近年来,分子钟定年方法(molecular dating methods)得以广泛运用,为宏观进化研究尤其是生物多样性及其格局形成历史的相关研究提供了不可或缺且十分详尽的进化时间框架。贝叶斯方法(Bayesianmethods)和马尔可夫链蒙特卡罗方法(Markov ch...近年来,分子钟定年方法(molecular dating methods)得以广泛运用,为宏观进化研究尤其是生物多样性及其格局形成历史的相关研究提供了不可或缺且十分详尽的进化时间框架。贝叶斯方法(Bayesianmethods)和马尔可夫链蒙特卡罗方法(Markov chain Monte Carlo)可容纳多维度、多类型的数据和参数设置,因此以BEAST、PAML-MCMCTree等软件为代表的贝叶斯节点标记法(Bayesian node-dating methods)逐渐成为分子钟定年方法中最为广泛使用的类型。贝叶斯框架的优势之一在于其可以利用复杂模型考虑各种不确定性因素,但是该类方法中各类模型和参数的设置都可能引入误差,从而影响进化分化时间估算的可靠性。本文介绍了贝叶斯分子钟定年方法的原理和主要类型,并以贝叶斯节点标记法为例,重点讨论了分子钟模型、化石标记的选择与放置、采样频率及化石标记点年龄先验分布等因素对节点定年的影响;提供了贝叶斯时间树构建软件的使用建议、节点年龄的讨论原则和不同模型下时间树的比较方法,针对常见的引起节点年龄潜在高估和低估风险的情况作了分析并给出了合理化建议。我们认为,合理整合多种贝叶斯方法和模型得出的结果并从中择优,能够提高定年结果的可靠性;研究人员应对时间树构建结果与其参数设置的关系开展讨论,从而为其他学者提供参考;化石记录的更新与分子钟定年方法的改进应同步不断跟进。展开更多
A plethora of studies investigating the origin and evolution of diverse mountain taxa has assumed a causal link between geological processes （orogenesis） and a biological response （diversification）. Yet, a substan...A plethora of studies investigating the origin and evolution of diverse mountain taxa has assumed a causal link between geological processes （orogenesis） and a biological response （diversification）. Yet, a substantial delay （up to 30 Myr） between the start of orogenesis and diversification is often observed. Evolutionary biologists should therefore identify alternative drivers of diversification and maintenance of biodiversity in mountain systems. Using phylogenetic, biogeographic, and diversification rate analyses, we could identify two independent processes that most likely explain the diversity of the widespread genus Allium in the Qinghai-Tibet Plateau （QTP） region： （1） While the QTP-related taxa of the subgenus Melanocrommyum diversified in situ, （2） QTP-related taxa of other subgenera migrated into the QTP from multiple source areas. Furthermore, shifts in diversification rates within Allium could not be attributed spatially and temporally to the uplift history of the QTP region. Instead, global cooling and climate oscillations in the Quaternary were major contributors to increased speciation rates in three clades of AUium. Our study therefore adds to the growing evidence supporting the ＂mountain-geo-biodiversity hypothesis＂, which highlights the role of climate oscillations for the diversification of mountain organisms.展开更多
Lagerstroemia L.(Lythraceae)is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia,with numerous species highly valued as ornamentals.Althoug...Lagerstroemia L.(Lythraceae)is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia,with numerous species highly valued as ornamentals.Although the plastomes of many species in this genus have been sequenced,the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined.We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses.Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods.Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility.These results as well as analyses of non-synonymous and synonymous mutations,indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution.In addition,divergence events within the Lagerstroemia were dated for the first time.Several of the divergence estimates corresponded to well-known Earth history events,such as the reduction in global temperatures at the Eocene/Oligocene boundary.Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders,as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species.展开更多
Animal genetic resources are playing a vital role in livestock production and are essential to food security. The present study aims to contribute to a better understanding genetic local sheep breeds and to elucidate ...Animal genetic resources are playing a vital role in livestock production and are essential to food security. The present study aims to contribute to a better understanding genetic local sheep breeds and to elucidate the phylogenetic relationships through the evolution of the SRY gene in four different lineages of Ladoum sheep raised in Senegal. After a brief analysis of genetic diversity, the phylogenetic relationships and molecular dating were inferred through haplotype networks and four phylogenetic reconstruction methods. The different haplotype networks are constructed with NETWORK ver. 5.0.0.0 using the Median-Joining method. Phylogenetic trees were reconstructed using neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference. The robustness of the nodes in phylogenetic trees of the three first methods was assessed by 1000 bootstraps. For Bayesian inference, the posterior probability distribution of the trees was estimated by 4 MCMC chains. 