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PubMed1988

Maintenance of multiplication rate stability by cell populations in the face of heterogeneity among individual cells.

We addressed the question of how a population of cells can maintain a constant multiplication rate given the heterogeneity of its individual members. Using the NIH 3T3 line of mouse embryo cells, comparisons were made of multiplication rates between offspring subclones and the parental clones from which the subclones were derived. Parents at all levels of multiplication rate produced offspring with a wide range of multiplication rates. Offspring from parent cells with the highest growth rates rarely exceeded their parents in rate of multiplication. Offspring from slow-growing parents, however, often exceeded the parents. It is concluded that the multiplication of NIH 3T3 populations represents constant diversification in multiplication rate: heterogeneous parents producing heterogeneous offspring. Population growth rates can remain stable because the fastest-growing parents generally produce offspring that multiply slower than the parents while the slowest parents often produce offspring that multiply faster than the parents.

Animals↗
PubMed2000

Colonization and diversification of the species Brachyderes rugatus (Coleoptera) on the Canary Islands: evidence from mitochondrial DNA COII gene sequences.

The genus Brachyderes Schönherr (Coleoptera: Curculionidae) is represented by the species B. rugatus Wollaston on the Canary Islands, with one subspecies on each of the islands of Gran Canaria, Tenerife, La Palma, and El Hierro. These four subspecies are associated with the endemic pine tree Pinus canariensis, and their distributions are broadly coincident. Eighty-eight individual Canarian Brachyderes, sampled from across the distributions of each subspecies, have been sequenced for 570 bp of the mitochondrial DNA (mtDNA) cytochrome oxidase II gene (COII). No mitotypes are shared among islands. Both maximum-likelihood and distance-based phylogenetic analyses have shown that: Tenerife is composed of a single monophyletic clade of mitotypes, El Hierro is composed of a single monophyletic clade occurring within a larger clade comprising all the La Palma mitotypes, and the mitotypes of these three islands form a monophyletic group distinct from Gran Canaria. New methods for estimating divergence times without the assumption of rate constancy have been used to reconstruct the direction and approximate timing of colonizations among the islands. Colonization has occurred from older to progressionally younger islands, and these colonizations are estimated to have occurred less than 2.6 million years ago, although the timing of the initial colonization of the archipelago is not discernable. New methods for the estimation of diversification rates that use branching times as the analyzed variable have been applied to each island fauna. Hypothesized effects of different levels of recent volcanism among islands were not apparent. All islands exhibit a gradually decreasing rate of genetic diversification that is marked by periodic sudden changes in rate.

Animals↗
PubMed2006

A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects.

BACKGROUND: A full understanding of the patterns and processes of biological diversification requires the dating of evolutionary events, yet the fossil record is inadequate for most lineages under study. Alternatively, a molecular clock approach, in which DNA or amino acid substitution rates are calibrated with fossils or geological/climatic events, can provide indirect estimates of clade ages and diversification rates. The utility of this approach depends on the rate constancy of molecular evolution at a genetic locus across time and across lineages. Although the nuclear ribosomal internal transcribed spacer region (nrITS) is increasingly being used to infer clade ages in plants, little is known about the sources or magnitude of variation in its substitution rate. Here, we systematically review the literature to assess substitution rate variation in nrITS among angiosperms, and we evaluate possible correlates of the variation. RESULTS: We summarize 28 independently calibrated nrITS substitution rates ranging from 0.38 x 10(-9) to 8.34 x 10(-9) substitutions/site/yr. We find that herbaceous lineages have substitution rates almost twice as high as woody plants, on average. We do not find any among-lineage phylogenetic constraint to the rates, or any effect of the type of calibration used. Within life history categories, both the magnitude of the rates and the variance among rates tend to decrease with calibration age. CONCLUSION: Angiosperm nrITS substitution rates vary by approximately an order of magnitude, and some of this variation can be attributed to life history categories. We make cautious recommendations for the use of nrITS as an approximate plant molecular clock, including an outline of more appropriate phylogenetic methodology and caveats against over interpretation of results. We also suggest that for lineages with independent calibrations, much of the variation in nrITS substitution rates may come from uncertainty in calibration date estimates, highlighting the importance of accurate and/or multiple calibration dates.

Amino Acid Substitution↗
PubMed2004

Environmental energy and evolutionary rates in flowering plants.

