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PubMed2006

Differences in potential for amino acid change after mutation reveals distinct strategies for kappa and lambda light-chain variation.

B cells generate varied yet functional clones under high rates of mutation of their V genes. It has been proposed that as a result of the opposing demands of diversification and preservation of integrity, the V genes of heavy and light chains have evolved to overexpress codons prone to amino acid change in their complementarity determining regions (CDR) compared with the framework (FW) regions. We have analyzed the germ-line V genes of heavy and light chains (both kappa and lambda), comparing codons of CDR and FW of the germ-line V regions both to each other and to control regions. We found that in both germ-line heavy chains and lambda chains, CDR codons are prone to replacement mutations, whereas in the FW, the opposite is true. Furthermore, the difference between CDR and FW in heavy chains and lambda chains is based on codons that are prone to nonconservative changes of amino acid. In contrast, in germ-line kappa chains, the codons in both CDR and FW are more prone to replacement mutations. We also demonstrated that negative selection during immune responses is more sensitive to nonconservative amino acid substitutions than overall amino acid change, demonstrating the applicability of our analysis to real-time process of selection in the immune system. The differences in germ-line kappa and lambda light chains' potential reaction to mutation suggests that via these two differently evolved light-chain types, the B cell repertoire encompasses two different strategies to balance diversity and stability in an immune response.

Amino Acids↗
PubMed2004

Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution.

To study the evolutionary effects of polyploidy on plant gene functions, we analyzed functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in Arabidopsis thaliana. Genes retained in duplicate are not distributed evenly among Gene Ontology or Munich Information Center for Protein Sequences functional categories, which indicates a nonrandom process of gene loss. Genes involved in signal transduction and transcription have been preferentially retained, and those involved in DNA repair have been preferentially lost. Although the two members of each gene pair must originally have had identical transcription profiles, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. We identified several cases where groups of duplicated gene pairs have diverged in concert, forming two parallel networks, each containing one member of each gene pair. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. We also find that the rate of protein sequence evolution has been significantly asymmetric in >20% of duplicate pairs. Together, these results suggest that functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids.

Arabidopsis↗
PubMed1999

Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus.

Predatory snails in the marine gastropod genus Conus stun prey by injecting a complex mixture of peptide neurotoxins. These conotoxins are associated with trophic diversification and block a diverse array of ion channels and neuronal receptors in prey species, but the evolutionary genesis of this functional diversity is unknown. Here we show that conotoxins with little amino acid similarity are in fact products of recently diverged loci that are rapidly evolving by strong positive selection in the vermivorous cone, Conus abbreviatus, and that the rate of conotoxin evolution is higher than that of most other known proteins. Gene duplication and diversifying selection result in the formation of functionally variable conotoxins that are linked to ecological diversification and evolutionary success of this genus.

Amino Acid Sequence↗
PubMed1999

Rapid evolution of the ribonuclease A superfamily: adaptive expansion of independent gene clusters in rats and mice.

The two eosinophil ribonucleases, eosinophil-derived neurotoxin (EDN/RNase 2) and eosinophil cationic protein (ECP/RNase 3), are among the most rapidly evolving coding sequences known among primates. The eight mouse genes identified as orthologs of EDN and ECP form a highly divergent, species-limited cluster. We present here the rat ribonuclease cluster, a group of eight distinct ribonuclease A superfamily genes that are more closely related to one another than they are to their murine counterparts. The existence of independent gene clusters suggests that numerous duplications and diversification events have occurred at these loci recently, sometime after the divergence of these two rodent species ( approximately 10-15 million years ago). Nonsynonymous substitutions per site (d(N)) calculated for the 64 mouse/rat gene pairs indicate that these ribonucleases are incorporating nonsilent mutations at accelerated rates, and comparisons of nonsynonymous to synonymous substitution (d(N) / d(S)) suggest that diversity in the mouse ribonuclease cluster is promoted by positive (Darwinian) selection. Although the pressures promoting similar but clearly independent styles of rapid diversification among these primate and rodent genes remain uncertain, our recent findings regarding the function of human EDN suggest a role for these ribonucleases in antiviral host defense.