5,000,000 generations were performed for each of the chains by sampling the different parameters every 1000 generations. Results show a low polymorphism. Haplotypic diversity is much higher than the average nucleotide divergence between all pairs of haplotypes. The majority and central haplotype indicates a close relationship between “Batling” and “Tyson” individuals. “Birahim” lineage is very distinct from the rest. Phylogenetic trees confirm two genetically separate clades between “Birahim” and the other lineages. The period of divergence between “Birahim” lineage versus the common ancestor of the other three lineages was 2504 years ago. The polyphyly revealed in “Birahim” lindicates that this lineage does not contain the common ancestor of all individuals who compose it. It could therefore be derived from two or more sheep breeds with a common ancestor, Ovis aries. The monophyletic clade appears to be a group including a common ancestor and all of its genetic descendants. This group, bringing together the other three lineag展开更多
A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable. A possible method for eudicots is to use a large phylogen...A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable. A possible method for eudicots is to use a large phylogeny calibrated using deep fossils including tricolpate pollen as a fixed （124 mya） calibration point. This method was used to calculate node ages within three species-poor disjunct basal eudicot genera, Caulophyllum, Podophyllum and Pachysandra, and sensitivity of these ages to effects such as taxon sampling were then quantified. By deleting from one to three accessions related to each genus in 112 different combinations, a confidence range describing variation due only to taxon sampling was generated. Ranges for Caulophyllum, Podophyllum and Pachysandra were 8.4-10.6, 7.6-20.0, and 17.6-25.0 mya, respectively. However, the confidence ranges calculated using bootstrapping were much wider, at 3-19, 0-32 and 11-32 mya, respectively. Furthermore, deleting 10 adjacent taxa had a large effect in Pachysandra only, indicating that undersampling effects are significant among Buxales. Changes to sampling density in neighboring clades, or to the position of the fixed fossil calibration point had small to negligible effects. Non-parametric rate smoothing was more sensitive to taxon sampling effects than was penalized likelihood. The wide range for Podophyllum, compared to the other two genera, was probably due to a high degree of rate heterogeneity within this genus. Confidence ranges calculated by this method could be narrowed by sampling more individuals within the genus of interest, and by sequencing multiple DNA regions from all species in the phylogeny.展开更多
Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and th...Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to （i） demonstrate the effects of partitioned phylo- genetic analyses on phylogeny reconstruction of cyprinid fishes; （ii） provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major mono- phyletic groups within Cyprinidae： （Cyprininae, Labeoninae）, （（Acheilognathinae, （（Leuciscinae, Tincinae）, Gobioninae））, Xenocyprirlinae）. The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family.展开更多
苋科(Amaranthaceaesensulato)是石竹目(Caryophyllales)第二大科,目前被普遍接受的苋科为其广义概念,含狭义苋科(Amaranthaceae sensu stricto)和藜科(Chenopodiaceae)。然而到目前为止,藜科是否应作为独立的科还存在争议。此外,广义...苋科(Amaranthaceaesensulato)是石竹目(Caryophyllales)第二大科,目前被普遍接受的苋科为其广义概念,含狭义苋科(Amaranthaceae sensu stricto)和藜科(Chenopodiaceae)。然而到目前为止,藜科是否应作为独立的科还存在争议。此外,广义苋科内部各亚科之间的系统关系也尚未厘清。对广义苋科所有13个亚科代表类群进行取样(共59种),基于8个叶绿体序列片段重建其系统发育关系,并结合分子钟估算,对该科及其主要分支的起源与分化时间进行推测。结果表明,广义苋科与狭义苋科都是很好的单系,但藜科并非单系,因此不支持藜科在科级水平的地位,支持广义苋科的观点。除了多节草亚科(Polycnemoideae)之外,其它亚科的系统位置均得到很好的分辨。分子钟估算结果表明,广义苋科于白垩纪晚期约69.9Ma分化出该科的2个主要分支,且该科在白垩纪-古近纪边界附近时期(约66.0Ma)可能发生过快速辐射分化事件。展开更多
