In June 2013,the fi rst human H6N1 infl uenza virus infec-tion was confirmed in Taiwan.However,the origin and molecular characterization of this virus,A/Taiwan/2/2013(H6N1),have not been well studied thus far.In the p...In June 2013,the fi rst human H6N1 infl uenza virus infec-tion was confirmed in Taiwan.However,the origin and molecular characterization of this virus,A/Taiwan/2/2013(H6N1),have not been well studied thus far.In the present report,we performed phylogenetic and coalescent analy-ses of this virus and compared its molecular profi le/char-acteristics with other closely related strains.Molecular characterization of H6N1 revealed that it is a typical avian infl uenza virus of low pathogenicity,which might not rep-licate and propagate well in the upper airway in mammals.Phylogenetic analysis revealed that the virus clusters with A/chicken/Taiwan/A2837/2013(H6N1)in seven genes,except PB1.For the PB1 gene,A/Taiwan/2/2013 was clus-tered with a different H6N1 lineage from A/chicken/Taiwan/A2837/2013.Although a previous study demonstrated that the PB2,PA,and M genes of A/Taiwan/2/2013 might be derived from the H5N2 viruses,coalescent analyses revealed that these H5N2 viruses were derived from more recent strains than that of the ancestor of A/Taiwan/2/2013.Therefore,we propose that A/Taiwan/2/2013 is a reassor-tant from different H6N1 lineages circulating in chickens in Taiwan.Furthermore,compared to avian isolates,a sin-gle P186L(H3 numbering)substitution in the hemaggluti-nin H6 of the human isolate might increase the mammali-an receptor binding and,hence,this strain’s pathogenicity in humans.Overall,human infection with this virus seems an accidental event and is unlikely to cause an infl uenza pandemic.However,its co-circulation and potential reas-sortment with other infl uenza subtypes are still worthy of attention.展开更多
This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five n...This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny （A00）, species tree estimation when the assignment and species delimitation are fixed （A01）, species delimitation using a fixed guide tree （A10）, and joint species delimitation and species-tree estimation or unguided species delimitation （A11）. For the joint analysis （A11）, two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis [Current Zoology 61 （5）： 854-865, 2015].展开更多
Colletotrichum is one of the most important plant pathogenic genera that is responsible for numerous diseases which can have a profound impact on the agricultural sector.Species delineation is difficult due to a lack ...Colletotrichum is one of the most important plant pathogenic genera that is responsible for numerous diseases which can have a profound impact on the agricultural sector.Species delineation is difficult due to a lack of distinctive phenotypic vari-ation.Therefore,in this study three different genomic approaches based on phylogenetic,evolutionary and coalescent-based methods are applied to establish robust species boundaries.The reliability of five different DNA barcodes was also assessed to provide further insights into species delineation.The ITS region can resolve the placement of taxa up to the species complex level.The GAPDH and TUB2 markers are determined to be the most informative for most complexes.However,no single marker could discriminate between species in all complexes,therefore different molecular approaches based on multi-locus datasets are recommended.This is the first study to provide an estimated divergence time for all species complexes in Colle-totrichum.The estimated divergence time for species complexes ranged between 4.8 to 32.2 MYA.Based on the high level of congruent results obtained from the different molecular approaches,a new species complex,the Colletotrichum agaves complex is introduced.This complex consists of five taxa which are characterised by the presence of straight or slightly curved conidia with obtuse apices.This study shows that coalescent approaches and multi-locus phylogeny are crucial to establish species boundaries in Colletotrichum.The taxonomic placement of three singleton taxa Colletotrichum axonopodi,C.cariniferi and C.parallelophorum is revised.We accept 248 species and provide recommendations regarding species boundaries in the graminicola-caudatum complex.展开更多
