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PubMed2004

Diversification of Ig superfamily genes in an invertebrate.

The freshwater snail Biomphalaria glabrata possesses a diverse family of fibrinogen-related proteins (FREPs), hemolymph polypeptides that consist of one or two amino-terminal immunoglobulin superfamily (IgSF) domains and a carboxyl-terminal fibrinogen domain. Here, we show that the IgSF1 domain of the FREP3 subfamily is diversified at the genomic level at higher rates than those recorded for control genes. All sequence variants are derived from a small set of nine source sequences by point mutation and recombinatorial processes. Diverse FREP3 transcripts are also produced. We hypothesize a mechanism present in snails that is capable of diversifying molecules involved in internal defense.

Alleles↗
PubMed1981

The HLA loci of th Hopi and Navajo.

The purpose of this paper is to present the genetic distribution at the HLA-A, B, C, and DR loci in the Hopi and the Navajo. A sample of 100 out-patients from each tribe was selected at the Public Health Service Indian Hospital in Keam's Canyon, Arizona, and was typed for the antigens at the four loci. The distributions of the alleles and the haplotypes are similar in each tribe. A distance measure, f, confirms the genetic similarity of the two populations. It is concluded that the great cultural diversity of the Hopi and the Navajo is the result of a cultural evolution and diversification that has greatly outstripped the genetic evolution at the major histocompatibility loci over the past 20,000 years.

Arizona↗
PubMed2000

The diversity of parasites.

Parasitism is one of the most successful modes of life displayed by living organisms, as measured by how often it evolved and how many parasitic species are presently in existence. Studying the diversity of parasites is particularly relevant because sympatric diversification may be important in some parasite taxa, and because of the opportunity for independent tests of evolutionary hypotheses in the many separate lineages in which parasitism evolved. Our incomplete knowledge of existing parasite species--the result of a range of phenomena that includes inadequate sampling effort or the lumping of different cryptic species under one name--is not always a major obstacle for the study of parasite diversity. Patterns in the diversity of parasites may be associated with either host or parasite characteristics. The distribution of parasite diversity among host taxa does not simply reflect the species diversity of the host taxa themselves; life history and ecological traits of hosts appear to play important roles. These may determine the likelihood that hosts are colonized by parasite species over evolutionary time. It is not yet clear whether some host traits also favor intrahost speciation and diversification of parasites, and the formation of new parasite species. Certain features of parasites may also be associated with speciation and diversification. Only parasite body size has received much attention; the patterns observed are not greatly different from those of free-living species, with small-bodied parasite taxa being more speciose than related large-bodied taxa. Epidemiological parameters such as the basic reproductive rate of parasites, or R0, can also generate predictions regarding the distribution or evolution of parasite diversity. For instance, parasite taxa characterized by high R0 values may be more speciose than related taxa with lower values of R0; such predictions remain untested. Large-scale biogeographical patterns of diversity have only been well studied for metazoan parasites of marine fish; for these parasites, latitudinal patterns can be explained by effects of temperature on speciation rates and epidemiological variables, though other causes are possible. The emphasis for future research must shift from pattern description to the elucidation of the processes responsible for the structure and diversity of parasite faunas. A better integration of ecological and historical (or phylogenetic) approaches to the study of parasite diversity should make this objective possible.

Animals↗
PubMed1991

Shared epitopes among HLA class II alleles: gene conversion, common ancestry and balancing selection.

The extent and pattern of HLA class II sequence polymorphism raise a variety of evolutionary questions, notably those concerning the genetic mechanisms for generating diversity, the rate of change and the nature of the selection pressure maintaining this variation. Phylogenetic analysis of primate MHC class II sequences suggests that the allelic lineages are ancient, having diverged long before separation of the hominoid species. For the beta-chain loci, however, considerable allelic diversification within these lineages has occurred after speciation. The striking patchwork pattern of polymorphism with different alleles containing common sequence motifs can be accounted for by common ancestry, by gene conversion or by convergent evolution, depending on the location of the shared epitope.

Alleles↗
PubMed2004

A phylogenetic approach to cultural evolution.

