Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds

We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates. We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. In particular, we use soft bounds, so that the probability that the true divergence time is outside the bounds is small but nonzero. A strict molecular clock is assumed in the current implementation, although this assumption may be relaxed. We apply our new algorithm to two data sets concerning divergences of several primate species, to examine the effects of the substitution model and of the prior for divergence times on Bayesian time estimation. We also conduct computer simulation to examine the differences between soft and hard bounds. We demonstrate that divergence time estimation is intrinsically hampered by uncertainties in fossil calibrations, and the error in Bayesian time estimates will not go to zero with increased amounts of sequence data. Our analyses of both real and simulated data demonstrate potentially large differences between divergence time estimates obtained using soft versus hard bounds and a general superiority of soft bounds. Our main findings are as follows. (1) When the fossils are consistent with each other and with the molecular data, and the posterior time estimates are well within the prior bounds, soft and hard bounds produce similar results. (2) When the fossils are in conflict with each other or with the molecules, soft and hard bounds behave very differently; soft bounds allow sequence data to correct poor calibrations, while poor hard bounds are impossible to overcome by any amount of data. (3) Soft bounds eliminate the need for "safe" but unrealistically high upper bounds, which may bias posterior time estimates. (4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict.     

Biogeographic calibrations for the molecular clock

Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.     

The impact of fossils and taxon sampling on ancient molecular dating analyses

The number and complexity of molecular dating studies has increased over the past decade. Along with a broadening acceptance of their utility has come significant controversy over the methods and models that are appropriate, as well as the accuracy of the estimates yielded by molecular clock analyses. Radically different age estimates have been published for the same divergences from analyses of different datasets with different fossil constraints obtained with different methods, and the underlying explanation for these differences is often unclear. Here we utilize two previously published datasets to examine the effect of fossil calibrations and taxon sampling on the age estimates for two deep eukaryote divergences in an attempt to discern the relative impact of these factors. Penalized likelihood, non-parametric rate smoothing, and Bayesian methods were utilized to generate age estimates for the origin of the Metazoa from a 7-gene dataset and for the divergence of Eukaryotes from a 129-gene dataset. From these analyses, it is clear that the fossil calibrations chosen and the method for applying constraints to these nodes have a large impact on age estimates, while the degree of taxon sampling within a dataset is less important in terms of the resulting age estimates. Concerns and recommendations for addressing these two factors when initiating a dating analysis are discussed.     

Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.     

Exploring uncertainty in the calibration of the molecular clock

Calibration is a critical step in every molecular clock analysis but it has been the least considered. Bayesian approaches to divergence time estimation make it possible to incorporate the uncertainty in the degree to which fossil evidence approximates the true time of divergence. We explored the impact of different approaches in expressing this relationship, using arthropod phylogeny as an example for which we established novel calibrations. We demonstrate that the parameters distinguishing calibration densities have a major impact upon the prior and posterior of the divergence times, and it is critically important that users evaluate the joint prior distribution of divergence times used by their dating programmes. We illustrate a procedure for deriving calibration densities in Bayesian divergence dating through the use of soft maximum constraints.     

Fossil calibrations and molecular divergence time estimates in centrarchid fishes (Teleostei: Centrarchidae)

Molecular clock methods allow biologists to estimate divergence times, which in turn play an important role in comparative studies of many evolutionary processes. It is well known that molecular age estimates can be biased by heterogeneity in rates of molecular evolution, but less attention has been paid to the issue of potentially erroneous fossil calibrations. In this study we estimate the timing of diversification in Centrarchidae, an endemic major lineage of the diverse North American freshwater fish fauna, through a new approach to fossil calibration and molecular evolutionary model selection. Given a completely resolved multi-gene molecular phylogeny and a set of multiple fossil-inferred age estimates, we tested for potentially erroneous fossil calibrations using a recently developed fossil cross-validation. We also used fossil information to guide the selection of the optimal molecular evolutionary model with a new fossil jackknife method in a fossil-based model cross-validation. The centrarchid phylogeny resulted from a mixed-model Bayesian strategy that included 14 separate data partitions sampled from three mtDNA and four nuclear genes. Ten of the 31 interspecific nodes in the centrarchid phylogeny were assigned a minimal age estimate from the centrarchid fossil record. Our analyses identified four fossil dates that were inconsistent with the other fossils, and we removed them from the molecular dating analysis. Using fossil-based model cross-validation to determine the optimal smoothing value in penalized likelihood analysis, and six mutually consistent fossil calibrations, the age of the most recent common ancestor of Centrarchidae was 33.59 million years ago (mya). Penalized likelihood analyses of individual data partitions all converged on a very similar age estimate for this node, indicating that rate heterogeneity among data partitions is not confounding our analyses. These results place the origin of the centrarchid radiation at a time of major faunal turnover as the fossil record indicates that the most diverse lineages of the North American freshwater fish fauna originated at the Eocene-Oligocene boundary, approximately 34 mya. This time coincided with major global climate change from warm to cool temperatures and a signature of elevated lineage extinction and origination in the fossil record across the tree of life. Our analyses demonstrate the utility of fossil cross-validation to critically assess individual fossil calibration points, providing the ability to discriminate between consistent and inconsistent fossil age estimates that are used for calibrating molecular phylogenies.     

