- 8606853482
Frederick Cohan
Wesleyan University, Biology, Faculty Member
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ABSTRACT The full power of functional genomics analyses comes from studying genomes of organisms that are known to be relevant to a system, as this permits a connection between metabolic networks within and across organisms within the... more
ABSTRACT The full power of functional genomics analyses comes from studying genomes of organisms that are known to be relevant to a system, as this permits a connection between metabolic networks within and across organisms within the systems these individuals inhabit. A genome is most effectively studied in an ecological and an evolutionary context, that is, with a view towards the relationships of the individual with other individuals within species and guilds that comprise a community and that mediate community function. We use examples from our own long-term studies of microbial mat communities found between ∼50°C and ∼72°C in alkaline siliceous hot springs of Yellowstone National Park, which are constructed by cyanobacteria (Synechococcus spp.), filamentous (Chloroflexus spp., Roseiflexus spp.) and other newly discovered anoxygenic phototrophic bacteria (Candidatus Chloracidobacterium thermophilum, Chlorobi), to illustrate that (i) isolates from systems are often numerically, genetically, and physiologically unrepresentative of the ecological diversity of predominant species, (ii) seemingly small genetic differences can be extremely important when attempting to infer system function from functions of an isolate, (iii) individuals group into ecologically distinct species populations that may or may not be typified by the characteristics of an individual and its genome, and (iv) co-evolution may be important for understanding metabolic networks among individuals of different species. Metagenomics, metatranscriptomics, metaproteomics and metabolomic/stable isotope technologies will soon enable global studies of the metabolic networking from the individual to the community level of biocomplexity. To interpret the results, we will need to understand the principles of networking at all biological levels and we will be better off if our knowledge of networking within individuals is based on the study of isolates relevant to ecological systems.
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Eight recently collected Australasian populations of D. melanogaster were each divided into eight selection lines. Two of these lines from each population were maintained on one of four types of selection media: standard food supplemented... more
Eight recently collected Australasian populations of D. melanogaster were each divided into eight selection lines. Two of these lines from each population were maintained on one of four types of selection media: standard food supplemented with 0%, 3%, 6% and 9% ethanol. After 30 generations the selection lines were tested for tolerance to 9% ethanol medium and after another 20 generations adults were tested for tolerance to concentrated ethanol fumes. Significant differences in tolerance were found among lines selected on different media which were consistent across the eight populations. On the 9% test media, the 6% and 9% selection lines, as compared with the control lines selected on 0% ethanol, were more likely to survive as pre-adults or adults, faster to develop as preadults, and heavier and more productive as adults. However, the tolerance of the 3% lines to the 9% test media was less than that of the 0% control lines in preadult and adult survival, intermediate between that of the 0% and the 6% and 9% lines in productivities, and apparently superior to the 6% and 9% lines in development times and adult weights. The 3%, 6% and 9% lines showed similar tolerances to the ethanol vapour. Previous work showed that 3% ethanol can be a metabolic benefit to D. melanogaster but 6% and 9% are metabolic costs. The present results suggest that the phenotype selected on 3% to obtain a metabolic benefit differs in many respects from that selected on 6% and 9% to minimise their detrimental effects.
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We have investigated the potential for genetic exchange by transformation within a Mojave Desert population of Bacillus subtilis. Almost all strains surveyed were competent for transformation, and the strains varied over almost three... more
We have investigated the potential for genetic exchange by transformation within a Mojave Desert population of Bacillus subtilis. Almost all strains surveyed were competent for transformation, and the strains varied over almost three orders of magnitude in their levels of competence. This high degree of variation suggests that natural selection toward an optimal level of competence is, at most, very weak in this population. Six of 24 competent strains showed sexual isolation from laboratory strain 168 (i.e., heterogamic transformation was reduced). Direct crosses between selected pairs of Mojave strains indicated sexual isolation within the Mojave population. Levels of sexual isolation observed within this population of B. subtilis were much less than those previously observed for transformation between named Bacillus species. Sexual isolation between 168 and Mojave strains, and among Mojave strains, was due to differences in restriction-modification systems and to DNA sequence divergence.