SFTS virus(SFTSV)is a novel bunyavirus,which was discovered as the etiological agent of severe fever with thrombocytopenia syndrome(SFTS)in China in 2009,and was now prevalent in at least 25 provinces in China.SFTS wa...SFTS virus(SFTSV)is a novel bunyavirus,which was discovered as the etiological agent of severe fever with thrombocytopenia syndrome(SFTS)in China in 2009,and was now prevalent in at least 25 provinces in China.SFTS was subsequently identified in South Korea and Japan in 2012.To explore themolecular evolution and genetic characteristics of this newly identified pathogen,we reported 72 whole genome sequences of SFTSV,and built a dataset of SFTSV genome sequences containing 292 L-segment,302 M-segment and 502 S-segment.We clearly divided SFTSV into six genotypes,Genotype A-F.It was found that genotype F was the dominant epidemic genotype of Japan,South Korea,and Zhejiang province of China.The coalescent analysis supported that SFTSV originated in the early 18th century from Zhejiang province,and Genotype F was the most primitive one.Henan,Hubei,and Anhui provinces which are located in Dabie Mountain area weremainly epidemic of Genotype A,which emerged relatively late but distributed widely.A total of 37 recombination events were identified,making SFTSV with a high recombination frequency(L segment 5.1%,Msegment 3.6%,S segment 0.8%)among negative-strand segmented RNA viruses.It was identified that 19 reassortant strains belonged to 12 reassortment forms of SFTSV genome containing 6 newly identified forms.The reassortment virus and recombination in tick were both found for the first time.We also found many of genotype-specific mutation sites,7 of which could be considered as potential molecular marker for genotype classification.This study promoted a more comprehensive understanding of the phylogeny and origin,and the genetic diversity of SFTSV,and it could help the studies of other newly discovered tick-borne bunyavirus as reference data and research ideas.展开更多
DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, par...DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the frame-work of the multi-species coalescent （MSC）. In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation （and their limitations） are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today＇s technologies [Current Zoology 61 （5）： 846-853,2015].展开更多
Rationale:Acute otitis media is a common disease in early childhood,and is usually caused by Streptococcus pneumoniae(S.pneumoniae).Acute mastoiditis is a complication of acute otitis media and can involve not only th...Rationale:Acute otitis media is a common disease in early childhood,and is usually caused by Streptococcus pneumoniae(S.pneumoniae).Acute mastoiditis is a complication of acute otitis media and can involve not only the mucoperiosteum of the middle ear but can also spread to the periosteum by destroying the mastoid bone(acute coalescent mastoiditis).In addition,the infection can extend through the surrounding bones or the emissary veins beyond the mastoid’s air cells,leading to subperiosteal abscesses.Patient’s Concern:A 16-month-old female patient was hospitalized due to the purulent discharge of the left ear and the symptoms of right mastoiditis(swelling and redness of the skin).Diagnosis:Bilateral acute coalescent mastoiditis caused by S.pneumoniae infection.The computer tomography revealed bilateral bone destruction of the mastoid and abscesses found behind the auricle on both sides.Interventions:The patient underwent intravenous antibiotic therapy and surgical treatment.Outcomes:The patient was discharged 14 days after hospitalization with an improved condition.Lessons:Improperly treated acute coalescent mastoiditis can lead to extracranial and intracranial complications,sometimes serious and even life-threatening.Complications are prevalent in children under 2 years,in whom the disease progresses more rapidly and severely.The vaccination with a 13-valent vaccine may not result in sufficient immunity against S.pneumoniae,a predominant pathogen in children affected by acute coalescent mastoiditis.展开更多
Identical-by-descent(IBD)is a fundamental genomic characteristic in population genetics and has been widely used for population history reconstruction.However,limited by the nature of IBD,which could only capture the ...Identical-by-descent(IBD)is a fundamental genomic characteristic in population genetics and has been widely used for population history reconstruction.However,limited by the nature of IBD,which could only capture the relationship between two individuals/haplotypes,existing IBD-based history inference is constrained to two populations.In this study,we propose a framework by leveraging IBD sharing in multipopulation and develop a method,MatrixiBD,to reconstruct recent multi-population migration history.Specifically,we employ the structured coalescent theory to precisely model the genealogical process and then estimate the IBD sharing across multiple populations.Within our model,we establish a theoretical connection between migration history and IBD sharing.Our method is rigorously evaluated through simulations,revealing its remarkable accuracy and robustness.Furthermore,we apply MatrixiBD to Central and South Asia in the Human Genome Diversity Project and successfully reconstruct the recent migration history of three closely related populations in South Asia.By taking into account the IBD sharing across multiple populations simultaneously,MatrixlBD enables us to attain clearer and more comprehensive insights into the history of regions characterized by complex migration dynamics,providing a holistic perspective on intricate patterns embedded within the recent population migration history.展开更多