Amino Acid Motifs↗
PubMed1993

Numerical experiments with model monophyletic and paraphyletic taxa.

The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere "taxonomic noise" in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.

Algorithms↗
PubMed1995

The genetic diversification of the HIV type 1 gag p17 gene in patients infected from a common source.

An evolutionary analysis was undertaken of HIV-1 gag p17 sequences taken from a small cohort of hemophilia B patients infected from a common batch of clotting factor concentrate. The sequence population found at seroconversion was highly homogeneous, suggesting that the infecting batch also contained little sequence variation. Genetic diversification was found in follow-up sequences taken approximately 3 years later and was generally found to be complex. Greater rates of synonymous to nonsynonymous substitution were observed, especially when comparing distantly related isolates, and the rate of synonymous substitution was used to estimate times of divergence for a number of isolates of HIV-1 including the origin of the subtypes A to H. The p17 region is therefore proposed as a useful marker for future epidemiological studies.

Amino Acid Sequence↗
PubMedDate not supplied

Selection, recombination and history in a parasitic flatworm (Echinococcus) inferred from nucleotide sequences.

Three species of flatworms from the genus Echinococcus (E. granulosus, E. multilocularis and E. vogeli) and four strains of E. granulosus (cattle, horse, pig and sheep strains) were analysed by the PCR-SSCP method followed by sequencing, using as targets two non-coding and two coding (one nuclear and one mitochondrial) genomic regions. The sequencing data was used to evaluate hypothesis about the parasite breeding system and the causes of genetic diversification. The calculated recombination parameters suggested that cross-fertilisation was rare in the history of the group. However, the relative rates of substitution in the coding sequences showed that positive selection (instead of purifying selection) drove the evolution of an elastase and neutrophil chemotaxis inhibitor gene (AgB/1). The phylogenetic analyses revealed several ambiguities, indicating that the taxonomic status of the E. granulosus horse strain should be revised.

Animals↗
PubMed2003

Genomic diversification among archival strains of Salmonella enterica serovar typhimurium LT7.

To document genomic changes during long periods of storage, we analyzed Salmonella enterica serovar Typhimurium LT7, a mutator strain that was previously reported to have higher rates of mutations compared to other serovar Typhimurium strains such as LT2. Upon plating directly from sealed agar stabs that had been stocked at room temperature for up to four decades, many auxotrophic mutants derived from LT7 gave rise to colonies of different sizes. Restreaking from single colonies consistently yielded colonies of diverse sizes even when we repeated single-colony isolation nine times. Colonies from the first plating had diverse genomic changes among and even within individual vials, including translocations, inversions, duplications, and point mutations, which were detected by rare-cutting endonuclease analysis with pulsed-field gel electrophoresis. Interestingly, even though the colony size kept diversifying, all descendents of the same single colonies from the first plating had the same sets of detected genomic changes. We did not detect any colony size or genome structure diversification in serovar Typhimurium LT7 stocked at -70 degrees C or in serovar Typhimurium LT2 stocked either at -70 degrees C or at room temperature. These results suggest that, although colony size diversification occurred during rapid growth, all detected genomic changes took place during the storage at room temperature and were carried over to their descendents without further changes during rapid growth in rich medium. We constructed a genomic cleavage map on the LT7 strain that had been stocked at -70 degrees C and located all of the detected genomic changes on the map. We speculated on the significance of mutators for survival and evolution under environmentally stressed conditions.

Biological Specimen Banks↗
PubMed1999

Molecular phylogeny and evolution of Sorex shrews (Soricidae: insectivora) inferred from mitochondrial DNA sequence data.