Melastomeae come full circle: biogeographic reconstruction and molecular clock dating

Rhexia, with 11 species in the Coastal Plain province of North America, is the only temperate zone endemic of the tropical eudicot family Melastomataceae. It is a member of the only pantropical tribe of that family, Melastomeae. Based on the chloroplast gene ndhF, we use a fossil-calibrated molecular clock to address the question of the geographic origin and age of Rhexia. Sequences from 37 species in 21 genera representing the tribe's geographical range were analyzed together with five outgroups. To obtain better clade support, another chloroplast region, the rpl16 intron, was added for 24 of the species. Parsimony analysis of the combined data and maximum-likelihood analysis of ndhF alone indicate that the deepest split is between Rhexia plus its sister group, a small Central American genus, and all other Melastomeae. Old World Melastomeae are monophyletic and nested within New World Melastomeae. Although likelihood-ratio tests of clock and nonclock substitution models for the full or moderately pruned datasets rejected the clock, these models yielded identical topologies (for 30 taxa) with few significantly different branch lengths as assessed by a Student's t-test. Age estimates obtained were 22 million years ago (Mya) for the divergence of Rhexia from its sister group, 12 Mya for the dispersal of Melastomeae from the New World to West Africa, and 1 Mya for the diversification of Melastoma in Southeast Asia. The only other genus of Melastomeae to have reached Southeast Asia from Africa or Madagascar is Osbeckia. The age and geographic distribution of fossils, which come from Miocene sites throughout Eurasia, suggest that Melastomeae once ranged from Eurasia across Beringia to North America from whence they reached South America and subsequently Africa and Southeast Asia. Climate deterioration led to their extinction in the Northern Hemisphere, with Rhexia possibly surviving in Coastal Plain refugia.     

Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards

Background  

Although current molecular clock methods offer greater flexibility in modelling evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate the evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates.     

Bayesian identification of admixture events using multilocus molecular markers

Bayesian statistical methods for the estimation of hidden genetic structure of populations have gained considerable popularity in the recent years. Utilizing molecular marker data, Bayesian mixture models attempt to identify a hidden population structure by clustering individuals into genetically divergent groups, whereas admixture models target at separating the ancestral sources of the alleles observed in different individuals. We discuss the difficulties involved in the simultaneous estimation of the number of ancestral populations and the levels of admixture in studied individuals' genomes. To resolve this issue, we introduce a computationally efficient method for the identification of admixture events in the population history. Our approach is illustrated by analyses of several challenging real and simulated data sets. The software (baps), implementing the methods introduced here, is freely available at http://www.rni.helsinki.fi/~jic/bapspage.html.     

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra‐ and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within‐population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter‐ and intraspecies branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior on Bayesian divergence time estimates by analysing computer‐simulated data sets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non‐Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyse data sets containing both populations and species variation when its computational efficiency is needed.     

Tectonic blocks and molecular clocks

Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.     

The origin of a mega‐diverse genus: dating Begonia (Begoniaceae) using alternative datasets,calibrations and relaxed clock methods

Begonia is a mega‐diverse genus comprising c. 1500 species of herbs, shrubs and epiphytes with a near pantropical distribution. Previous date estimates for the most recent common ancestor of Begonia have placed the evolution of this genus into a broad temporal context, but the issue of an absolute date estimate remains open. In this study, we attempt to estimate absolute DNA divergence dates for Begonia and, in doing so, address some of many the factors that can affect such estimates. The largest source of variance in our estimates was because of uncertainty with the calibration constraints and phylogenetic distance between these constraints and Begonia. Another large source of variance was due to the alternative methods of analysis investigated. Less variance was as a result of the alternative DNA datasets and combinations of calibration constraints assessed. Our date estimates suggest that the most recent common ancestor of Begonia could have diversified from the end of the Cretaceous to the beginning of the Neogene, probably during a period of global cooling from the mid Eocene to early Oligocene. These estimates imply that the near pantropical distribution of extant Begonia was generated by intercontinental dispersal after the ancient inferred break up of the supercontinent, Gondwana. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 363–380.     

Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences

The temperate South American lizard genus Liolaemus is the one of the most widely distributed and species‐rich genera of lizards on earth. The genus is divided into two subgenera, Liolaemus sensu stricto (the ‘Chilean group’) and Eulaemus (the ‘Argentino group’), a division that is supported by recent molecular and morphological data. Owing to a lack of reliable fossil data, previous studies have been forced to use either global molecular clocks, a standardized mutation rate adopted from previous studies, or the use of geological events as calibration points. However, simulations indicate that these types of assumptions may result in less accurate estimates of divergence times when clock‐like models or mutation rates are violated. We used a multilocus data set combined with a newly described fossil to provide the first calibrated phylogeny for the crown groups of the clade Eulaemus, and derive new fossil‐calibrated substitution rates (with error) of both nuclear and mtDNA gene regions for Eulaemus specifically. Divergence date estimates for each of the crown groups and appropriate rate estimates will provide the foundation for understanding rates of speciation, historical biogeography, and phylogeographical history for various clades in one of the most diverse lizard genera in the poorly studied Patagonian region. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 825–835.     