The latitudinal gradient in species richness is a pervasive feature of the living world, but its underlying causes remain unclear. We evaluated the hypothesis that environmental energy drives evolutionary rates and thereby diversification in flowering plants. We estimated energy levels across angiosperm family distributions in terms of evapotranspiration, temperature and UV radiation taken from satellite and climate databases. Using the most comprehensive DNA-based phylogenetic tree for angiosperms to date, analysis of 86 sister-family comparisons shows that molecular evolutionary rates have indeed been faster in high-energy regions, but that this is not an intermediate step between energy and diversity. Energy has strong, but independent effects on both species richness and molecular evolutionary rates.

Biodiversity↗
PubMed2003

Evolution and microsynteny of the apyrase gene family in three legume genomes.

Apyrases have been suggested to play important roles in plant nutrition, photomorphogenesis, and nodulation. To help trace the evolution of these genes in the legumes--and possibly, the acquisition of new functions for nodulation--apyrase-containing BACs were sequenced from three legume genomes. Genomic sequences from Medicago truncatula, Glycine max and Lotus japonicus were compared to one another and to corresponding regions in Arabidopsis thaliana. A phylogenetic analysis of apyrase homologs from these regions and sequences from other legume species, as well as other plant families, identified a potentially legume-specific clade that contains a well-characterized soybean ( G. soja) apyrase, Gs52, as well as homologs from Dolichos, Lotus, Medicago and Pisum. Sister clades contain homologs from members of Brassicaceae, Solanaceae, Poaceae and Fabaceae. Comparisons of rates of change at synonymous and nonsynonymous sites in the Gs52 and sister clades show rapid evolution in the potentially legume-specific Gs52 clade. The genomic organization of the apyrase-containing BACs shows evidence of gene duplication, genomic rearrangement, and gene conversion among Gs52 homologs. Taken together, these results suggest a scenario of local apyrase gene duplication in an ancestor of the legumes, followed by functional diversification and increased rates of change in the new genes, and further duplications in the Galegae (which include the genera Medicago and Pisum). The study also provides a detailed comparison of genomic regions between two model genomes which are now being sequenced ( M. truncatulaand L. japonicus), and a genome from an economically important legume species ( G. max).

Apyrase↗
PubMed1999

MtDNA phylogeography and recent intra-island diversification among Canary Island Calathus beetles.

The genus Calathus Bonelli comprises 24 species on the Canary Islands. Sequences of 927 and 687 bp of the mitochondrial cytochrome oxidase I and II genes, respectively, as well as the intervening tRNA leu gene in 21 of the 24 species, have identified three genetically divergent and unequivocally monophyletic groupings. A phylogeographic analysis is presented for the major monophyletic group comprising all the species of Gran Canaria, La Gomera, and El Hierro, and two Tenerifean species. A distance-based phylogenetic analysis and maximum parsimony analysis have clearly shown that this clade is composed of four distinct lineages. DNA sequence data suggest a recent origin for this clade and that lineages have not evolved at the same rate. Compared with diversification patterns observed in other Coleoptera on the Canary Islands, diversification has been recent relative to the time of colonization within the islands of Gran Canaria and La Gomera. Calathus diversification on La Gomera has been greater than on Gran Canaria. The influences of geological and ecological history are discussed in relation to Calathus diversification.

Animals↗
PubMed2005

Intraspecific variability and timing in ancestral ecology reconstruction: a test case from the cape flora.

Thamnochortus (ca. 32 species) is an ecologically diverse genus of Restionaceae. Restionaceae comprise a major component of the southern African Cape flora, wherein eco-diversification might have been important in the generation of high levels of species richness. In an attempt to reconstruct the macroecological history of Thamnochortus, it was found that standard procedures for character state optimization make two inappropriate assumptions. The first is that ancestors are monomorphic (i.e., ecologically uniform) and the second is that eco-diversification follows, or is slower than, lineage diversification. We demonstrate a variety of coding schemes with which the assumption of monomorphy can be avoided. For unordered discrete ecological characters, presence coding and generalized frequency coding (GFC) are suboptimal because they occasionally yield illogical assignments of no state to ancestors. Polymorphism coding or use of the program DIVA are preferable in this respect but are applicable only with parsimony. For continuous eco-characters (e.g., a rainfall gradient, where individual species occur in ranges), GFC and MaxMin coding provide equally valid solutions to optimizing ranges with parsimony. However, MaxMin can be extended to likelihood approaches and is therefore preferable. With respect to rates and timing, all algorithms currently employed for ancestral ecology reconstruction bias toward slow rates of eco-diversification relative to lineage diversification. An alternative to this bias is provided by DIVA, which biases toward accelerated rates of eco-diversification and thus inferences of ecology-driven speciation. We see no way of choosing between these biases; however, phylogeneticists should be aware of them. Applying these methods to Thamnochortus, we find there to be important differences in details, yet general congruence, regarding the historical ecology of this clade. We infer the most recent common ancestor of Thamnochortus to have been a post-fire resprouting species distributed on rocky, well-drained, sandstone-derived soils at lower-middle elevations, in regions of moderate levels of yearly (primarily winter) rainfall. This species would have been distributed in habitats much like those of the southwestern Cape mountains today. Major ecological trends include shifts to lower rainfall regimes and shifts from sandstone to limestone-derived alkaline soils at lower altitudes.