Shrews of the genus Sorex are characterized by a Holarctic distribution, and relationships among extant taxa have never been fully resolved. Phylogenies have been proposed based on morphological, karyological, and biochemical comparisons, but these analyses often produced controversial and contradictory results. Phylogenetic analyses of partial mitochondrial cytochrome b gene sequences (1011 bp) were used to examine the relationships among 27 Sorex species. The molecular data suggest that Sorex comprises two major monophyletic lineages, one restricted mostly to the New World and one with a primarily Palearctic distribution. Furthermore, several sister-species relationships are revealed by the analysis. Based on the split between the Soricinae and Crocidurinae subfamilies, we used a 95% confidence interval for both the calibration of a molecular clock and the subsequent calculation of major diversification events within the genus Sorex. Our analysis does not support an unambiguous acceleration of the molecular clock in shrews, the estimated rate being similar to other estimates of mammalian mitochondrial clocks. In addition, the data presented here indicate that estimates from the fossil record greatly underestimate divergence dates among Sorex taxa.

Animals↗
PubMed1999

A translocated mitochondrial cytochrome b pseudogene in voles (Rodentia: Microtus)

A full-length cytochrome b pseudogene was found in rodents; it has apparently been translocated from a mitochondrion to the nuclear genome in the subfamily Arvicolinae. The pseudogene (psi cytb) differed from its mitochondrial counterpart at 201 of 1143 sites (17.6%) and by four indels. Cumulative evidence suggests that the pseudogene has been translocated to the nucleus. Phylogenetic reconstruction indicates that the pseudogene arose before the diversification of M. arvalis/M. rossiaemeridionalis from M. oeconomus, but after the divergence of the peromyscine/sigmodontine/ arvicoline clades some approximately 10 MYA. Published rates of divergence between mitochondrial genes and their nuclear pseudogenes suggest that the translocation of this mitochondrial gene to the nuclear genome occurred some 6 MYA, in agreement with the phylogenetic evidence.

Animals↗
PubMed1999

Mechanisms of dominance: coexistence of picocyanobacterial genotypes in a freshwater ecosystem

The autotrophic picoplankton of the pelagic zone of the mesotrophic Lake Constance is dominated by phycoerythrin-rich unicellular cyanobacteria phylogenetically related to the marine Synechococcus and Prochlorococcus cluster. In Lake Constance, the abundance of picocyanobacteria shows a recurrent pattern of seasonal variations. Evidence of diverse subpopulations was obtained by electron-microscopic examination of natural water samples and isolated strains that unveiled different surface structures of picocyanobacteria. Further evidence was obtained by DNA analysis of 26 clonal isolates representing 12 different genotypes. Variations in light and nutrient supply revealed distinct abilities of the genetically different strains to cope with these stress situations. Furthermore, cultured heterotrophic nanoflagellates exhibited differential feeding preferences for certain Synechococcus strains. The findings imply that growth and loss rates of the natural cyanobacterial community may be influenced by its genetic composition. Phylogenetic analyses of isolated strains indicated that the physiological diversification of pelagic Synechococcus spp. has occurred during a recent adaptive radiation. An example for genetic mechanisms underlying physiological diversification is indicated by mobile DNA elements found in a Synechocystis strain also isolated from the pelagic zone of Lake Constance. The observations suggest that dominance of Synechococcus spp. was achieved by evolutionary adaptation and coexistence of numerous genotypes generating a physiologically highly diversified population.

Journal Article↗
PubMed1989

The evolution of ecological tolerance in prokaryotes.

The ecological ranges of Archaeobacteria and Eubacteria are constrained by a requirement for liquid water and the physico-chemical stability limits of biomolecules, but within this broad envelope, prokaryotes have evolved adaptations that permit them to tolerate a remarkable spectrum of habitats. Laboratory experiments indicate that prokaryotes can adapt rapidly to novel environmental conditions, yet geological studies suggest early diversification and long-term stasis within the prokaryotic kingdoms. These apparently contradictory perspectives can be reconciled by understanding that, in general, rates and patterns of prokaryotic evolution reflect the developmental history of the Earth's surface environments. Our understanding of modern microbial ecology provides a lens through which our accumulating knowledge of physiology, molecular phylogeny and the Earth's history can be integrated and focussed on the phenomenon of prokaryotic evolution.