There has been a rapid increase in the use of phylogenetic methods to study the evolution of languages and culture. Languages fit a tree model of evolution well, at least in their basic vocabulary, challenging the view that blending, or admixture among neighbouring groups, was predominant in cultural history. Here, we argue that we can use language trees to test hypotheses about not only cultural history and diversification, but also bio-cultural adaptation. Phylogenetic comparative methods take account of the non-independence of cultures (Galton's problem), which can cause spurious statistical associations in comparative analyses. Advances in phylogenetic methods offer new possibilities for the analysis of cultural evolution, including estimating the rate of evolution and the direction of coevolutionary change of traits on the tree. They also enable phylogenetic uncertainty to be incorporated into the analyses, so that one does not have to treat phylogenetic trees as if they were known without error.

Journal Article↗
PubMed1997

Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor.

From a database containing the published nuclear hormone receptor (NR) sequences I constructed an alignment of the C, D and E domains of these molecules. Using this alignment, I have performed tree reconstruction using both distance matrix and parsimony analysis. The robustness of each branch was estimated using bootstrap resampling methods. The trees constructed by these two methods gave congruent topologies. From these analyses I defined six NR subfamilies: (i) a large one clustering thyroid hormone receptors (TRs), retinoic acid receptors (RARs), peroxisome proliferator-activated receptors (PPARs), vitamin D receptors (VDRs) and ecdysone receptors (EcRs) as well as numerous orphan receptors such as RORs or Rev-erbs; (ii) one containing retinoid X receptors (RXRs) together with COUP, HNF4, tailless, TR2 and TR4 orphan receptors; (iii) one containing steroid receptors; (iv) one containing the NGFIB orphan receptors; (v) one containing FTZ-F1 orphan receptors; and finally (vi) one containing to date only one gene, the GCNF1 orphan receptor. The relationships between the six subfamilies are not known except for subfamilies I and IV which appear to be related. Interestingly, most of the liganded receptors appear to be derived when compared with orphan receptors. This suggests that the ligand-binding ability of NRs has been gained by orphan receptors during the course of evolution to give rise to the presently known receptors. The distribution into six subfamilies correlates with the known abilities of the various NRs to bind to DNA as homo- or heterodimers. For example, receptors heterodimerizing efficiently with RXR belong to the first or the fourth subfamilies. I suggest that the ability to heterodimerize evolved once, just before the separation of subfamilies I and IV and that the first NR was able to bind to DNA as a homodimer. From the study of NR sequences existing in vertebrates, arthropods and nematodes, I define two major steps of NR diversification: one that took place very early, probably during the multicellularization event leading to all the metazoan phyla, and a second occurring later on, corresponding to the advent of vertebrates. Finally, I show that in vertebrate species the various groups of NRs accumulated mutations at very different rates.

Animals↗
PubMed1990

Bursectomy of chicken embryos at 60 hours of incubation leads to an oligoclonal B cell compartment and restricted Ig diversity.

Chickens that have been surgically bursectomized at 60 h of embryonic development usually generate Ig producing B cells; however, the bursectomized chickens are incapable of specific antibody responses, even after repeated immunization. In the present work, we analyzed the molecular basis of this immunodeficiency. In the bursectomized chickens, DNA sequencing revealed a repertoire of Ig L and H chains with a low number of different V-J and V-D-J joints, indicating an oligoclonal B cell compartment. In addition, the L and H chains belonging to each B cell clone had similar gene conversion events in the V region. In situ hybridization to Harderian gland tissue sections showed, that B cells of the bursectomized chickens were, however, capable of terminal plasma cell maturation. Thus, in chickens that were lacking the bursal microenvironment, 1) only a few B cell precursors differentiated into mature Ig-producing B cells, 2) low rate of gene conversion resulted in restricted Ig diversity. Regarding the chicken B cell differentiation, the present data support a model that the induction of B cell differentiation is a bursa-independent event, whereas the bursa of Fabricius has a crucial role in the amplification and diversification of the embryonic B cell repertoire.

Amino Acid Sequence↗
PubMed2006

Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage.