Base Sequence↗
PubMed2001

Timing of the HIV-1 subtype C epidemic in Ethiopia based on early virus strains and subsequent virus diversification.

OBJECTIVE: To trace the introduction of HIV-1 subtype C into Ethiopia based on virus diversification during the epidemic. DESIGN: A set of 474 serum samples obtained in Ethiopia in 1982-1985 was tested for HIV-1. HIV-1 env gp120 V3 and gag or pol regions were sequenced and analysed together with sequences from later stages of the epidemic. RESULTS: None of 98 samples from 1982-1983, one of 193 samples from 1984, and one of 183 samples from 1985 were HIV-1 positive. Phylogenetic analysis of virus sequences from positive samples revealed that they belong to the Ethiopian C, and not the C', cluster. Analysis of 81 Ethiopian C V3 sequences from 1984-1997 revealed that the consensus sequence of the Ethiopian epidemic has been stable over time. Both the 1984 and 1985 V3 sequences, in contrast with three out of 27 (11%) of the 1988 and none out of 51 of the 1992-1997 sequences, had no synonymous substitutions compared to the reconstructed common ancestor of the Ethiopian C viruses. A highly significant correlation between sampling years of the V3 sequences and their synonymous distances to the common ancestor was demonstrated. CONCLUSIONS: The increasing genetic heterogeneity together with stable consensus sequence of the Ethiopian HIV-1 C population demonstrates that evolution of the virus population is characterized by an unbiased expansion around a stationary consensus. Based on the rate of synonymous diversification of HIV-1 strains within the Ethiopian population, we were able to estimate 1983 (95% confidence interval, 1980-1984) as the year of HIV-1 C introduction into Ethiopia.

Adult↗
PubMed2001

Evolutionary assembly of the milkweed fauna: cytochrome oxidase I and the age of Tetraopes beetles.

The insects that feed on the related plant families Apocynaceae and Asclepiadaceae (here collectively termed "milkweeds") comprise a "component community" of highly specialized, distinctive lineages of species that frequently sequester toxic cardiac glycosides from their host plants for defense against predators and are thus often aposematic, advertising their consequent unpalatability. Such sets of specialized lineages provide opportunities for comparative studies of the rate of adaptation, diversification, and habitat-related effects on molecular evolution. The cerambycid genus Tetraopes is the most diverse of the new world milkweed herbivores and the species are generally host specific, being restricted to single, different species of Asclepias, more often so than most other milkweed insects. Previous work revealed correspondence between the phylogeny of these beetles and that of their hosts. The present study provides analyses of near-complete DNA sequences for Tetraopes and relatives that are used to establish a molecular clock and temporal framework for Tetraopes evolution with their milkweed hosts.

Adaptation, Physiological↗
PubMed2002

Genomic analysis of the terpenoid synthase ( AtTPS) gene family of Arabidopsis thaliana.