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Research Interests: Evolutionary Biology, Genetics, Microbiology, Microbial Ecology, Medical Microbiology, and 15 moreBiology, Medicine, Phylogeny, Pyruvate Kinase, Bacillus, Gene, ribosomal RNA, Ecosystem, Molecular Marker, Systematic, Biological markers, Species Specificity, Genetic Markers, Nucleotides, and DNA sequence
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We have investigated the rates of recombination and migration in native populations of two closely related, naturally competent Bacillus species. Native soil isolates of Bacillus subtilis and Bacillus mojavensis were obtained from three... more
We have investigated the rates of recombination and migration in native populations of two closely related, naturally competent Bacillus species. Native soil isolates of Bacillus subtilis and Bacillus mojavensis were obtained from three continents and, within North America, from populations at a range of geographical distances from one another. The rate of recombination within populations of each species was estimated from restriction-site data for three genes. Recombination was shown to occur within each species at about the same rate as neutral mutation, whatever the geographical scale or phylogenetic scale over which strains were sampled. The rate of migration between populations was estimated by a cladistic analysis and was shown to be high (i.e., Nm > 1), even among populations on different continents. The level of migration within each species is sufficient to prevent neutral geographical divergence within species.
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Research Interests: Evolutionary Biology, Genetics, Microbiology, Microbial Ecology, Biology, and 14 moreHorizontal Gene Transfer, Medicine, Gene expression, Multidisciplinary, Bacillus, Gene, Biological evolution, Phenotype, Microarray Analysis, Adaptive evolution, Genetic variation, Species Specificity, Resource Utilization, and Sodium Chloride
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We have investigated the rates of recombination and migration in native populations of two closely related, naturally competent Bacillus species. Native soil isolates of Bacillus subtilis and Bacillus mojavensis were obtained from three... more
We have investigated the rates of recombination and migration in native populations of two closely related, naturally competent Bacillus species. Native soil isolates of Bacillus subtilis and Bacillus mojavensis were obtained from three continents and, within North America, from populations at a range of geographical distances from one another. The rate of recombination within populations of each species was estimated from restriction-site data for three genes. Recombination was shown to occur within each species at about the same rate as neutral mutation, whatever the geographical scale or phylogenetic scale over which strains were sampled. The rate of migration between populations was estimated by a cladistic analysis and was shown to be high (i.e., Nm > 1), even among populations on different continents. The level of migration within each species is sufficient to prevent neutral geographical divergence within species.
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Research Interests: Evolutionary Biology, Genetics, Human Genetics, Biology, Horizontal Gene Transfer, and 12 moreDNA repair, Genetic Algorithm, Genetica, Pubmed, Bacteria, Biological evolution, Reproductive Isolation, Genetic Recombination, Species Specificity, Recombination, DNA Restriction Enzymes, and Springer Ebooks
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Organisms of the Microcystis aeruginosa complex form harmful algal blooms (HABs) in nutrient-rich water bodies worldwide. MAC HABs are difficult to manage owing to the production of potent toxins (microcystins) that resist water treatment.
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Multi-drug resistant bacterial pathogens are alarmingly on the rise, signaling that the golden age of antibiotics may be over. Phage therapy is a classic approach that often employs strictly lytic bacteriophages (bacteria-specific viruses... more
Multi-drug resistant bacterial pathogens are alarmingly on the rise, signaling that the golden age of antibiotics may be over. Phage therapy is a classic approach that often employs strictly lytic bacteriophages (bacteria-specific viruses that kill cells) to combat infections. Recent success in using phages in patient treatment stimulates greater interest in phage therapy among Western physicians. But there is concern that widespread use of phage therapy would eventually lead to global spread of phage-resistant bacteria and widespread failure of the approach. Here, we argue that various mechanisms of horizontal genetic transfer (HGT) have largely contributed to broad acquisition of antibiotic resistance in bacterial populations and species, whereas similar evolution of broad resistance to therapeutic phages is unlikely. The tendency for phages to infect only particular bacterial genotypes limits their broad use in therapy, in turn reducing the likelihood that bacteria could acquire ...
