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Coalescence Times (coalescence + time)

Distribution by Scientific Domains
Life Sciences57%

Selected Abstracts

PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES

EVOLUTION, Issue 6 2000
ScottV.
Abstract Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (,) to T and the effect of uncertainty in , on estimates of population divergence (,) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on , decrease when the range over which ancestral population size , is assumed to be distributed decreases and when increases; they generally exclude zero when /(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding = 0 is roughly that l/(4Ne)> 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time. [source]

Binary coalescence of air bubbles in viscous liquids in presence of non-ionic surfactant

THE CANADIAN JOURNAL OF CHEMICAL ENGINEERING, Issue 4 2008
K. Giribabu
Abstract Coalescence of air bubbles is important in gas,liquid reactors and food processing operations. Bubbles can be stabilized by using non-ionic surfactants. Binary coalescence of air bubbles in ethylene glycol and aqueous glycerol solutions were studied in this work in presence of Span 80. A novel set-up was developed to study long coalescence times. Coalescence time was observed to follow broad stochastic distributions in all systems. The distributions were fitted with a stochastic model developed earlier. The surface tension of ethylene glycol and glycerol solutions was measured at various concentrations of Span 80. These data were fitted using a surface equation of state derived from the Langmuir isotherm. The effect of surfactant concentration on coalescence time was explained in terms of the surface excess of the surfactant and the repulsive force generated at the air,liquid interface. The results from this work illustrate the stochastic nature of bubble coalescence in viscous liquids. This work also demonstrates how non-ionic surfactants can stabilize bubbles in such liquids. La coalescence des bulles d'air est importante dans les réacteurs gaz-liquide et les opérations de l'industrie alimentaire. Les bulles peuvent être stabilisées en utilisant des surfactants non ioniques. La coalescence binaire de bulles d'air dans des solutions aqueuses d'éthylène glycol et de glycérol a été étudiée dans ce travail en présence de Span 80. Un nouveau montage a été mis au point pour caractériser les temps de coalescence longs. Le temps de coalescence a été observé afin de suivre les distributions de modèle stochastique dans tous les systèmes. Les distributions ont été calées à un modèle stochastique mis au point antérieurement. La tension de surface des solutions d'éthylène glycol et de glycérol a été mesurée à différentes concentrations de Span 80. Ces données ont été calées à l'aide d'une équation d'état de surface calculée à partir de l'isotherme de Langmuir. L'effet de la concentration de surfactant sur le temps de coalescence est expliqué par l'excès de surface du surfactant et la force répulsive créée à l'interface air-liquide. Les résultats de ce travail illustrent la nature stochastique de la coalescence des bulles dans les liquides visqueux. Ce travail démontre également comment les surfactants non ioniques peuvent stabiliser les bulles dans de tels liquides. [source]

PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES

EVOLUTION, Issue 6 2000
ScottV.
Abstract Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (,) to T and the effect of uncertainty in , on estimates of population divergence (,) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on , decrease when the range over which ancestral population size , is assumed to be distributed decreases and when increases; they generally exclude zero when /(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding = 0 is roughly that l/(4Ne)> 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time. [source]

Binary coalescence of air bubbles in viscous liquids in presence of non-ionic surfactant

THE CANADIAN JOURNAL OF CHEMICAL ENGINEERING, Issue 4 2008
K. Giribabu
Abstract Coalescence of air bubbles is important in gas,liquid reactors and food processing operations. Bubbles can be stabilized by using non-ionic surfactants. Binary coalescence of air bubbles in ethylene glycol and aqueous glycerol solutions were studied in this work in presence of Span 80. A novel set-up was developed to study long coalescence times. Coalescence time was observed to follow broad stochastic distributions in all systems. The distributions were fitted with a stochastic model developed earlier. The surface tension of ethylene glycol and glycerol solutions was measured at various concentrations of Span 80. These data were fitted using a surface equation of state derived from the Langmuir isotherm. The effect of surfactant concentration on coalescence time was explained in terms of the surface excess of the surfactant and the repulsive force generated at the air,liquid interface. The results from this work illustrate the stochastic nature of bubble coalescence in viscous liquids. This work also demonstrates how non-ionic surfactants can stabilize bubbles in such liquids. La coalescence des bulles d'air est importante dans les réacteurs gaz-liquide et les opérations de l'industrie alimentaire. Les bulles peuvent être stabilisées en utilisant des surfactants non ioniques. La coalescence binaire de bulles d'air dans des solutions aqueuses d'éthylène glycol et de glycérol a été étudiée dans ce travail en présence de Span 80. Un nouveau montage a été mis au point pour caractériser les temps de coalescence longs. Le temps de coalescence a été observé afin de suivre les distributions de modèle stochastique dans tous les systèmes. Les distributions ont été calées à un modèle stochastique mis au point antérieurement. La tension de surface des solutions d'éthylène glycol et de glycérol a été mesurée à différentes concentrations de Span 80. Ces données ont été calées à l'aide d'une équation d'état de surface calculée à partir de l'isotherme de Langmuir. L'effet de la concentration de surfactant sur le temps de coalescence est expliqué par l'excès de surface du surfactant et la force répulsive créée à l'interface air-liquide. Les résultats de ce travail illustrent la nature stochastique de la coalescence des bulles dans les liquides visqueux. Ce travail démontre également comment les surfactants non ioniques peuvent stabiliser les bulles dans de tels liquides. [source]

PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES

EVOLUTION, Issue 6 2000
ScottV.
Abstract Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (,) to T and the effect of uncertainty in , on estimates of population divergence (,) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on , decrease when the range over which ancestral population size , is assumed to be distributed decreases and when increases; they generally exclude zero when /(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding = 0 is roughly that l/(4Ne)> 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time. [source]

Historical male-mediated introgression in horseshoe bats revealed by multilocus DNA sequence data

MOLECULAR ECOLOGY, Issue 7 2010
XIUGUANG MAO
Abstract Instances of hybridization between mammalian taxa in the wild are rarely documented. To test for introgression between sibling species of horseshoe bat (Rhinolophus yunanensis and R. pearsoni) and two subspecies of the latter (R. p. pearsoni and R. p. chinensis), we sequenced two mtDNA and two ncDNA markers in individuals sampled from multiple localities within their overlapping ranges. The interspecific mtDNA gene tree corresponded to the expected taxonomic divisions, and coalescent-based analyses suggested divergence occurred around 4 MYA. However, these relationships strongly conflicted with those recovered from two independent nuclear gene trees, in which R. yunanensis clustered with R. p. pearsoni to the exclusion of R. p. chinensis. This geographically widespread discordance is best explained by large-scale historical introgression of ncDNA from R. yunanensis to R. pearsoni by male-mediated exchange in mixed species colonies during Pleistocene glacial periods, when ranges may have contracted and overlapped more than at present. Further species tree,gene tree conflicts were detected between R. p. pearsoni and R. p. chinensis, also indicating past and/or current introgression in their overlapping regions. However, here the patterns point to asymmetric mtDNA introgression without ncDNA introgression. Analyses of coalescence times indicate this exchange has occurred subsequent to the divergence of these subspecies from their common ancestor. Our work highlights the importance of using multiple data sets for reconstructing phylogeographic histories and resolving taxonomic relationships. [source]

Binary coalescence of air bubbles in viscous liquids in presence of non-ionic surfactant

THE CANADIAN JOURNAL OF CHEMICAL ENGINEERING, Issue 4 2008
K. Giribabu
Abstract Coalescence of air bubbles is important in gas,liquid reactors and food processing operations. Bubbles can be stabilized by using non-ionic surfactants. Binary coalescence of air bubbles in ethylene glycol and aqueous glycerol solutions were studied in this work in presence of Span 80. A novel set-up was developed to study long coalescence times. Coalescence time was observed to follow broad stochastic distributions in all systems. The distributions were fitted with a stochastic model developed earlier. The surface tension of ethylene glycol and glycerol solutions was measured at various concentrations of Span 80. These data were fitted using a surface equation of state derived from the Langmuir isotherm. The effect of surfactant concentration on coalescence time was explained in terms of the surface excess of the surfactant and the repulsive force generated at the air,liquid interface. The results from this work illustrate the stochastic nature of bubble coalescence in viscous liquids. This work also demonstrates how non-ionic surfactants can stabilize bubbles in such liquids. La coalescence des bulles d'air est importante dans les réacteurs gaz-liquide et les opérations de l'industrie alimentaire. Les bulles peuvent être stabilisées en utilisant des surfactants non ioniques. La coalescence binaire de bulles d'air dans des solutions aqueuses d'éthylène glycol et de glycérol a été étudiée dans ce travail en présence de Span 80. Un nouveau montage a été mis au point pour caractériser les temps de coalescence longs. Le temps de coalescence a été observé afin de suivre les distributions de modèle stochastique dans tous les systèmes. Les distributions ont été calées à un modèle stochastique mis au point antérieurement. La tension de surface des solutions d'éthylène glycol et de glycérol a été mesurée à différentes concentrations de Span 80. Ces données ont été calées à l'aide d'une équation d'état de surface calculée à partir de l'isotherme de Langmuir. L'effet de la concentration de surfactant sur le temps de coalescence est expliqué par l'excès de surface du surfactant et la force répulsive créée à l'interface air-liquide. Les résultats de ce travail illustrent la nature stochastique de la coalescence des bulles dans les liquides visqueux. Ce travail démontre également comment les surfactants non ioniques peuvent stabiliser les bulles dans de tels liquides. [source]