Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies

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

Estimation of time of divergence from phylogenetic studies.

Recent studies with comparative data on base sequences of homologous DNA's or amino acid sequences of homologous proteins indicate that simultaneous estimation of phylogenetic structure and time of divergence is often cumbersome and time consuming. On the other hand, when the topology of an evolutionary tree is known, it is shown in this paper that the least squares theory may be applied to obtain simple estimates of the relative time lengths for each segment of the tree under the assumption of uniform random substitutions in each segment. The method is illustrated with amino acid sequence data on various globin molecules and cytochrome c. The evolutionary significance of some of the estimates is also discussed.     

Molecular distance and divergence time in carnivores and primates

Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the results of empirical studies conflict and are difficult to compare because they differ widely in their choice of taxa, genetic techniques, or methods for calibrating rates of molecular evolution. We use a single methodology to analyze the relationship of molecular distance and divergence time in 86 taxa (72 carnivores and 14 primates). These taxa have divergence times of 0.01-55 Myr and provide a graded series of phylogenetic divergences such that the shape of the curve relating genetic distance and divergence time is often well defined. The techniques used to obtain genetic distance estimates include one- and two-dimensional protein electrophoresis, DNA hybridization, and microcomplement fixation. Our results suggest that estimates of molecular distance and divergence time are highly correlated. However, rates of molecular evolution are not constant; rather, in general they decline with increasing divergence time in a linear fashion. The rate of decline may differ according to technique and taxa. Moreover, in some cases the variability in evolutionary rates changes with increasing divergence time such that the accuracy of nodes in a phylogenetic tree varies predictably with time.     

新疆裂腹鱼类的系统发生关系及物种分化时间

文章采用线粒体COI、ND4、16S rRNA基因联合数据分析了新疆分布的裂腹鱼类4属10个种或亚种的分子系统发育,并通过鲤亚科的分化时间、黄河上游和青海湖隔离的地质时间来校正分子钟,进而探讨了裂腹鱼类分化时间与塔里木盆地周边地区主要地质事件和气候变化的关系。结果发现,扁吻鱼属未能形成独立的分支,与塔里木裂腹鱼、厚唇裂腹鱼聚在一起。进一步基于COI基因序列,利用Kimura双参数模型计算遗传距离,发现扁吻鱼属和裂腹鱼属间的遗传距离未达到属间区别,扁吻鱼可能是裂腹鱼属内特化的物种;聚类分析结果不同于裂腹鱼属的形态学分类方法,不支持裂腹鱼属鱼类的亚属划分;原始等级裂腹鱼类(包括裂腹鱼属和扁吻鱼属)两个族群的分化时间(8.18 Ma)与新疆裸重唇鱼和斑重唇鱼的分化时间(7.67 Ma)均发生于晚中新世,这可能与8Ma左右青藏高原北缘和北天山抬升、塔里木盆地气候干旱化等重大地质事件和气候转型导致青藏高原北缘(昆仑山)和北天山水系间出现分离相关。而塔里木盆地裂腹鱼属鱼类现今的分布格局可能与第四纪喜马拉雅运动使盆地形成西高东低的地势、罗布泊成为塔里木盆地周边高山发源河流的汇水中心相关。     

Exploring the impact of fossil constraints on the divergence time estimates of derived liverworts

In this study, we evaluate the impact of fossil assignments and different models of calibration on divergence time estimates carried out as Bayesian analyses. Estimated ages from preceding studies and liverwort inclusions from Baltic amber are used as constraints on a molecular phylogeny of Cephaloziineae (Jungermanniopsida) obtained from sequences of two chloroplast coding regions: rbcL and psbA. In total, the comparison of 12 different analyses demonstrates that an increased reliability of the chronograms is linked to the number of fossils assigned and to the accuracy of their assignments. Inclusion of fossil constraints leads to older ages of most crown groups, but has no influence on lineage through time plots suggesting a nearly constant accumulation of diversity since the origin of Cephaloziineae in the early to Middle Jurassic. Our results provide a note of caution regarding the interpretation of chronograms derived from DNA sequence variation of extant species based on a single calibration point and/or low accuracy of the assignment of fossils to nodes in the phylogeny.     

