Detecting Small Amounts of Gene Flow from Phylogenies of Alleles

The method of coalescents is used to find the probability that none of the ancestors of alleles sampled from a population are immigrants. If that is the case for samples from two or more populations, then there would be concordance between the phylogenies of those alleles and the geographic locations from which they are drawn. This type of concordance has been found in several studies of mitochondrial DNA from natural populations. It is shown that if the number of sequences sampled from each population is reasonably large (10 or more), then this type of concordance suggests that the average number of individuals migrating between populations is likely to be relatively small (Nm less than 1) but the possibility of occasional migrants cannot be excluded. The method is applied to the data of E. Bermingham and J. C. Avise on mtDNA from the bowfin, Amia calva.     

Detecting Isolation by Distance Using Phylogenies of Genes

We introduce a method for analyzing phylogenies of genes sampled from a geographically structured population. A parsimony method can be used to compute s, the minimum number of migration events between pairs of populations sampled, and the value of s can be used to estimate the effective migration rate M, the value of Nm in an island model with local populations of size N and a migration rate m that would yield the same value of s. Extensive simulations show that there is a simple relationship between M and the geographic distance between pairs of samples in one- and two-dimensional models of isolation by distance. Both stepping-stone and lattice models were simulated. If two demes k steps apart are sampled, then, s, the average value of s, is a function only of k/(Nm) in a one-dimensional model and is a function only of k/(Nm)2 in a two-dimensional model. Furthermore, log(M) is approximately a linear function of log(k). In a one-dimensional model, the regression coefficient is approximately -1 and in a two-dimensional model the regression coefficient is approximately -0.5. Using data from several locations, the regression of log(M) on log(distance) may indicate whether there is isolation by distance in a population at equilibrium and may allow an estimate of the effective migration rate between adjacent sampling locations. Alternative methods for analyzing DNA sequence data from a geographically structured population are discussed. An application of our method to the data of R. L. Cann, M. Stoneking and A. C. Wilson on human mitochondrial DNA is presented.     

洱海鲤属鱼类同域分化形成的分子遗传学证据

对洱海的 3种鲤鱼———洱海鲤 (C .barbatus)、春鲤 (C .longipectoralis)和杞麓鲤 (C .carpiochila)线粒体DNA(mtDNA)进行了限制性片段长度多态 (RFLP)分析和mtDNA控制区 (D loop)序列测定。RFLP分析结果表明 ,16种酶在洱海鲤、春鲤和杞麓鲤 3个种共 14个个体上 ,仅DraⅠ在春鲤的一个个体上检出一个位点的限制性片段长度多态 ,独立为单倍型Ⅱ ,3个种的其余 13个个体共享单倍型Ⅰ ,种间遗传距离为 0 %～ 0 0 0 75 % ,此种间差异值比已报道的鱼类的种间差异甚至种内差异都低得多。D loop区的序列测定结果表明 ,长为 4 4 9bp的序列共显示有 7个变异位点 ,均为碱基替换 ,变异比例为 1 5 6 % ,在 14个鲤鱼个体中共检出 6种单倍型 ,种间的遗传距离为 0 0 82 %～ 0 171% ,与已研究的其他几种异域分布的鲤鱼相比 ,也至少小一个数量级。mtDNA的RFLP及D loop区的序列比较都揭示出洱海 3种鲤鱼之间的遗传差异远小于异域分布的鲤属鱼类物种之间及其他鱼类的同属种间的遗传差异。对洱海鲤属鱼类种间如此小的遗传差异唯一合理的解释就是 :它们确是由同域分化而形成的。     

犁头鳅属鱼类物种地理分化过程

犁头鳅属为中国的特有属,包括犁头鳅和长鳍犁头鳅两个物种,犁头鳅广泛分布于长江中上游,而长鳍犁头鳅则局限分布于闽江水系。本研究对采自长江中上游的犁头鳅20个个体和闽江水系的长鳍犁头鳅8个个体的线粒体细胞色素b（cyt b）基因序列进行分析,以期对犁头鳅属鱼类的物种地理分化过程进行研究。结果显示,犁头鳅不同单倍型之间的遗传变异水平为0.1%—1.8％,平均为0.7%;长鳍犁头鳅各单倍型之间的遗传变异水平为0.6%—1.3%,平均为0.7%;犁头鳅和长鳍犁头鳅单倍型之间的遗传差异也较小,仅为0.2%—1.8%,平均为0.9%。采用邻接(NJ)法和贝叶斯(BI)法构建的分子系统发育树一致显示,该研究中的犁头鳅属鱼类构成一个单系;所有长鳍犁头鳅样本构成一个单系,位于系统发育树的顶部位置;犁头鳅的样本不构成单系,而是形成并系。从形态上看,犁头鳅和长鳍犁头鳅均为有效种。由此推测,在第四纪冰期,长江中下游的犁头鳅沿东海大陆架向南扩散到东南沿海水系,长鳍犁头鳅可能是犁头鳅的一个种群扩散到闽江水系后,由于适应新的环境条件而分化成的一个新物种,剩下的长江流域的犁头鳅种群则构成一个并系类群。本文对于类似的地理物种形成方式也进行了讨论。     