Phosphonatase functions in the 2-aminoethylphosphonate (AEP) degradation pathway of bacteria, catalyzing the hydrolysis of the C-P bond in phosphonoacetaldehyde (Pald) via formation of a bi-covalent Lys53ethylenamine/Asp12 aspartylphosphate intermediate. Because phosphonatase is a member of the haloacid dehalogenase superfamily, a family predominantly comprised of phosphatases, the question arises as to how this new catalytic activity evolved. The source of general acid-base catalysis for Schiff-base formation and aspartylphosphate hydrolysis was probed using pH-rate profile analysis of active-site mutants and X-ray crystallographic analysis of modified forms of the enzyme. The 2.9 A X-ray crystal structure of the mutant Lys53Arg complexed with Mg2+ and phosphate shows that the equilibrium between the open and the closed conformation is disrupted, favoring the open conformation. Thus, proton dissociation from the cap domain Lys53 is required for cap domain-core domain closure. The likely recipient of the Lys53 proton is a water-His56 pair that serves to relay the proton to the carbonyl oxygen of the phosphonoacetaldehyde (Pald) substrate upon addition of the Lys53. The pH-rate profile analysis of active-site mutants was carried out to test this proposal. The proximal core domain residues Cys22 and Tyr128 were ruled out, and the role of cap domain His56 was supported by the results. The X-ray crystallographic structure of wild-type phosphonatase reduced with NaBH4 in the presence of Pald was determined at 2.4A resolution to reveal N epsilon-ethyl-Lys53 juxtaposed with a sulfate ligand bound in the phosphate site. The position of the C2 of the N-ethyl group in this structure is consistent with the hypothesis that the cap domain N epsilon-ethylenamine-Lys53 functions as a general base in the hydrolysis of the aspartylphosphate bi-covalent enzyme intermediate. Because the enzyme residues proposed to play a key role in P-C bond cleavage are localized on the cap domain, this domain appears to have evolved to support the diversification of the HAD phosphatase core domain for catalysis of hydrolytic P-C bond cleavage.

Aspartic Acid↗
PubMed2004

Phenological resonance and quantum life history.

The principle of 'quantum life history' is proposed here as a complementary viewpoint to current modeling of body size and life history evolution which usually considers a 'fast-slow continuum' of covarying life history traits. This principle emphasizes the discrete (and primary) nature of development time caused by the effect of phenological resonance (the compliance of development time with periodicities of earth rotation). The body mass, in turn, complies with development time, which generates body mass attractors. This principle is illustrated with mammals as exemplary group. The adaptive radiation of Cenozoic mammals is supposed to proceed as a competition-driven diversification of body sizes and development times around the strongest (year-long) resonant mode of development time corresponding to body mass of about 1 kg. Mammals with this body mass are shown here to have a largest genome size and a lowest (body mass-corrected) basal metabolic rate. This extends the previously reported negative relation between genome size and metabolic rate to the realm of nonlinearity, and suggests that selection against the accumulation of non-coding DNA in the genome is relaxed in mammals with this body mass.

Animals↗
PubMed2006

Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication.

It is widely accepted that gene duplication is a primary source of genetic novelty. However, the evolutionary fate of duplicated genes remains largely unresolved. The classical Ohno's Duplication-Retention-Non/Neofunctionalization theory, and the recently proposed alternatives such as subfunctionalization or duplication-degeneration-complementation, and subneofunctionalization, each can explain one or more aspects of gene fate after duplication. Duplicated genes are also affected by epigenetic changes. We constructed a phylogenetic tree using Dof (DNA binding with one finger) protein sequences from poplar (Populus trichocarpa) Torr. & Gray ex Brayshaw, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa). From the phylogenetic tree, we identified 27 pairs of paralogous Dof genes in the terminal nodes. Analysis of protein motif structure of the Dof paralogs and their ancestors revealed six different gene fates after gene duplication. Differential protein methylation was revealed between a pair of duplicated poplar Dof genes, which have identical motif structure and similar expression pattern, indicating that epigenetics is involved in evolution. Analysis of reverse transcription-PCR, massively parallel signature sequencing, and microarray data revealed that the paralogs differ in expression pattern. Furthermore, analysis of nonsynonymous and synonymous substitution rates indicated that divergence of the duplicated genes was driven by positive selection. About one-half of the motifs in Dof proteins were shared by non-Dof proteins in the three plants species, indicating that motif co-option may be one of the forces driving gene diversification. We provided evidence that the Ohno's Duplication-Retention-Non/Neofunctionalization, subfunctionalization/duplication-degeneration-complementation, and subneofunctionalization hypotheses are complementary with, not alternative to, each other.