A family of 40 terpenoid synthase genes ( AtTPS) was discovered by genome sequence analysis in Arabidopsis thaliana. This is the largest and most diverse group of TPS genes currently known for any species. AtTPS genes cluster into five phylogenetic subfamilies of the plant TPS superfamily. Surprisingly, thirty AtTPS closely resemble, in all aspects of gene architecture, sequence relatedness and phylogenetic placement, the genes for plant monoterpene synthases, sesquiterpene synthases or diterpene synthases of secondary metabolism. Rapid evolution of these AtTPS resulted from repeated gene duplication and sequence divergence with minor changes in gene architecture. In contrast, only two AtTPS genes have known functions in basic (primary) metabolism, namely gibberellin biosynthesis. This striking difference in rates of gene diversification in primary and secondary metabolism is relevant for an understanding of the evolution of terpenoid natural product diversity. Eight AtTPS genes are interrupted and are likely to be inactive pseudogenes. The localization of AtTPS genes on all five chromosomes reflects the dynamics of the Arabidopsis genome; however, several AtTPS genes are clustered and organized in tandem repeats. Furthermore, some AtTPS genes are localized with prenyltransferase genes ( AtGGPPS, geranylgeranyl diphosphate synthase) in contiguous genomic clusters encoding consecutive steps in terpenoid biosynthesis. The clustered organization may have implications for TPS gene evolution and the evolution of pathway segments for the synthesis of terpenoid natural products. Phylogenetic analyses highlight events in the divergence of the TPS paralogs and suggest orthologous genes and a model for the evolution of the TPS gene family.

Alkyl and Aryl Transferases↗
PubMed1992

Genetic variation and quasi-species.

During the past year the relative fitness, that is, overall replication ability, and the fitness gain of animal virus variants have been quantified, providing new insight into the dynamics for the generation of RNA virus quasi-species. Measurements of mutant frequencies and rates of genetic diversification have confirmed the extreme complexity of RNA virus and retrovirus populations.

Genetic Variation↗
PubMed2006

Genome architecture drives protein evolution in ciliates.

Studies of microbial eukaryotes have been pivotal in the discovery of biological phenomena, including RNA editing, self-splicing RNA, and telomere addition. Here we extend this list by demonstrating that genome architecture, namely the extensive processing of somatic (macronuclear) genomes in some ciliate lineages, is associated with elevated rates of protein evolution. Using newly developed likelihood-based procedures for studying molecular evolution, we investigate 6 genes to compare 1) ciliate protein evolution to that of 3 other clades of eukaryotes (plants, animals, and fungi) and 2) protein evolution in ciliates with extensively processed macronuclear genomes to that of other ciliate lineages. In 5 of the 6 genes, ciliates are estimated to have a higher ratio of nonsynonymous/synonymous substitution rates, consistent with an increase in the rate of protein diversification in ciliates relative to other eukaryotes. Even more striking, there is a significant effect of genome architecture within ciliates as the most divergent proteins are consistently found in those lineages with the most highly processed macronuclear genomes. We propose a model whereby genome architecture-specifically chromosomal processing, amitosis within macronuclei, and epigenetics-allows ciliates to explore protein space in a novel manner. Further, we predict that examination of diverse eukaryotes will reveal additional evidence of the impact of genome architecture on molecular evolution.

Animals↗
PubMed1984

Structural determinants of hospital closure.

In a retrospective case-control study, structural characteristics of hospitals that closed during the years 1976-1980 were contrasted with three comparison groups: hospitals that were acquired in a merger; hospitals that joined a multihospital system; and hospitals that remained autonomously opened, to investigate these characteristics as predictors of closure. Characteristics investigated included environmental, structural, and process variables. The independent variables were measured 5 years prior to outcome. Findings indicate that closed hospitals resemble hospitals acquired in a merger ("failure"), and likewise autonomous hospitals resemble hospitals that join a multihospital system ("success"). The most important predictors of hospital failure were the physician-to-population ratio, the East North Central and West North Central census regions, the level of diversification, low occupancy rate, location in a standard metropolitan statistical area, the chief executive officer's lack of affiliation in the American College of Hospital Administrators, profit status, bed size of less than 50, and presence in a state with a rate-setting agency. Surprisingly, this study shows the bed-to-population ratio to be unrelated to closure. In addition, the findings strongly support the open-system perspective, which, unlike the closed-system perspective, is concerned with the vulnerability of the organization to the uncontrollable and often unpredictable influences of the environment.

Bed Occupancy↗
PubMed2004

The role of Quaternary environmental change in plant macroevolution: the exception or the rule?