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Prokaryotic systematics has defined species as phenotypically distinct groups that form clusters based on a fixed level of molecular similarity. These criteria have provided stability for species demarcation but yield enormous levels of... more
Prokaryotic systematics has defined species as phenotypically distinct groups that form clusters based on a fixed level of molecular similarity. These criteria have provided stability for species demarcation but yield enormous levels of ecological diversity within a typical species taxon. Investigations of prokaryotic diversification have not focused on the broadly defined species taxa of systematics but rather on the more newly divergent lineages expected to have dynamic properties attributed to species. Regardless of whether species are demarcated as clusters or by evolutionary properties, full genome sequences provide an efficient way to discover diversity at the species level and to infer the ecological roles of species.
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Research Interests: Evolutionary Biology, Microbiology, Microbial Ecology, Biology, Ecology, and 15 moreMedicine, Multidisciplinary, Applied, Applied Environmental Microbiology, Microbial Mat, Light, Cluster Analysis, Genotype, Oxygen, Genetic variation, Geologic Sediments, Molecular Sequence Data, Hot Springs, bacteroidetes, and Distribution Pattern
Research Interests: Evolutionary Biology, Microbiology, Microbial Ecology, Medical Microbiology, Biology, and 13 moreEcology, Evolution, Ecological Niche Modeling, Horizontal Gene Transfer, Medicine, Natural Selection, Genetic Diversity, Bacteria, Plasmids, Biological evolution, Genetic Recombination, Genetic variation, and Niche
Research Interests: Evolutionary Biology, Genetics, Genomics, Comparative Genomics, Biology, and 15 moreCyanobacteria, Metagenomics, Medicine, Gene expression, Heredity, Cytogenetics, Evolutionary theory, Environmental genomics, Microbial Mat, Key words, Ecological, Ecosystem, Genome sequence, Environment, and Microbial community
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Research Interests: Biology, ALGORITMA GENETIKA, Universitas Lampung, Universitas Riau, Undip, and 15 moreUniversitas, Universitas Gadjah Mada, Peternakan, Universitas Hasanuddin, Genetik, Sosial Ekonomi Peternakan, buku Genetika, Universitas Negeri Surabaya, Genetika, Dasar Genetika, Bio Genetika, Kegiatan Peternakan Di Dalam Dan Luar Negeri, Fakultas Peternakan Dan Pertanian, Manajemen Peternakan, and Perencanaan Pembangunan Peternakan
Previous studies have shown that genetic exchange in bacteria is too rare to prevent neutral sequence divergence between ecological populations. That is, despite genetic exchange, each population should diverge into its own DNA... more
Previous studies have shown that genetic exchange in bacteria is too rare to prevent neutral sequence divergence between ecological populations. That is, despite genetic exchange, each population should diverge into its own DNA sequence-similarity cluster. In those studies, each selective sweep was limited to acting within a single ecological population. Here we postulate the existence of globally adaptive mutations, which may confer a selective advantage to all ecological populations constituting a metapopulation. Such adaptations cause global selective sweeps, which purge the divergence both within and between populations. We found that the effect of recurrent global selective sweeps on neutral sequence divergence is highly dependent on the mechanism of genetic exchange. Global selective sweeps can prevent populations from reaching high levels of neutral sequence divergence, but they cannot cause two populations to become identical in neutral sequence characters. The model support...
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Despite the important roles of soil microbes, especially the most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter the stability and functions of the rare microbial biosphere... more
Despite the important roles of soil microbes, especially the most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter the stability and functions of the rare microbial biosphere remains unknown. We reciprocally transplanted field soils across a latitudinal gradient to simulate climate change, and sampled the soils annually after harvesting the maize over the following six years (from 2005 to 2011). By sequencing microbial 16S ribosomal RNA gene amplicons, we found that changing climate regimes significantly altered the composition and dynamics of soil microbial communities. Continuous succession of the rare and abundant communities was observed. Rare microbial communities were more stable under changing climatic regimes, with lower variations in temporal dynamics, and higher stability and constancy of diversity. More nitrogen cycling gene was detected in the rare members than in the abundant members, including amoA, napA, nifH, nirK, nirS, norB, and nrfA. Random forest analysis and receiver operating characteristics analysis showed that rare taxa may act as potential contributors to maize yield under changing climatics. The study indicates that the taxonomically and functionally diverse rare biosphere has the potential to increase functional redundancy and enhance the ability of soil communities to counteract environmental disturbances. With ongoing global climate change, exploring the succession process and functional changes of rare taxa may be important in elucidating the ecosystem stability and multifunctionality that are mediated by microbial communities. This article is protected by copyright. All rights reserved.