Sequence divergence at the putative flowering time locus COL1 in Brassicaceae

An insertion/deletion polymorphism (Ind2) in the Brassica nigra CONSTANS LIKE 1 (Bni COL1) gene was previously found to be associated with variation in flowering time. In the present study we examine the inter-specific divergence of COL1 in the family Brassicaceae. Analysis of codon substitution models did not reveal evidence of positive Darwinian selection, but comparisons of the COL1 gene in different species revealed a surprising number of indels. A total of 24 indels were found in the 650 bp of the middle variable region of the gene. This high number of indels could reflect a lack of constraint on length of this region of the protein, or the effect of positive selection. The number of indels was close to that expected in non-coding DNA, but the indels were longer in COL1 than those observed in non-coding regions. Reconstruction of indel evolution indicated that most indels resulted from deletions rather than insertions. The Ind2 indel that has shown association with flowering time in Brassica nigra exhibited a remarkable distribution in the Brassicaceae family, indicating that the polymorphism may have persisted more than ten million years. Considering presumed historic populations sizes of Brassicaceae species, such a long persistence time seems unlikely for a neutral polymorphism.     

以演化时间为新增指标构建真菌分类系统

随着分子系统发育研究的普及,真菌各分类类群逐渐被修订为单系发生类群,通常结合形态学特征为代表的表型特征("单系+表型特征")对不同的分类等级命名是最为普遍的方法.历史上存在的大量多系名称被逐步修订、补充和完善,各个不同等级类群的分类系统变得更加合理、客观和趋于自然,这是分类学进程中巨大的进步.然而系统发育重建所揭示的单...     

Calibrated tree priors for relaxed phylogenetics and divergence time estimation

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently, Bayesian Markov chain Monte Carlo has become the dominant method of divergence time estimation, and fossil evidence has been reinterpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting hashave not been carefully investigated. Here, we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis.     

The roles of speciation and divergence time in the loss of duplicate gene expression

In 50 million years the tetraploid catostomid fishes have lost the expression of approximately half of their duplicate genes, with species rich taxa having lost more than species poor taxa. We have constructed a phylogenetic tree of the catostomids based primarily on morphological data, and have estimated the divergence times from the fossil record and genetic distances. The losses of duplicate gene expression were then analyzed conditionally given this tree. Three probabilistic models were generated to describe the process of loss of gene expression: gene dysfunction depends on (1) time alone, (2) the number of speciation events alone, or (3) a combination of speciation and time. A maximum likelihood analysis revealed that the two component model fits the data better than the other models. The loss of duplicate gene expression is mediated by null mutations at structural and/or regulatory genes, and the rate of fixation of these nulls might have been enhanced by any reductions in population size accompanying speciation events. This reduction may explain the lower number of duplicate genes expressed in the more speciose taxa.     

Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation

The selection of fossil data to use as calibration age priors in molecular divergence time estimates inherently links neontological methods with paleontological theory. However, few neontological studies have taken into account the possibility of a taphonomic bias in the fossil record when developing approaches to fossil calibration selection. The Sppil-Rongis effect may bias the first appearance of a lineage toward the recent causing most objective calibration selection approaches to erroneously exclude appropriate calibrations or to incorporate multiple calibrations that are too young to accurately represent the divergence times of target lineages. Using turtles as a case study, we develop a Bayesian extension to the fossil selection approach developed by Marshall (2008. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibrations points. Am. Nat. 171:726-742) that takes into account this taphonomic bias. Our method has the advantage of identifying calibrations that may bias age estimates to be too recent while incorporating uncertainty in phylogenetic parameter estimates such as tree topology and branch lengths. Additionally, this method is easily adapted to assess the consistency of potential calibrations to any one calibration in the candidate pool.     