The Quaternary has been described as an important time for genetic diversification and speciation. This is based on the premise that Quaternary climatic conditions fostered the isolation of populations and, in some instances, allopatric speciation. However, the 'Quaternary Ice-Age speciation model' rests on two key assumptions: (i) that biotic responses to climate change during the Quaternary were significantly different from those of other periods in Earth's history; and (ii) that the mechanisms of isolation during the Quaternary were sufficient in time and space for genetic diversification to foster speciation. These assumptions are addressed by examining the plant fossil record for the Quaternary (in detail) and for the past 410 Myr, which encompasses previous intervals of icehouse Earth. Our examination of the Quaternary record indicates that floristic responses to climate changes during the past 1.8 Myr were complex and that a distinction has to be made between those plants that were able to withstand the extremes of glacial conditions and those that could not. Generation times are also important as are different growth forms (e.g. herbaceous annuals and arborescent perennials), resulting in different responses in terms of genetic divergence rates during isolation. Because of these variations in the duration of isolation of populations and genomic diversification rates, no canonical statement about the predominant floristic response to climatic changes during the Quaternary (i.e. elevated rates of speciation or extinction, or stasis) is currently possible. This is especially true because of a sampling bias in terms of the fossil record of tree species over that of species with non-arborescent growth forms. Nevertheless, based on the available information, it appears that the dominant response of arborescent species during the Quaternary was extinction rather than speciation or stasis. By contrast, our examination of the fossil record of vascular plants for the past 410 Myr indicates that speciation rates often increased during long intervals of icehouse Earth (spanning up to 50 Myr). Therefore, longer periods of icehouse Earth than those occurring during the Quaternary may have isolated plant populations for sufficiently long periods of time to foster genomic diversification and allopatric speciation. Our results highlight the need for more detailed study of the fossil record in terms of finer temporal and spatial resolution than is currently available to examine the significance of intervals of icehouse Earth. It is equally clear that additional and detailed molecular studies of extant populations of Quaternary species are required in order to determine the extent to which these 'relic' species have genomically diversified across their current populations.

Biological Evolution↗
PubMed2004

Exploring the concept of clonality in bacteria.

Isolates of bacterial species that are indistinguishable in genotype are assigned as a clone, with the implication that they are descended from the same recent ancestor. Clones are difficult to define with precision since bacteria are not truly asexual, and recombinational replacements result in diversification of the ancestral genotype of a clone, to produce a cluster of increasingly diverse genotypes (a clonal complex). The rate at which clonal diversification occurs depends on the extent of recombination, which varies among bacteria, so that some species have rather stable clones (e.g., Salmonella enterica), whereas in other species (e.g., Helicobacter pylori) clones may be so transient that they cannot readily be discerned. Clones and clonal complexes need to be assigned by indexing genetic variation that is selectively neutral, and currently this is best achieved using multilocus sequence typing. Some species of bacterial pathogens are very diverse, whereas others are genetically uniform, and some are, in essence, a single clone of a mother species that has been raised to species status due to the distinctiveness of the disease it causes (e.g., Yersinia pestis, Salmonella typhi, or Burkholderia mallei). The population structures of bacteria depend on the rate of recombination, and comparative measures of the extent of recombination during clonal diversification can be obtained from multilocus sequence typing data, as can measures of the longer-term impact of recombination. These studies show a wide range of recombination rates among bacterial species, and indicate that recombination in many bacteria has been sufficiently extensive that a reliable evolutionary history of the species cannot be inferred.

Bacteria↗
PubMed2002

Shifts in hexapod diversification and what Haldane could have said.

Data on species richness and taxon age are assembled for the extant hexapod orders (insects and their six-legged relatives). Coupled with estimates of phylogenetic relatedness, and simple statistical null models, these data are used to locate where, on the hexapod tree, significant changes in the rate of cladogenesis (speciation-minus-extinction rate) have occurred. Significant differences are found between many successive pairs of sister taxa near the base of the hexapod tree, all of which are attributable to a shift in diversification rate after the origin of the Neoptera (insects with wing flexion) and before the origin of the Holometabola (insects with complete metamorphosis). No other shifts are identifiable amongst supraordinal taxa. Whilst the Coleoptera have probably diversified faster than either of their putative sister lineages, they do not stand out relative to other closely related clades. These results suggest that any Creator had a fondness for a much more inclusive clade than the Coleoptera, definitely as large as the Eumetabola (Holometabola plus bugs and their relatives), and possibly as large as the entire Neoptera. Simultaneous, hence probable causative events are discussed, of which the origin of wing flexion has been the focus of much attention.

Animals↗
PubMed2006

Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns.

The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.

Evolution, Molecular↗