Amino Acid Sequence↗
PubMed1997

[The effect of system restructuring on absenteeism due to sickness in the work place. I. Sickness absenteeism during the period 19989-1994].

The current transformation of property relations and economic restructuring, along with many other factors, influence the health condition of workers. The objective of the study was to illustrate the size of the problem and to identify the major causes of work disability among persons employed in enterprises undergoing those processes during the years 1989-94 against the situation observed in the whole country during the same period. The study was carried out in one of the largest industrial plants undergoing the process of economic restructuring. The group investigated was composed of 8,588 workers (including 62.6% of males). In individual years the number of workers in this group was decreasing, and in 1994 the employment status in the group accounted for 37% in relation to the number of workers employed during the first year under observation. The analysis of work disability was based on the rate of sickness absenteeism calculated as a relationship between the number of days of work disability and the number of working days during that particular period. Due to the application of this method it was feasible to consider both workers employed and persons who left the plant, regardless of their employment duration during a year. The study showed a 20 per cent increase in sickness absenteeism during the period of 1989-94. The highest rate (8.60) was noted in 1994. It was higher by 16% in comparison to the rate for the whole country. The greatest difference between these rates was observed in 1990 (the rate in the group investigated was higher by 46%). As to the causes of work disability, the main differences concerned two categories of illnesses, diseases of the circulatory system, a major cause of sickness absenteeism in the group studied (21%), and diseases of the musculoskeletal system, a major cause of sickness absenteeism in Poland. The change in the relationship between sickness absenteeism and the age during the period of the plant restructuring resulted from the fact that a large number of workers left the job. It was observed that the rate of the sickness absenteeism was almost directly proportional to the percentage of persons leaving the plant in individual years. The study showed that changes in the size and the structure of employment resulting from the plant restructuring influence the level of sickness absenteeism, and the age-related diversification in causes of diseases, and in consequence alter the established regularities.

Absenteeism↗
PubMed2003

Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa.

Multicellular animals, or Metazoa, appear in the fossil records between 575 and 509 million years ago (MYA). At odds with paleontological evidence, molecular estimates of basal metazoan divergences have been consistently older than 700 MYA. However, those date estimates were based on the molecular clock hypothesis, which is almost always violated. To relax this hypothesis, we have implemented a Bayesian approach to describe the change of evolutionary rate over time. Analysis of 22 genes from the nuclear and the mitochondrial genomes under the molecular clock assumption produced old date estimates, similar to those from previous studies. However, by allowing rates to vary in time and by taking small species-sampling fractions into account, we obtained much younger estimates, broadly consistent with the fossil records. In particular, the date of protostome-deuterostome divergence was on average 582 +/- 112 MYA. These results were found to be robust to specification of the model of rate change. The clock assumption thus had a dramatic effect on date estimation. However, our results appeared sensitive to the prior model of cladogenesis, although the oldest estimates (791 +/- 246 MYA) were obtained under a suboptimal model. Bayes posterior estimates of evolutionary rates indicated at least one major burst of molecular evolution at the end of the Precambrian when protostomes and deuterostomes diverged. We stress the importance of assumptions about rates on date estimation and suggest that the large discrepancies between the molecular and fossil dates of metazoan divergences might partly be due to biases in molecular date estimation.

Algorithms↗
PubMed1993

Genetic diversity and phylogenetic relationships between birches and alders using ITS, 18S rRNA and rbcL gene sequences.