The Gamma-Dirichlet algebra corresponds to the decomposition of the gamma process into the independent product of a gamma random variable and a Dirichlet process. This structure allows us to study the properties of th...The Gamma-Dirichlet algebra corresponds to the decomposition of the gamma process into the independent product of a gamma random variable and a Dirichlet process. This structure allows us to study the properties of the Dirichlet process through the gamma process and vice versa. In this article, we begin with a brief survey of several existing results concerning this structure. New results are then obtained for the large deviations of the jump sizes of the gamma process and the quasi-invariance of the two-parameter Poisson-Dirichlet distribution. We finish the paper with the derivation of the transition function of the Fleming-Viot process with parent independent mutation from the transition function of the measure-valued branching diffusion with immigration by exploring the Gamma-Dirichlet algebra embedded in these processes. This last result is motivated by an open R. C. Gritfiths. problem proposed by S. N. Ethier and展开更多
Genetic variability plays a key role in the biology and medical treatment of RNA viruses. As an RNA virus, Hepatitis C virus (HCV) replicate as complex distributions of closely related genomes termed viral quasispecie...Genetic variability plays a key role in the biology and medical treatment of RNA viruses. As an RNA virus, Hepatitis C virus (HCV) replicate as complex distributions of closely related genomes termed viral quasispecies. The behavior of the evolving HCV quasispecies population is influenced by the ensemble of mutants that compose the viral population. One such influence is the presence of minority subpopulations, termed memory genomes, in the mutant spectra. Biologically relevant mutants have been previously observed to be present as memory genomes in RNA viral populations. For that reason, an in-depth analysis of HCV quasispecies populations is crucial for our understanding viral evolution, drug resistance and therapy outcome. Recently developed next-generation sequencing (NGS) platforms make it possible to investigate viral quasispecies at much greater detail. In order to gain insight into these matters, we have performed a Bayesian coalescent analysis of hypervariable region 1 (HVR1) sequences of a HCV quasispecies population circulating in a chronic patient, recently obtained by ultra-deep sequencing. The results of these studies revealed a mean rate of evolution of HCV HVR1 of the intra-host quasispecies population of 4.80 × 10-2 amino acid substitutions/site/year. A sharp and rapid diversification of the HCV quasispecies isolated from the patient in three different sub-populations was observed. The most abundant sequence in the quasispecies population was not found to be the center of a tight and complex network around this sequence, suggesting that the quasispecies population as a whole efficiently explore a wide sequence space. Co-evolution of relevant amino acid sites had been identified in the HVR1. This speaks of the possible roll of these residues in HVR1 to allow the virus to shift between combinations of residues to escape the immune system while retaining its structure and functions. The results of these studies highlight the importance of minority genomes in HCV population history and evolution, t展开更多