Adaptation, Biological↗
PubMed2006

Evolutionary patterns in early tetrapods. II. Differing constraints on available character space among clades.

Radiations of large clades often accompany rapid morphological diversification. Evolutionary biologists debate the impact of external restrictions imposed by ecology, and intrinsic constraints imposed by development and genetics, on the rate at which morphological innovations are gained. These issues are particularly interesting for groups such as tetrapods, which evolved novel body plans relative to their piscine ancestors and which also invaded new ecosystems following terrestrialization. Prior studies have addressed these issues by looking at either ranges of morphological variation or rates of character change. Here, we address a related but distinct issue: the numbers of characters that freely vary within a clade. We modify techniques similar to those used by ecologists to infer species richnesses to estimate the number of potentially varying characters given the distributions of changes implied by a model phylogeny. Our results suggest both increasing constraints/restrictions and episodes of 'character release' (i.e. increasing the number of potentially varying characters). In particular, we show that stem lissamphibians had a restricted character space relative to that of stem amniotes, and that stem amniotes both had restrictions on some parts of character space but also invaded new character space that had been unavailable to stem tetrapods.

Amphibians↗
PubMed2005

A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites.

A recent molecular timescale for major lineages of the Galliformes indicated that Megapodiidae and possibly Cracidae, originated in the Cretaceous, while the remaining families originated in the Tertiary. This timescale was based on clock-like evolution in genetic and taxonomic partitions of mitochondrial ND2 and cyt b DNA sequences, and assumed that ordinal diversification of Galloanserae around 90 million years ago and imposed, whenever appropriate, minimum age constraints based on the fossil record. This approach is not ideal, as it did not account for uncertainty in estimating branch lengths and time, including the calibration time, and heterogeneity in the rate of DNA substitution among sites and in different lineages. Furthermore all the information available in the DNA sequences was not included, and may have been affected by stochastic error in individual gene partitions. Here, we present a follow-up analysis by estimating divergence times using a Bayesian framework that accounts for these possible sources of uncertainty. Our results based on combined and separate analyses of mitochondrial DNA sequences comprised of 1756 sites of 12S rDNA, ND2 and cyt b indicated that (1) Megapodiidae and Cracidae, and likely Odontophoridae, originated in the Cretaceous; (2) estimates based on concatenated genes are less affected by stochastic error among sites and less influenced by the phylogenetic signals of individual gene partitions, which are unequally distributed along the phylogenetic tree; and (3) the use of only an external molecular calibration results in lower estimation of most ingroup node ages. We also point out that galliform fossils may not be as useful for point calibrations as was previously suggested, but instead may be better employed as priors for the estimation of node ages under a Bayesian approach.

Animals↗
PubMed2004

Origin and diversification of the endemic Hawaiian tree snails (Achatinellidae: Achatinellinae) based on molecular evidence.

Tree snails of the endemic subfamily Achatinellinae comprise a diverse and important component of the Hawaiian fauna. In recent decades anthropogenic impacts have resulted in devastating extinction rates in Hawaiian tree snails. To address long-standing biogeographic, systematic, and evolutionary questions we used cytochrome c oxidase subunit I (COI) gene sequences to reconstruct the phylogeny of 23 extant species spanning the range of the subfamily from five Hawaiian Islands. To investigate family-level relationships, data were analyzed from 11 terrestrial pulmonate families. Although nodal support for monophyly of the endemic Pacific family Achatinellidae and endemic Hawaiian subfamily Achatinellinae was strong, bifurcation order among deeper ingroup nodes was not well-supported by bootstrap resampling. We hypothesize that lineage extinction and rapidity of lineage formation may have rendered evolutionary reconstruction difficult using a standard phylogenetic approach. Use of an optimized evolutionary model, however, improved resolution and recovered three main clades. The diversification pattern inferred contradicts the traditional biogeographic hypothesis of a Maui origin of the achatinelline lineage. Taxa comprising the basal ingroup clade (Achatinella spp.) and seeding lineages for subsequent clades originated on O'ahu. Therefore it appears that the ancestral colonizing species of achatinellines arrived first on O'ahu from an unknown source, and that O'ahu is the Hawaiian origin of the subfamily. Species previously defined by morphological criteria were generally found to be phylogenetically distinct, and the overall colonization pattern follows the island-age progression rule with several instances of generic polyphyly and back-colonization.