The Betuleae is one of the two Betulaceae tribes and contains two genera, the actinorhizal genus Alnus and the nonactinorhizal genus Betula. To elucidate the phylogenetic relationships within the tribe and compare the relative amounts of genetic diversity between the genera Alnus and Betula, rbcL and 18S rRNA gene sequences as well as rDNA internal transcribed spacer (ITS1 and ITS2) sequences were obtained and compared. In rbcL and 18S rRNA, several substitutions were detected between Alnus and Betula but no variation was observed within Alnus. Minimal length variation was observed among ITS sequences. The numbers of substitutions per site for ITS were, on average, close to 10 times those estimated for 18S between Alnus and Betula. In ITS, numbers of substitutions were, on average, more than twice as large between genera than within genera. Phylogenies from ITS sequences were estimated using neighbor-joining analysis of substitution rates, maximum likelihood and parsimony methods. Each of the two genera appeared monophyletic, which was supported by high bootstrap estimates. Relationships among the three sections of Betula analyzed were also better resolved than those among the three subgenera of Alnus analyzed. Phylogenies estimated from ITS sequences suggested a relatively recent diversification of each genus, in agreement with fossil data.

DNA, Ribosomal↗
PubMed2004

Enhanced macrocyclizing activity of the thioesterase from tyrocidine synthetase in presence of nonionic detergent.

Macrocyclization carried out by thioesterase domains of multimodular nonribosomal peptide synthetases (NRPSs) is a key step in the biosynthesis of many biologically active peptides. The thioesterase excised from tyrocidine synthetase is a versatile macrocyclization catalyst and a useful tool for chemoenzymatic synthesis of diverse cyclic peptides. However, its utility is limited by its short lifetime of catalytic activity as well as significant flux of the acyl-enzyme intermediate to hydrolysis. The addition of Brij 58, a nonionic detergent, above the critical micelle concentration, has dramatic effects on enzyme activity: catalytic activity is extended to >60 min and the rate of cyclization (but not hydrolysis) increases 6-fold, resulting in a net 150- to 300-fold increase in cyclic product yields. This enhanced activity allowed enzymatic macrocyclization of a solid phase library of tyrocidine decapeptides to identify acceptable substitutions at the Orn9 position which had previously been inaccessible for diversification.

Amino Acid Substitution↗
PubMed2005

Molecular phylogeny and evidence for an adaptive radiation of geophagine cichlids from South America (Perciformes: Labroidei).

Nucleotide sequences from the mitochondrial ND4 gene and the nuclear RAG2 gene were used to derive the most extensive molecular phylogeny to date for the Neotropical cichlid subfamily Geophaginae. Previous hypotheses of relationships were tested in light of these new data and a synthesis of all existing molecular information was provided. Novel phylogenetic findings included support for : (1) a 'Big Clade' containing the genera Geophagus sensu lato, Gymnogeophagus, Mikrogeophagus, Biotodoma, Crenicara, and Dicrossus; (2) a clade including the genera Satanoperca, Apistogramma, Apistogrammoides, and Taeniacara; and (3) corroboration for Kullander's clade Acarichthyini. ND4 demonstrated saturation effects at the third code position and lineage-specific rate heterogeneity, both of which influenced phylogeny reconstruction when only equal weighted parsimony was employed. Both branch lengths and internal branch tests revealed extremely short basal nodes that add support to the idea that geophagine cichlids have experienced an adaptive radiation sensu Schluter that involved ecomorphological specializations and life history diversification.

Animals↗
PubMed2004

Factors affecting the decision to exit dairy farming: a two-stage regression analysis.

Substantial attention has focused on the dairy industry because of a concern that many producers are getting out of dairying. Although low milk prices are postulated as a primary reason for exits from dairying, other factors may be important as well. Data from a representative 64-farm subset of a 2002 survey of dairy producers in Maine were used in the current study. Of the 64 farms, 15 indicated an imminent exit from dairying, whereas 49 dairy farms expected to remain in business for > or =5 yr. A binary choice logit regression model, based upon the dependent variable decision to exit or remain in the industry, was used as part of a 2-stage regression process to ascertain why dairy producers are choosing to leave the industry. The hypothesis states that the decision is a function of 3 independent variable categories: demographic, efficiency, and opportunity costs. Four variables were revealed that significantly influence the exit decision. Older producers, higher off-farm income, lower returns over variable cost, and greater diversification of farm income were more likely associated with a decision to leave dairy farming. Because factors other than milk price are involved in exit decisions, perhaps national or regional dairy programs should consider strategies beyond price supports to provide for a stable dairy industry and a reduction in the rate of dairy farm exits.