Revisiting the phylogeny of Ranunculeae: Implications for divergence time estimation and historical biogeography

Previous studies based on different molecular datasets have generated conflicting topologies for Ranunculeae. Here, we revisit the phylogeny of Ranunculeae by analyzing the individual matK/trnK, psbJ-petA, and internal transcribed spacer (ITS) data, the combined matK/trnK, psbJ-petA, and ITS dataset, and the combinedrbcL, trnL-F, matK/trnK, psbJ-petA, and ITS dataset. Based on the tree-based comparisons, blast searches against NCBI of the sequences, and close examination of the alignment, we found that 10 psbJ-petA sequences previously used were questionable (erroneous or problematic) and responsible for previous conflicting topologies. After omitting these questionable sequences, we provide a new phylogeny for Ranunculeae, in which Beckwithia–Cyrtorhyncha, Kumlienia, andPeltocalathos were replaced. These new replacements are supported by corresponding morphological characters. Moreover, three previously proposed intercontinental disjunct distributions within Ranunculus were also refuted. In our framework, our divergence time and biogeographic analyses indicate that divergence time estimates and the ancestral areas reconstructed for 10 of the 15 nodes in the genus-level phylogeny were influenced by elimination of the questionable sequences. The most recent common ancestor of Ranunculeae was inferred to be present in Europe and North America during the late Eocene. Clades I and II began to diversify in Europe and North America, respectively, and subsequently migrated to other continents. This study shows that it is necessary to analyze individual chloroplast DNA region datasets separately to detect questionable sequences early in the study. The combined dataset including the questionable sequences resulted in an erroneous phylogenetic tree, and the use of this tree subsequently affected age estimates and biogeographic analyses.     

Precision and accuracy of divergence time estimates from STR and SNPSTR variation

Inference of intraspecific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels of homoplasy and varying mutational properties, often leading to inaccurate inference of population divergence. A SNPSTR is a genetic system that consists of an STR polymorphism closely linked (typically < 500 bp) to one or more single-nucleotide polymorphisms (SNPs). SNPSTR systems are characterized by lower levels of homoplasy than are STR loci. Divergence time estimates based on STR variation (on the derived SNP allele background) should, therefore, be more accurate and precise. We use coalescent-based simulations in the context of several models of demographic history to compare divergence time estimates based on SNPSTR haplotype frequencies and STR allele frequencies. We demonstrate that estimates of divergence time based on STR variation on the background of a derived SNP allele are more accurate (3% to 7% bias for SNPSTR versus 11% to 20% bias for STR) and more precise than STR-based estimates, conditional on a recent SNP mutation. These results hold even for models involving complex demographic scenarios with gene flow, population expansion, and population bottlenecks. Varying the timing of the mutation event generating the SNP revealed that estimates of divergence time are sensitive to SNP age, with more recent SNPs giving more accurate and precise estimates of divergence time. However, varying both mutational properties of STR loci and SNP age demonstrated that multiple independent SNPSTR systems provide less biased estimates of divergence time. Furthermore, the combination of estimates based separately on STR and SNPSTR variation provides insight into the age of the derived SNP alleles. In light of our simulations, we interpret estimates from data for human populations.     

Gene arrangement,phylogeny and divergence time estimation of mitogenomes in Thrips

Molecular Biology Reports - The metazoan mitogenomes usually display conserved gene arrangement while thrips are known for their extensive gene rearrangement, and duplication of the control region....     

Transmission of single and multiple viral variants in primary HIV-1 subtype C infection