Background: Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to conver...Background: Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a consistent topology, including introgression, incomplete lineage sorting, different data types, or insufficient data.Methods: We generated three novel whole genome assemblies for Gallus species, which we combined with data from the published genomes of Gallus gallus and Bambusicola thoracicus(a member of the sister genus to Gallus). To determine why previous studies have failed to converge on a single topology, we extracted large numbers of orthologous exons, introns, ultra-conserved elements, and conserved non-exonic elements from the genome assemblies. This provided more than 32 million base pairs of data that we used for concatenated maximum likelihood and multispecies coalescent analyses of Gallus.Results: All of our analyses, regardless of data type, yielded a single, well-supported topology. We found some evidence for ancient introgression involving specific Gallus lineages as well as modest data type effects that had an impact on support and branch length estimates in specific analyses. However, the estimated gene tree spectra for all data types had a relatively good fit to their expectation given the multispecies coalescent.Conclusions: Overall, our data suggest that conflicts among previous studies probably reflect the use of smaller datasets(both in terms of number of sites and of loci) in those analyses. Our results demonstrate the importance of sampling large numbers of loci, each of which has a sufficient number of sites to provide robust estimates of gene trees. Low-coverage whole genome sequencing, as we did here, represents a cost-effective means to generate the very large data sets that include multiple data types that enabled us to obtain a robust estimate of Gallus phylogeny.展开更多
Chaotic genetic patchiness （CGP） refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene f...Chaotic genetic patchiness （CGP） refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene flow via larval dispersal. Here we review and discuss 4 mechanisms that could generate such unexpected patterns： selection, sweepstakes reproductive success, collective dispersal, and temporal shifts in local population dynamics. First, we review examples where genetic differentiation at specific loci was driven by diversifying selection, which was historically the first process invoked to explain CGP. Second, we turn to neutral demographic processes that may drive genome-wide effects, and whose effects on CGP may be enhanced when they act together. We discuss how sweepstakes reproductive success accelerates genetic drift and can thus generate genetic structure, provided that gene flow is not too strong. Collective dispersal is another mechanism whereby genetic structure can be maintained regardless of dispersal intensity, because it may prevent larval cohorts from becoming entirely mixed. Theoretical analyses of both the sweepstakes and the collective dispersal ideas are presented. Finally, we discuss an idea that has received less attention than the other ones just mentioned, namely temporal shifts in local population dynamics.展开更多
基金the National Basic Research Pro-gram(973 Program)(Nos.2010CB530303,2011CB504703,and 2012CB955501an intramural special grant for influenza virus research from the Chinese Academy of Sciences(KSZD-EW-Z-002)the Doctoral Starting up Foundation of Taishan Medical College.GFG is a leading principal investigator of the Innova-tive Research Group of the National Natural Science Foundation of China(Grant No.81021003)。
文摘In June 2013,the fi rst human H6N1 infl uenza virus infec-tion was confirmed in Taiwan.However,the origin and molecular characterization of this virus,A/Taiwan/2/2013(H6N1),have not been well studied thus far.In the present report,we performed phylogenetic and coalescent analy-ses of this virus and compared its molecular profi le/char-acteristics with other closely related strains.Molecular characterization of H6N1 revealed that it is a typical avian infl uenza virus of low pathogenicity,which might not rep-licate and propagate well in the upper airway in mammals.Phylogenetic analysis revealed that the virus clusters with A/chicken/Taiwan/A2837/2013(H6N1)in seven genes,except PB1.For the PB1 gene,A/Taiwan/2/2013 was clus-tered with a different H6N1 lineage from A/chicken/Taiwan/A2837/2013.Although a previous study demonstrated that the PB2,PA,and M genes of A/Taiwan/2/2013 might be derived from the H5N2 viruses,coalescent analyses revealed that these H5N2 viruses were derived from more recent strains than that of the ancestor of A/Taiwan/2/2013.Therefore,we propose that A/Taiwan/2/2013 is a reassor-tant from different H6N1 lineages circulating in chickens in Taiwan.Furthermore,compared to avian isolates,a sin-gle P186L(H3 numbering)substitution in the hemaggluti-nin H6 of the human isolate might increase the mammali-an receptor binding and,hence,this strain’s pathogenicity in humans.Overall,human infection with this virus seems an accidental event and is unlikely to cause an infl uenza pandemic.However,its co-circulation and potential reas-sortment with other infl uenza subtypes are still worthy of attention.