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Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of... more
Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, a...
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Recent work shows that genetic exchange in prokaryotes is less frequent but more promiscuous than that in eukaryotes. As a result, genetic exchange plays very different roles in determining the patterns of evolutionary divergence in these... more
Recent work shows that genetic exchange in prokaryotes is less frequent but more promiscuous than that in eukaryotes. As a result, genetic exchange plays very different roles in determining the patterns of evolutionary divergence in these major groups. Because sexual isolation is not a prerequisite for divergence in the prokaryotic world, the biological species concept is not appropriate for bacteria. However, there is a species concept that may apply universally.
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We have introduced a device for selecting Drosophila for increased resistance to very high concentrations of ethanol fumes. This device has enabled us to: 1) select quickly and easily over a thousand flies at a time, and 2) score the... more
We have introduced a device for selecting Drosophila for increased resistance to very high concentrations of ethanol fumes. This device has enabled us to: 1) select quickly and easily over a thousand flies at a time, and 2) score the knockdown time of every fly in the distribution, while causing very little injury to the flies. A sample of nine west coast populations of Drosophila melanogaster showed a significant trend toward higher knockdown resistance in more northern populations. A population's level of knockdown resistance was virtually uncorrelated with its alcohol dehydrogenase (Adh) allele frequencies. Five of the above nine populations were then subjected to selection for further knockdown resistance. Each population was divided randomly into four groups of 256 flies: two lines to be selected, and two lines to remain unselected as control lines. In every generation each selected line was measured for knockdown resistance, and the last quartile of flies to be knocked down was saved to continue the selection cycle. Population sizes of the selected and unselected lines were all maintained at 256. Realized heritability, based on the responses to selection of the first four generations, was calculated for each selected line. The five populations were significantly heterogeneous for heritability estimates; the average heritability of the five populations pooled was 0.143 ± 0.019. Over the course of twelve generations, the ten selected lines increased their knockdown times by an average factor of 2.40. Before selection, the five populations were heterogeneous for knockdown resistance, and resistance was greatest among the most northern populations. The amount of change of knockdown resistance over the course of selection was also correlated with latitude: the most southern population increased its knockdown time by a factor of 2.23, and the most northern population increased it by a factor of 2.55. After ten generations of selection, the cline of knockdown resistance was about 4.5 times as steep as that before selection. Small phenotypic differences among populations before selection were thus exaggerated by the action of selection. The differences among populations in their rates of response to selection were attributed to genetic differences that existed before selection. The pattern of change of Adh frequencies over the course of selection was very inconsistent, both among and within populations. From this inconsistency of change of Adh alleles with selection, and the lack of correlation between Adh frequencies and knockdown resistance before selection, we concluded that Adh frequency changes could not have had much effect on the responses of the selected lines.
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The experiments usedDrosophila melanogaster lines previously selected for increased knockdown resistance to ethanol. Selected lines utilized ethanol as a metabolic resource to a greater extent than unselected lines. Lines were... more
The experiments usedDrosophila melanogaster lines previously selected for increased knockdown resistance to ethanol. Selected lines utilized ethanol as a metabolic resource to a greater extent than unselected lines. Lines were characterized by their olfactory responses to ethanol, ethyl acetate, and acetaldehyde in a wind tunnel. Selected lines were less attracted to ethanol than unselected lines but did not differ consistently in their responses to other chemicals. This suggests that increased tolerance and utilization of ethanol are not necessarily accompanied by increased attraction to this chemical.