Animals↗
PubMed2006

Evolution of rattlesnakes (Viperidae; Crotalus) in the warm deserts of western North America shaped by Neogene vicariance and Quaternary climate change.

During Pleistocene, the Laurentide ice sheet rearranged and diversified biotic distributions in eastern North America, yet had minimal physical impact in western North America where lineage diversification is instead hypothesized to result from climatic changes. If Pleistocene climatic fluctuations impacted desert species, the latter would reflect patterns of restricted gene flow concomitant with indications of demographic bottlenecks. Accordingly, molecular evidence for refugia should be present within these distributions and for subsequent range expansions as conditions improved. We sought answers to these questions by evaluating mitochondrial DNA (mtDNA) sequences from four species of rattlesnakes [Crotalus mitchellii (speckled rattlesnake), Crotalus cerastes (sidewinder), Crotalus tigris (tiger rattlesnake), Crotalus ruber (red diamond rattlesnake)] with distributions restricted to desert regions of southwestern North America. We inferred relationships using parsimony and maximum likelihood, tested intraspecific clades for population expansions, applied an isolation-with-migration model to determine bi-directional migration rates (m) among regions, and inferred divergence times for species and clades by applying a semiparametric penalized likelihood approach to our molecular data. Evidence for significant range expansion was present in two of eight regions in two species (Crotalus mitchellii pyrrhus, C. tigris region north). Two species (C. cerastes, C. mitchellii) showed a distribution concomitant with northward displacement of Baja California from mainland México, followed by vicariant separation into subclades. Effects of Pleistocene climate fluctuations were found in the distributions of all four species. Three regional diversification patterns were identified: (i) shallow genetic diversity that resulted from Pleistocene climatic events (C. tigris, C. ruber); (ii) deep Pleistocene divisions indicating allopatric segregation of subclades within refugia (C. mitchellii, C. cerastes); and (iii) lineage diversifications that extended to Pliocene or Late Miocene (C. mitchellii, C. cerastes). Clade-diversifying and clade-constraining effects impacted the four species of rattlesnakes unequally. We found relatively high levels of molecular diversification in the two most broadly distributed species (C. mitchellii, C. cerastes), and lower levels of genetic diversification in the two species (C. tigris, C. ruber) whose ranges are relatively more restricted. Furthermore, in several cases, the distributions of subspecies were not congruent with our molecular information. We suggest regional conservation perspectives for southwestern deserts cannot rely upon subspecies as biodiversity surrogates, but must instead employ a molecular and deep historical perspective as a primary mechanism to frame biodiversity reserves within this region.

Adenosine Triphosphatases↗
PubMedDate not supplied

Estimating the relative contributions of mutation and recombination to clonal diversification: a comparison between Neisseria meningitidis and Streptococcus pneumoniae.

Both Neisseria meningitidis and Streptococcus pneumoniae are naturally transformable species and are known to be freely recombining in the wild. Large multilocus sequence typing (MLST) datasets have been generated for these species. Here we outline an approach which exploits these data sets in order to quantify the extent of recombination, thus enabling meaningful comparisons between the two species. Two parameters are estimated; the rate at which recombination changes alleles, compared to point mutation, and the rate at which recombination changes individual nucleotide sites, compared to point mutation. Estimates for the former parameter are 4:1 in the meningococcus (i.e. alleles are changed four-fold more frequently by recombination than by mutation), and 10:1 in the pneumococcus. However, estimates for the latter parameter are at least 80:1 in the meningococcus (i.e. an individual nucleotide site is at least 80-fold more likely to change by recombination than by mutation) and 50:1 in the pneumococcus. These data imply that recombination events, compared to mutational events, may be more common in the pneumococcus than in the meningococcus. However, because it is a more diverse species, each recombinational exchange in the meningococcus results in more nucleotide changes on average.

Genetic Variation↗