The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses

Background  

Ectomycorrhizae (ECM) are symbioses formed by polyphyletic assemblages of fungi (mostly Agaricomycetes) and plants (mostly Pinaceae and angiosperms in the rosid clade). Efforts to reconstruct the evolution of the ECM habit in Agaricomycetes have yielded vastly different results, ranging from scenarios with many relatively recent origins of the symbiosis and no reversals to the free-living condition; a single ancient origin of ECM and many subsequent transitions to the free-living condition; or multiple gains and losses of the association. To test the plausibility of these scenarios, we performed Bayesian relaxed molecular clock analyses including fungi, plants, and other eukaryotes, based on the principle that a symbiosis cannot evolve prior to the origin of both partners. As we were primarily interested in the relative ages of the plants and fungi, we did not attempt to calibrate the molecular clock using the very limited fossil record of Agaricomycetes.     

Phylogenetics of global Camellia (Theaceae) based on three nuclear regions and its implications for systematics and evolutionary history

Camellia contains tea, oil camellia, and camellias which benefit people globally. Its infrageneric classification is, however, controversial and unstable, and former phylogenetic analyses failed to yield robust and consistent trees. Here, we aimed to reconstruct a robust phylogenetic tree, date all clades and discuss the evolutionary history of Camellia. Emphasizing the taxonomically comprehensive sampling rather than more DNA data, orthologous nuclear RPB2 introns 11–15 and 23, and waxy were sequenced for 99 taxa of Camellia to reconstruct its phylogenetic history. Ten clades are identified in Camellia: Camellia II, Camelliopsis, Corallina, Furfuracea, Heterogenea, Paracamellia, Piquetia, Stereocarpus, Thea and Yellow camellias II. Camellia grijsii and C. shensiensis are not closely related with other oil camellias that form the clade Paracamellia. Sections Camelliopsis and Theopsis together form the clade Camelliopsis, while clade Furfuracea consists of sect. Furfuracea and C. hongkongensis. Camellia connata is separated from C. lanceolata but nested in the clade Heterogenea, and C. longissima is nested in the clade Thea, suggesting a new germplasm for tea breeding. Molecular dating using four fossil calibration points suggests that the crown age of Camellia is 39.5 Ma with clade Corallina probably the earliest infrageneric clade to diversify and the most widespread clade, Paracamellia, the latest. Our findings provide new insights into the phylogenetic relationships, systematics and evolutionary history of Camellia.     

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock

Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.     

Effects of taxon sampling on molecular dating for within-genus divergence events, when deep fossils are used for calibration

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.     

Multiple fossil calibrations,nuclear loci and mitochondrial genomes provide new insight into biogeography and divergence timing for true seals (Phocidae,Pinnipedia)

Aim To better understand the historical biogeography of the true seals, Phocidae, by combining nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) in a divergence time analysis using multiple fossil calibrations. Location Arctic, Antarctic, Pacific and Atlantic Oceans, Lake Baikal, Caspian Sea. Methods Fifteen nuclear genes totalling 8935 bp plus near‐complete mitochondrial genome sequences were used in a Bayesian divergence time analysis, incorporating eight soft‐bound fossil calibrations across the phylogeny. All species of true seals were included, plus the walrus, three otariids and seven carnivore outgroups. The majority of the nuclear sequences and four phocid mitochondrial genomes (plus three non‐phocid mitochondrial genomes) were newly generated for this study using DNA extracted from tissue samples; other sequences were obtained from GenBank. Results Using multiple nuclear genes and multiple fossil calibrations resulted in most divergence time estimations within Phocidae being much more recent than predicted by other molecular studies incorporating only mtDNA and using a single calibration point. A new phylogenetic hypothesis was recovered for the Antarctic seals. Main conclusions Incorporating multiple nuclear genes and fossil calibrations had a profound effect on the estimated divergence times. Most estimated divergences within Phocinae (Arctic seals) correspond to Arctic oceanic events and all occur within the last 12 Myr, a time when the Arctic and Atlantic oceans were freely exchanging and perennial Arctic sea ice existed, indicating that the Arctic seals may have had a longer association with ice than previously thought. The Monachinae (‘southern’ seals) split from the Phocinae c. 15 Ma on the eastern US coast. Several early trans‐Atlantic dispersals possibly occurred, leaving no living descendants, as divergence estimates suggest that the Monachus (monk seal) species divergences occurred in the western Atlantic c. 6 Ma, with the Mediterranean monk seal ancestor dispersing afterwards. The tribes Lobodontini (Antarctic seals) and Miroungini (elephant seals) are also estimated to have diverged in the eastern Atlantic c. 7 Ma and a single Lobodontini dispersal to Antarctica occurred shortly afterwards. Many of the newly estimated dates are used to infer how extinct lineages/taxa are allied with their living relatives.     

主流分子钟定年方法的原理、误差来源和使用建议

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(Bayesian methods)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。