The Permian Basin is a unique ecosystem located in the southwest of the USA.An unanswered question is whether the bacteria in the Permian Basin adapted to the changing paleomarine environment and survived in the remna...The Permian Basin is a unique ecosystem located in the southwest of the USA.An unanswered question is whether the bacteria in the Permian Basin adapted to the changing paleomarine environment and survived in the remnants of Permian groundwater.In our previous study,a novel bacterial strain,Permianibacter aggregans HW001T,was isolated from micro-algae cultures incubated with Permian Basin waters,and was shown to originate from the Permian Ocean.In this study,strain HW001T was shown to be the representative strain of a novel family,classified as‘Permianibacteraceae’.The results of molecular dating suggested that the strain HW001T diverged~447 million years ago(mya),which is the early Permian period(~250 mya).Genome analysis was used to access its potential energy utilization and biosynthesis capacity.A large number of transporters,carbohydrate-active enzymes and protein-degradation related genes have been annotated in the genome of strain HW001T.In addition,a series of important metabolic pathways,such as peptidoglycan biosynthesis,osmotic stress response system and multifunctional quorum sensing were annotated,which may confer the ability to adapt to vari-ous unfavorable environmental conditions.Finally,the evolutionary history of strain HW001T was reconstructed and the horizontal transfer of genes was predicted,indicating that the adaptation of P.aggregans to a changing marine environment depends on the evolution of their metabolic capabilities,especially in signal transmission.In conclusion,the results of this study provide genomic information for revealing the adaptive mechanism of strain HW001T to the changing ancient oceans.展开更多
Although significant achievements have shown that the coronavirus disease 2019(COVID‐19)resurgence in Beijing,China,was initiated by contaminated frozen products and transported via cold chain transportation,internat...Although significant achievements have shown that the coronavirus disease 2019(COVID‐19)resurgence in Beijing,China,was initiated by contaminated frozen products and transported via cold chain transportation,international travelers with asymptomatic symptoms or false‐negative nucleic acid may have another possible transmission mode that spread the virus to Beijing.One of the key differences between these two assumptions was whether the virus actively replicated since,so far,no reports showed viruses could stop evolution in alive hosts.We studied severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)sequences in this outbreak by a modified leaf‐dating method with the Bayes factor.The numbers of single nucleotide variants(SNVs)found in SARS‐CoV‐2 sequences were significantly lower than those called from B.1.1 records collected at the matching time worldwide(P=0.047).In addition,results of the leaf‐dating method showed ages of viruses sampled from this outbreak were earlier than their recorded dates of collection(Bayes factors>10),while control sequences(selected randomly with ten replicates)showed no differences in their collection dates(Bayes factors<10).Our results which indicated that the re‐emergence of SARS‐CoV‐2 in Beijing in June 2020 was caused by a virus that exhibited a lack of evolutionary changes compared to viruses collected at the corresponding time,provided evolutionary evidence to the contaminated imported frozen food should be responsible for the reappearance of COVID‐19 cases in Beijing.The method developed here might also be helpful to provide the very first clues for potential sources of COVID‐19 cases in the future.展开更多
Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based o...Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeog- raphy are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously be- lieved that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicaziance in several groups. Moreover, the possibility of speciation having occurred before the said geo- logical event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations al- ways result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided展开更多
Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitut...Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitution rates of Gnetales （Ephedra, Gnetum, and Welwitschia） has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species （and 7736 aligned nucleotides） to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.展开更多
文摘近年来,分子钟定年方法(molecular dating methods)得以广泛运用,为宏观进化研究尤其是生物多样性及其格局形成历史的相关研究提供了不可或缺且十分详尽的进化时间框架。贝叶斯方法(Bayesianmethods)和马尔可夫链蒙特卡罗方法(Markov chain Monte Carlo)可容纳多维度、多类型的数据和参数设置,因此以BEAST、PAML-MCMCTree等软件为代表的贝叶斯节点标记法(Bayesian node-dating methods)逐渐成为分子钟定年方法中最为广泛使用的类型。贝叶斯框架的优势之一在于其可以利用复杂模型考虑各种不确定性因素,但是该类方法中各类模型和参数的设置都可能引入误差,从而影响进化分化时间估算的可靠性。本文介绍了贝叶斯分子钟定年方法的原理和主要类型,并以贝叶斯节点标记法为例,重点讨论了分子钟模型、化石标记的选择与放置、采样频率及化石标记点年龄先验分布等因素对节点定年的影响;提供了贝叶斯时间树构建软件的使用建议、节点年龄的讨论原则和不同模型下时间树的比较方法,针对常见的引起节点年龄潜在高估和低估风险的情况作了分析并给出了合理化建议。我们认为,合理整合多种贝叶斯方法和模型得出的结果并从中择优,能够提高定年结果的可靠性;研究人员应对时间树构建结果与其参数设置的关系开展讨论,从而为其他学者提供参考;化石记录的更新与分子钟定年方法的改进应同步不断跟进。
基金the German Research Foundation for funding of staff (project no. MU 2934/2-1)the support of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig funded by the German Research Foundation (FZT 118) for funding of lab expenses
文摘A plethora of studies investigating the origin and evolution of diverse mountain taxa has assumed a causal link between geological processes （orogenesis） and a biological response （diversification）. Yet, a substantial delay （up to 30 Myr） between the start of orogenesis and diversification is often observed. Evolutionary biologists should therefore identify alternative drivers of diversification and maintenance of biodiversity in mountain systems. Using phylogenetic, biogeographic, and diversification rate analyses, we could identify two independent processes that most likely explain the diversity of the widespread genus Allium in the Qinghai-Tibet Plateau （QTP） region： （1） While the QTP-related taxa of the subgenus Melanocrommyum diversified in situ, （2） QTP-related taxa of other subgenera migrated into the QTP from multiple source areas. Furthermore, shifts in diversification rates within Allium could not be attributed spatially and temporally to the uplift history of the QTP region. Instead, global cooling and climate oscillations in the Quaternary were major contributors to increased speciation rates in three clades of AUium. Our study therefore adds to the growing evidence supporting the ＂mountain-geo-biodiversity hypothesis＂, which highlights the role of climate oscillations for the diversification of mountain organisms.
基金supported by the Zhejiang Provincial Natural Science Foundation of China(Grant No.LY21C160001)Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants.
文摘Lagerstroemia L.(Lythraceae)is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia,with numerous species highly valued as ornamentals.Although the plastomes of many species in this genus have been sequenced,the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined.We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses.Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods.Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility.These results as well as analyses of non-synonymous and synonymous mutations,indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution.In addition,divergence events within the Lagerstroemia were dated for the first time.Several of the divergence estimates corresponded to well-known Earth history events,such as the reduction in global temperatures at the Eocene/Oligocene boundary.Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders,as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species.
