly infected individuals were prospectively sampled from June 2000 to March 2002 in a geographically representative way, with known dates of diagnosis and information of probable route of transmission. Viral regions coding for two viral gene regions were directly sequenced from plasma viral RNA and phylogenetically analyzed. In addition, a larger region coding for the entire env gene was sequenced from one sample and studied for indications of possible recombinant structure. The Estonian HIV outbreak was found to be caused by simultaneous introduction of two strains: a minor subtype A strain very similar to the Eastern European subtype A strain (approximately 8% of cases), and a second major strain (77%) found to be most closely related to the CRF06-cpx strain, previously described only from African countries. The variability in the two clusters was very low, suggesting point source introductions. Ten percent of cases seemed to be newly generated recombinants of the A and CRF06-cpx strains. Analysis of viral diversification over time revealed a rate of change within the V3 region of 0.83%/year for the CRF06-cpx strain, consistent with findings from other subtypes. Due to the relatively frequently found novel recombinant forms, the Estonian HIV-1 epidemic may allow studies of coinfection and intersubtype recombination in detail.

Disease Outbreaks↗
PubMed1995

Triple combinations: present and future.

Three or more therapeutic agents have commonly been used to treat chronic infections and many malignant diseases. It is clear that monotherapy treatment of HIV infection, although effective in the short term, is not a viable long-term management option because of incomplete suppression of viral replication and the subsequent development of viral resistance. It is therefore generally accepted that multidrug combination therapy represents the most promising strategy for HIV management. The rationale for this approach is based on an understanding of viral pathogenesis and preliminary results from in vitro studies. It is anticipated that combination therapy will achieve greater reductions in viral load, leading to reduced rates of viral replication and diversification, which, in turn, will result in the delayed emergence of drug-resistant and cytopathic variants. This will probably result in the prevention of both immune system destruction and subsequent disease progression. Preliminary in vitro studies have provided evidence that double combinations are more effective than monotherapy. In vivo results from clinical trials comparing double combinations with monotherapy, however, have not been as impressive as expected, and show that suppression of viral replication, even with two drugs, is incomplete. Further in vitro evidence from sensitivity studies suggests that triple combinations are likely to be more effective. Further clinical trials of the most promising combinations need to be conducted. however, the selection of these combinations is not an easy task owing to the large number of possible regimens to choose from. The Inter-Company Collaboration on AIDS Drug Development, among others, has established protocols for rapid identification of promising combinations that should make this task easier. At present, early treatment with combinations of three or even more drugs represents the only logical long-term management option for patients infected with HIV.

Antiviral Agents↗
PubMed2007

How does resource supply affect evolutionary diversification?

The availability of different resources in the environment can affect the outcomes of evolutionary diversification. A unimodal distribution of diversity with resource supply has been widely observed and explained previously in the context of selection acting in a spatially heterogeneous environment. Here, we propose an alternative mechanism to explain the relationship between resource supply and diversification that is based on selection for exploitation of different resources. To test this mechanism, we conducted a selection experiment using the bacterium Pseudomonas fluorescens in spatially homogeneous environments over a wide range of resource supply rates. Our results show that niche diversification peaks at intermediate levels of resource availability. We suggest that this unimodal relationship is due to evolutionary diversification that is driven by competition for resources but constrained by the ecological opportunity represented by different resource types. These processes may underlie some general patterns of diversity, including latitudinal gradients in species richness and the effects of anthropogenic enrichment of the environment.

Adaptation, Biological↗