文摘This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny （A00）, species tree estimation when the assignment and species delimitation are fixed （A01）, species delimitation using a fixed guide tree （A10）, and joint species delimitation and species-tree estimation or unguided species delimitation （A11）. For the joint analysis （A11）, two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis [Current Zoology 61 （5）： 854-865, 2015].
基金the Thailand Research Fund,grant RDG6130001 entitled“Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion”the support from University of Mauritius and the Mauritius Research and Innovative Council(MRC/RUN/1705)RS Jayawardena thanks the National Research Council of Thailand,grant for new researcher NRCT5-TRG630010-01,entitled“Biodiversity,taxonomy,phylogeny and evolution of Colletotrichum in northern Thailand”.
文摘Colletotrichum is one of the most important plant pathogenic genera that is responsible for numerous diseases which can have a profound impact on the agricultural sector.Species delineation is difficult due to a lack of distinctive phenotypic vari-ation.Therefore,in this study three different genomic approaches based on phylogenetic,evolutionary and coalescent-based methods are applied to establish robust species boundaries.The reliability of five different DNA barcodes was also assessed to provide further insights into species delineation.The ITS region can resolve the placement of taxa up to the species complex level.The GAPDH and TUB2 markers are determined to be the most informative for most complexes.However,no single marker could discriminate between species in all complexes,therefore different molecular approaches based on multi-locus datasets are recommended.This is the first study to provide an estimated divergence time for all species complexes in Colle-totrichum.The estimated divergence time for species complexes ranged between 4.8 to 32.2 MYA.Based on the high level of congruent results obtained from the different molecular approaches,a new species complex,the Colletotrichum agaves complex is introduced.This complex consists of five taxa which are characterised by the presence of straight or slightly curved conidia with obtuse apices.This study shows that coalescent approaches and multi-locus phylogeny are crucial to establish species boundaries in Colletotrichum.The taxonomic placement of three singleton taxa Colletotrichum axonopodi,C.cariniferi and C.parallelophorum is revised.We accept 248 species and provide recommendations regarding species boundaries in the graminicola-caudatum complex.
基金supported by the National Major Science and Technol-ogy Project of China(2018ZX10711001,2016ZX10004222-002)。
文摘SFTS virus(SFTSV)is a novel bunyavirus,which was discovered as the etiological agent of severe fever with thrombocytopenia syndrome(SFTS)in China in 2009,and was now prevalent in at least 25 provinces in China.SFTS was subsequently identified in South Korea and Japan in 2012.To explore themolecular evolution and genetic characteristics of this newly identified pathogen,we reported 72 whole genome sequences of SFTSV,and built a dataset of SFTSV genome sequences containing 292 L-segment,302 M-segment and 502 S-segment.We clearly divided SFTSV into six genotypes,Genotype A-F.It was found that genotype F was the dominant epidemic genotype of Japan,South Korea,and Zhejiang province of China.The coalescent analysis supported that SFTSV originated in the early 18th century from Zhejiang province,and Genotype F was the most primitive one.Henan,Hubei,and Anhui provinces which are located in Dabie Mountain area weremainly epidemic of Genotype A,which emerged relatively late but distributed widely.A total of 37 recombination events were identified,making SFTSV with a high recombination frequency(L segment 5.1%,Msegment 3.6%,S segment 0.8%)among negative-strand segmented RNA viruses.It was identified that 19 reassortant strains belonged to 12 reassortment forms of SFTSV genome containing 6 newly identified forms.The reassortment virus and recombination in tick were both found for the first time.We also found many of genotype-specific mutation sites,7 of which could be considered as potential molecular marker for genotype classification.This study promoted a more comprehensive understanding of the phylogeny and origin,and the genetic diversity of SFTSV,and it could help the studies of other newly discovered tick-borne bunyavirus as reference data and research ideas.