文摘Animal genetic resources are playing a vital role in livestock production and are essential to food security. The present study aims to contribute to a better understanding genetic local sheep breeds and to elucidate the phylogenetic relationships through the evolution of the SRY gene in four different lineages of Ladoum sheep raised in Senegal. After a brief analysis of genetic diversity, the phylogenetic relationships and molecular dating were inferred through haplotype networks and four phylogenetic reconstruction methods. The different haplotype networks are constructed with NETWORK ver. 5.0.0.0 using the Median-Joining method. Phylogenetic trees were reconstructed using neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference. The robustness of the nodes in phylogenetic trees of the three first methods was assessed by 1000 bootstraps. For Bayesian inference, the posterior probability distribution of the trees was estimated by 4 MCMC chains. 5,000,000 generations were performed for each of the chains by sampling the different parameters every 1000 generations. Results show a low polymorphism. Haplotypic diversity is much higher than the average nucleotide divergence between all pairs of haplotypes. The majority and central haplotype indicates a close relationship between “Batling” and “Tyson” individuals. “Birahim” lineage is very distinct from the rest. Phylogenetic trees confirm two genetically separate clades between “Birahim” and the other lineages. The period of divergence between “Birahim” lineage versus the common ancestor of the other three lineages was 2504 years ago. The polyphyly revealed in “Birahim” lindicates that this lineage does not contain the common ancestor of all individuals who compose it. It could therefore be derived from two or more sheep breeds with a common ancestor, Ovis aries. The monophyletic clade appears to be a group including a common ancestor and all of its genetic descendants. This group, bringing together the other three lineag
基金NERC (fellowship NE/B500658/1) for the financial support that made this work possible
文摘A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable. A possible method for eudicots is to use a large phylogeny calibrated using deep fossils including tricolpate pollen as a fixed （124 mya） calibration point. This method was used to calculate node ages within three species-poor disjunct basal eudicot genera, Caulophyllum, Podophyllum and Pachysandra, and sensitivity of these ages to effects such as taxon sampling were then quantified. By deleting from one to three accessions related to each genus in 112 different combinations, a confidence range describing variation due only to taxon sampling was generated. Ranges for Caulophyllum, Podophyllum and Pachysandra were 8.4-10.6, 7.6-20.0, and 17.6-25.0 mya, respectively. However, the confidence ranges calculated using bootstrapping were much wider, at 3-19, 0-32 and 11-32 mya, respectively. Furthermore, deleting 10 adjacent taxa had a large effect in Pachysandra only, indicating that undersampling effects are significant among Buxales. Changes to sampling density in neighboring clades, or to the position of the fixed fossil calibration point had small to negligible effects. Non-parametric rate smoothing was more sensitive to taxon sampling effects than was penalized likelihood. The wide range for Podophyllum, compared to the other two genera, was probably due to a high degree of rate heterogeneity within this genus. Confidence ranges calculated by this method could be narrowed by sampling more individuals within the genus of interest, and by sequencing multiple DNA regions from all species in the phylogeny.
基金supported by the National Natural Science Foundation of China (Grant No. 30770300)Chinese Academy of Sciences (Grant No. KSCX2-EW-Q-12)the Cypriniformes Tree of Life Initiative supported by the USA National Science Foundation (Grant No. EF-0431326)
文摘Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to （i） demonstrate the effects of partitioned phylo- genetic analyses on phylogeny reconstruction of cyprinid fishes; （ii） provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major mono- phyletic groups within Cyprinidae： （Cyprininae, Labeoninae）, （（Acheilognathinae, （（Leuciscinae, Tincinae）, Gobioninae））, Xenocyprirlinae）. The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family.
文摘苋科(Amaranthaceaesensulato)是石竹目(Caryophyllales)第二大科,目前被普遍接受的苋科为其广义概念,含狭义苋科(Amaranthaceae sensu stricto)和藜科(Chenopodiaceae)。然而到目前为止,藜科是否应作为独立的科还存在争议。此外,广义苋科内部各亚科之间的系统关系也尚未厘清。对广义苋科所有13个亚科代表类群进行取样(共59种),基于8个叶绿体序列片段重建其系统发育关系,并结合分子钟估算,对该科及其主要分支的起源与分化时间进行推测。结果表明,广义苋科与狭义苋科都是很好的单系,但藜科并非单系,因此不支持藜科在科级水平的地位,支持广义苋科的观点。除了多节草亚科(Polycnemoideae)之外,其它亚科的系统位置均得到很好的分辨。分子钟估算结果表明,广义苋科于白垩纪晚期约69.9Ma分化出该科的2个主要分支,且该科在白垩纪-古近纪边界附近时期(约66.0Ma)可能发生过快速辐射分化事件。
基金Funding for this study was provided by the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory(Guang-zhou)(GML2019ZD0606)National Natural Science Foundation of China(92051118)+1 种基金Guangdong Science and Technology Department(2019A1515011139)2020 Li Ka Shing Foundation(LKSF)Cross-Disciplinary Research Grant(2020LKSFG07A).