To address whether sequences of viral gag and env quasispecies collected during the early post-acute period can be utilized to determine multiplicity of transmitted HIV's, recently developed approaches for analysis of viral evolution in acute HIV-1 infection [1,2] were applied. Specifically, phylogenetic reconstruction, inter- and intra-patient distribution of maximum and mean genetic distances, analysis of Poisson fitness, shape of highlighter plots, recombination analysis, and estimation of time to the most recent common ancestor (tMRCA) were utilized for resolving multiplicity of HIV-1 transmission in a set of viral quasispecies collected within 50 days post-seroconversion (p/s) in 25 HIV-infected individuals with estimated time of seroconversion. The decision on multiplicity of HIV infection was made based on the model's fit with, or failure to explain, the observed extent of viral sequence heterogeneity. The initial analysis was based on phylogeny, inter-patient distribution of maximum and mean distances, and Poisson fitness, and was able to resolve multiplicity of HIV transmission in 20 of 25 (80%) cases. Additional analysis involved distribution of individual viral distances, highlighter plots, recombination analysis, and estimation of tMRCA, and resolved 4 of the 5 remaining cases. Overall, transmission of a single viral variant was identified in 16 of 25 (64%) cases, and transmission of multiple variants was evident in 8 of 25 (32%) cases. In one case multiplicity of HIV-1 transmission could not be determined. In primary HIV-1 subtype C infection, samples collected within 50 days p/s and analyzed by a single-genome amplification/sequencing technique can provide reliable identification of transmission multiplicity in 24 of 25 (96%) cases. Observed transmission frequency of a single viral variant and multiple viral variants were within the ranges of 64% to 68%, and 32% to 36%, respectively.     

Electrophoretically estimated genetic distance and divergence time between chimpanzee and man

Amount of genetic differentiation between chimpanzee and man was estimated from the result of comparative electrophoretic screening of blood protein variations at 32 independent genetic loci. TheNei's genetic distance (D) was calculated as 0.4514, and from this value the divergence time between the two species was estimated as 2.26 million years; considering the variation among amino-acid substitution rate in different proteins, the corrected figures were given as genetic distance of 0.5706 and divergence time of 2.85 million years. This genetic difference is considered too small the two species to be allocated in different families, in accordance with the results of the similar kind of analyses byKing andWilson (1975) and Bruce andAyala (1979). Discussions were made for a discrepancy between the divergence times estimated by using and not by using the splitting time recognized by paleoprimatologists as a reference, and for the difference in the estimations made in different laboratories.     

Molecular phylogeny of the Canary Island lacertids (Gallotia): mitochondrial DNA restriction fragment divergence in relation to sequence divergence and geological time

Restriction fragment length polymorphisms of 6 base pair recognising endonucleases are used to reconstruct the phylogeny of the endemic Canary Island lacertid, Gallotia. The division into conventional species is upheld by this molecular analysis and the western Canary Island lizard (G. galloti) and eastern Canary Island lizard (G. atlantica) are hypothesized to be sister species. A more comprehensive study of the intraspecific relationships of G. galloti, based on nineteen restriction enzymes, indicates that there are distinct southern and northern lineages within this species. The phylogenetic analysis does not uphold the conventional subspecies, but suggests an alternative arrangement with one northern (La Palma, Tenerife) and one southern (Gomera, Hierro) subspecies. The inferred timing of molecular divergence of populations of G. galloti, based on RFLP analysis, is compatible with the geological timing for island origin and fossil data. Mantel tests show that mitochondrial RFLP divergence is correlated with mitrochondrial 12s rRNA and cytochrome oxidase I sequence divergence and highly correlated with mitochondrial cytochrome b sequence divergence.     

Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection

Estimates of species divergence times using DNA sequence data are playing an increasingly important role in studies of evolution, ecology and biogeography. Most work has centred on obtaining appropriate kinds of data and developing optimal estimation procedures, whereas somewhat less attention has focused on the calibration of divergences using fossils. Case studies with multiple fossil calibration points provide important opportunities to examine the divergence time estimation problem in new ways. We discuss two cross-validation procedures that address different aspects of inference in divergence time estimation. 'Fossil cross-validation' is a procedure used to identify the impact of different individual calibrations on overall estimation. This can identify fossils that have an exceptionally large error effect and may warrant further scrutiny. 'Fossil-based model cross-validation' is an entirely different procedure that uses fossils to identify the optimal model of molecular evolution in the context of rate smoothing or other inference methods. Both procedures were applied to two recent studies: an analysis of monocot angiosperms with eight fossil calibrations and an analysis of placental mammals with nine fossil calibrations. In each case, fossil calibrations could be ranked from most to least influential, and in one of the two studies, the fossils provided decisive evidence about the optimal molecular evolutionary model.