文摘DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the frame-work of the multi-species coalescent （MSC）. In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation （and their limitations） are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today＇s technologies [Current Zoology 61 （5）： 846-853,2015].
文摘Rationale:Acute otitis media is a common disease in early childhood,and is usually caused by Streptococcus pneumoniae(S.pneumoniae).Acute mastoiditis is a complication of acute otitis media and can involve not only the mucoperiosteum of the middle ear but can also spread to the periosteum by destroying the mastoid bone(acute coalescent mastoiditis).In addition,the infection can extend through the surrounding bones or the emissary veins beyond the mastoid’s air cells,leading to subperiosteal abscesses.Patient’s Concern:A 16-month-old female patient was hospitalized due to the purulent discharge of the left ear and the symptoms of right mastoiditis(swelling and redness of the skin).Diagnosis:Bilateral acute coalescent mastoiditis caused by S.pneumoniae infection.The computer tomography revealed bilateral bone destruction of the mastoid and abscesses found behind the auricle on both sides.Interventions:The patient underwent intravenous antibiotic therapy and surgical treatment.Outcomes:The patient was discharged 14 days after hospitalization with an improved condition.Lessons:Improperly treated acute coalescent mastoiditis can lead to extracranial and intracranial complications,sometimes serious and even life-threatening.Complications are prevalent in children under 2 years,in whom the disease progresses more rapidly and severely.The vaccination with a 13-valent vaccine may not result in sufficient immunity against S.pneumoniae,a predominant pathogen in children affected by acute coalescent mastoiditis.
基金supported by the Fundamental Research Funds for the Central Universities(2023JBMC011)the National Natural Science Foundation of China(NSFC)Grant(12271026)the Beijing Natural Science Foundation Grant(L222051).
文摘Identical-by-descent(IBD)is a fundamental genomic characteristic in population genetics and has been widely used for population history reconstruction.However,limited by the nature of IBD,which could only capture the relationship between two individuals/haplotypes,existing IBD-based history inference is constrained to two populations.In this study,we propose a framework by leveraging IBD sharing in multipopulation and develop a method,MatrixiBD,to reconstruct recent multi-population migration history.Specifically,we employ the structured coalescent theory to precisely model the genealogical process and then estimate the IBD sharing across multiple populations.Within our model,we establish a theoretical connection between migration history and IBD sharing.Our method is rigorously evaluated through simulations,revealing its remarkable accuracy and robustness.Furthermore,we apply MatrixiBD to Central and South Asia in the Human Genome Diversity Project and successfully reconstruct the recent migration history of three closely related populations in South Asia.By taking into account the IBD sharing across multiple populations simultaneously,MatrixlBD enables us to attain clearer and more comprehensive insights into the history of regions characterized by complex migration dynamics,providing a holistic perspective on intricate patterns embedded within the recent population migration history.