文摘The Permian Basin is a unique ecosystem located in the southwest of the USA.An unanswered question is whether the bacteria in the Permian Basin adapted to the changing paleomarine environment and survived in the remnants of Permian groundwater.In our previous study,a novel bacterial strain,Permianibacter aggregans HW001T,was isolated from micro-algae cultures incubated with Permian Basin waters,and was shown to originate from the Permian Ocean.In this study,strain HW001T was shown to be the representative strain of a novel family,classified as‘Permianibacteraceae’.The results of molecular dating suggested that the strain HW001T diverged~447 million years ago(mya),which is the early Permian period(~250 mya).Genome analysis was used to access its potential energy utilization and biosynthesis capacity.A large number of transporters,carbohydrate-active enzymes and protein-degradation related genes have been annotated in the genome of strain HW001T.In addition,a series of important metabolic pathways,such as peptidoglycan biosynthesis,osmotic stress response system and multifunctional quorum sensing were annotated,which may confer the ability to adapt to vari-ous unfavorable environmental conditions.Finally,the evolutionary history of strain HW001T was reconstructed and the horizontal transfer of genes was predicted,indicating that the adaptation of P.aggregans to a changing marine environment depends on the evolution of their metabolic capabilities,especially in signal transmission.In conclusion,the results of this study provide genomic information for revealing the adaptive mechanism of strain HW001T to the changing ancient oceans.
基金This work was supported by the National Natural Science Foundation of China(Grant number:82041023)the Bill&Melinda Gates Foundation(Grant number:INV‐016826)China Mega‐Projects for Infectious Disease(2018ZX10711001,2017ZX10104001).
文摘Although significant achievements have shown that the coronavirus disease 2019(COVID‐19)resurgence in Beijing,China,was initiated by contaminated frozen products and transported via cold chain transportation,international travelers with asymptomatic symptoms or false‐negative nucleic acid may have another possible transmission mode that spread the virus to Beijing.One of the key differences between these two assumptions was whether the virus actively replicated since,so far,no reports showed viruses could stop evolution in alive hosts.We studied severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)sequences in this outbreak by a modified leaf‐dating method with the Bayes factor.The numbers of single nucleotide variants(SNVs)found in SARS‐CoV‐2 sequences were significantly lower than those called from B.1.1 records collected at the matching time worldwide(P=0.047).In addition,results of the leaf‐dating method showed ages of viruses sampled from this outbreak were earlier than their recorded dates of collection(Bayes factors>10),while control sequences(selected randomly with ten replicates)showed no differences in their collection dates(Bayes factors<10).Our results which indicated that the re‐emergence of SARS‐CoV‐2 in Beijing in June 2020 was caused by a virus that exhibited a lack of evolutionary changes compared to viruses collected at the corresponding time,provided evolutionary evidence to the contaminated imported frozen food should be responsible for the reappearance of COVID‐19 cases in Beijing.The method developed here might also be helpful to provide the very first clues for potential sources of COVID‐19 cases in the future.
文摘Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeog- raphy are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously be- lieved that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicaziance in several groups. Moreover, the possibility of speciation having occurred before the said geo- logical event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations al- ways result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided
基金supported,in part,by the National Science Foundation (USA)-Emerging Frontiers,Assembling the Tree of Life,Collaborative Research:Gymnosperms on the Tree of Life:Resolving the Phylogeny of Seed Plants (Grant No. EF-0629657 to SMI-B)supported by the Swedish Research Council (grants to CR)
文摘Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitution rates of Gnetales （Ephedra, Gnetum, and Welwitschia） has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species （and 7736 aligned nucleotides） to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.
基金supported by the 100 Young Talents Program of Chinese Academy of Sciences and partly supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB26000000)~~