Animals↗
PubMed2005

Chromosomal phylogeny of Robertsonian races of the house mouse on the island of Madeira: testing between alternative mutational processes.

The ancestral karyotype of the house mouse (Mus musculus) consists of 40 acrocentric chromosomes, but numerous races exist within the domesticus subspecies characterized by different metacentric chromosomes formed by the joining at the centromere of two acrocentrics. An exemplary case is present on the island of Madeira where six highly divergent chromosomal races have accumulated different combinations of 20 metacentrics in 500-1000 years. Chromosomal cladistic phylogenies were performed to test the relative performance of Robertsonian (Rb) fusions, Rb fissions and whole-arm reciprocal translocations (WARTs) in resolving relationships between the chromosomal races. The different trees yielded roughly similar topologies, but varied in the number of steps and branch support. The analyses using Rb fusions/fissions as characters resulted in poorly supported trees requiring six to eight homoplasious events. Allowance for WARTs considerably increased nodal support and yielded the most parsimonious trees since homoplasy was reduced to a single event. The WART-based trees required five to nine WARTs and 12 to 16 Rb fusions. These analyses provide support for the role of WARTs in generating the extensive chromosomal diversification observed in house mice. The repeated occurrence of Rb fusions and WARTs highlights the contribution of centromere-related rearrangements to accelerated rates of chromosomal change in the house mouse.

Animals↗
PubMed2000

Correlations in fossil extinction and origination rates through geological time.

Recent analyses have suggested that extinction and origination rates exhibit long-range correlations, implying that the fossil record may be controlled by self-organized criticality or other scale-free internal dynamics of the biosphere. Here we directly test for correlations in the fossil record by calculating the autocorrelation of extinction [corrected] and origination rates through time. Our results show that extinction rates are uncorrelated beyond the average duration of a stratigraphic interval. Thus, they lack the long-range correlations predicted by the self-organized criticality hypothesis. In contrast, origination rates show strong autocorrelations due to long-term trends. After detrending, origination rates generally show weak positive correlations at lags of 5-10 million years (Myr) and weak negative correlations at lags of 10-30 Myr, consistent with aperiodic oscillations around their long-term trends. We hypothesize that origination rates are more correlated than extinction rates because originations of new taxa create new ecological niches and new evolutionary pathways for reaching them, thus creating conditions that favour further diversification.

Animals↗
PubMed1989

Stepwise progression of B cell malignancy occurred in a bone marrow stromal cell-dependent pre-B cell clone.

The murine long-term bone marrow culture system which can support the almost infinite growth of normal B lineage cells was used to establish the experimental model for spontaneous B cell leukemogenesis. At the early phase of the culture, B cell differentiation with diversification of immunoglobulin genes was induced. However, the culture was finally captured by a single B cell clone which had the fastest growth rate. The B cell clone was strictly dependent on stromal cells for in vitro growth and did not generate leukemia when injected into syngenic mice. After up to a year of maintenance of the clone, the leukemic cells developed spontaneously. The leukemic cell line isolated in vivo retained the stromal cell-dependency, and further in vitro selection process was required to establish the stromal cell-independent leukemic cell line. These leukemic cell lines highly expressed c-myc and Ha-ras genes regardless of stromal cell-dependency. We detected no chromosomal aberrations accompanied with the process of leukemic transformation. Our results suggest that spontaneous neoplastic transformation of B cells in long-term bone marrow culture occurs in a stepwise manner.

Animals↗