文摘The Gamma-Dirichlet algebra corresponds to the decomposition of the gamma process into the independent product of a gamma random variable and a Dirichlet process. This structure allows us to study the properties of the Dirichlet process through the gamma process and vice versa. In this article, we begin with a brief survey of several existing results concerning this structure. New results are then obtained for the large deviations of the jump sizes of the gamma process and the quasi-invariance of the two-parameter Poisson-Dirichlet distribution. We finish the paper with the derivation of the transition function of the Fleming-Viot process with parent independent mutation from the transition function of the measure-valued branching diffusion with immigration by exploring the Gamma-Dirichlet algebra embedded in these processes. This last result is motivated by an open R. C. Gritfiths. problem proposed by S. N. Ethier and
文摘Genetic variability plays a key role in the biology and medical treatment of RNA viruses. As an RNA virus, Hepatitis C virus (HCV) replicate as complex distributions of closely related genomes termed viral quasispecies. The behavior of the evolving HCV quasispecies population is influenced by the ensemble of mutants that compose the viral population. One such influence is the presence of minority subpopulations, termed memory genomes, in the mutant spectra. Biologically relevant mutants have been previously observed to be present as memory genomes in RNA viral populations. For that reason, an in-depth analysis of HCV quasispecies populations is crucial for our understanding viral evolution, drug resistance and therapy outcome. Recently developed next-generation sequencing (NGS) platforms make it possible to investigate viral quasispecies at much greater detail. In order to gain insight into these matters, we have performed a Bayesian coalescent analysis of hypervariable region 1 (HVR1) sequences of a HCV quasispecies population circulating in a chronic patient, recently obtained by ultra-deep sequencing. The results of these studies revealed a mean rate of evolution of HCV HVR1 of the intra-host quasispecies population of 4.80 × 10-2 amino acid substitutions/site/year. A sharp and rapid diversification of the HCV quasispecies isolated from the patient in three different sub-populations was observed. The most abundant sequence in the quasispecies population was not found to be the center of a tight and complex network around this sequence, suggesting that the quasispecies population as a whole efficiently explore a wide sequence space. Co-evolution of relevant amino acid sites had been identified in the HVR1. This speaks of the possible roll of these residues in HVR1 to allow the virus to shift between combinations of residues to escape the immune system while retaining its structure and functions. The results of these studies highlight the importance of minority genomes in HCV population history and evolution, t
基金the Florida International University Tropics Program and the Susan S.Levine Trust.RTK and ELB also received support from the United States National Science Foundation(DEB-1118823 and DEB-1655683).
文摘Background: Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a consistent topology, including introgression, incomplete lineage sorting, different data types, or insufficient data.Methods: We generated three novel whole genome assemblies for Gallus species, which we combined with data from the published genomes of Gallus gallus and Bambusicola thoracicus(a member of the sister genus to Gallus). To determine why previous studies have failed to converge on a single topology, we extracted large numbers of orthologous exons, introns, ultra-conserved elements, and conserved non-exonic elements from the genome assemblies. This provided more than 32 million base pairs of data that we used for concatenated maximum likelihood and multispecies coalescent analyses of Gallus.Results: All of our analyses, regardless of data type, yielded a single, well-supported topology. We found some evidence for ancient introgression involving specific Gallus lineages as well as modest data type effects that had an impact on support and branch length estimates in specific analyses. However, the estimated gene tree spectra for all data types had a relatively good fit to their expectation given the multispecies coalescent.Conclusions: Overall, our data suggest that conflicts among previous studies probably reflect the use of smaller datasets(both in terms of number of sites and of loci) in those analyses. Our results demonstrate the importance of sampling large numbers of loci, each of which has a sufficient number of sites to provide robust estimates of gene trees. Low-coverage whole genome sequencing, as we did here, represents a cost-effective means to generate the very large data sets that include multiple data types that enabled us to obtain a robust estimate of Gallus phylogeny.
文摘Chaotic genetic patchiness （CGP） refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene flow via larval dispersal. Here we review and discuss 4 mechanisms that could generate such unexpected patterns： selection, sweepstakes reproductive success, collective dispersal, and temporal shifts in local population dynamics. First, we review examples where genetic differentiation at specific loci was driven by diversifying selection, which was historically the first process invoked to explain CGP. Second, we turn to neutral demographic processes that may drive genome-wide effects, and whose effects on CGP may be enhanced when they act together. We discuss how sweepstakes reproductive success accelerates genetic drift and can thus generate genetic structure, provided that gene flow is not too strong. Collective dispersal is another mechanism whereby genetic structure can be maintained regardless of dispersal intensity, because it may prevent larval cohorts from becoming entirely mixed. Theoretical analyses of both the sweepstakes and the collective dispersal ideas are presented. Finally, we discuss an idea that has received less attention than the other ones just mentioned, namely temporal shifts in local population dynamics.