峨眉山2种重楼属植物同域分化的分子遗传学及其形态学证据初探

对峨眉山2种重楼－小重楼（Paris polyphylla Smith var. minora S.F.Wang）、黒籽重楼（P. thibetica Franch）DNA进行了AFLP (扩增的限制性片段长度多态性)分析和形态上的差异分析。AFLP分析可知小重楼和黑籽重楼在DNA分子水平上表现出极为丰富的遗传多样性,每个种内个体间的相似性很大,但有明显种间的遗传差异。形态对比分析可知小重楼和黑籽重楼在花部性状上有明显的差异。AFLP和形态分析结果表明小重楼和黑籽重楼无论是在形态还是遗传上均有明显差异。它们之间已经有了明显的分化。     

峨眉山2种重楼属植物同域分化的分子遗传学及其形态学证据初探

对峨眉山2种重楼-小重楼（Paris polyphylla Smith vat．minora S．F．Wang）、黑籽重楼（P．thibetica Franch）DNA进行了AFLP（扩增的限制性片段长度多态性）分析和形态上的差异分析。AFLP分析可知小重楼和黑籽重楼在DNA分子水平上表现出极为丰富的遗传多样性,每个种内个体间的相似性很大,但有明显种间的遗传差异。形态对比分析可知小重楼和黑籽重楼在花部性状上有明显的差异。AFLP和形态分析结果表明小重楼和黑籽重楼无论是在形态还是遗传上均有明显差异。它们之间已经有了明显的分化。     

A Cladistic Measure of Gene Flow Inferred from the Phylogenies of Alleles

A method for estimating the average level of gene flow among populations is introduced. The method provides an estimate of Nm, where N is the size of each local population in an island model and m is the migration rate. This method depends on knowing the phylogeny of the nonrecombining segments of DNA that are sampled. Given the phylogeny, the geographic location from which each sample is drawn is treated as multistate character with one state for each geographic location. A parsimony criterion applied to the evolution of this character on the phylogeny provides the minimum number of migration events consistent with the phylogeny. Extensive simulations show that the distribution of this minimum number is a simple function of Nm. Assuming the phylogeny is accurately estimated, this method provides an estimate of Nm that is as nearly as accurate as estimates obtained using FST and other statistics when Nm is moderate. Two examples of the use of this method with mitochondrial DNA data are presented.     

粉条儿菜属(肺筋草科)的地理分布及其物种多样性和分化中心

粉条儿菜属(AletrisL.)隶属于肺筋草科,全世界有23种1变种,东亚有18种1变种,北美东南部有5种,为典型的东亚-北美间断分布的属.本文在种(变种)的水平上,研究了粉条儿菜属的地理分布及其分布中心和多样化中心,并对其起源和分化以及现代洲际间断分布格局的成因进行了分析.结果表明,(1)中国共分布有粉条儿菜属植物15种1变种,而广义的横断山地区集中分布有13种1变种,是东亚粉条儿菜属植物分布最为集中的地区,而且包含该属植物各个进化阶段的代表.因此,广义的横断山地区是粉条儿菜属在东亚的分布中心和多样化中心.(2)根据粉条儿菜属及其近缘属的分布格局推测,该属可能在不晚于第三纪早期,起源于古北大陆.东亚和北美的粉条儿菜属植物形态区别明显,应该是隔离分化的结果.(3)该属植物可能曾经广布于北半球,后来地质、气候以及冰川等因素的变化,导致该属在一些地区灭绝,而仅存于东亚和北美东南部.(4)尽管横断山及其周边地区是东亚粉条儿菜属的多样化中心,但该地区很可能并不是粉条儿菜属最早的分化中心,因横断山地区周边的一些特有种可能是在晚近的时期形成的新特有种;另外,东亚粉条儿菜属一些原始的种类主要分布于我国中东部到日本一带.所以,中国中东部到日本一带可能是粉条儿菜属早期的分化中心.     

Congruent Avian Phylogenies Inferred from Mitochondrial and Nuclear DNA Sequences

Recent molecular studies addressing the phylogenetic relationships of avian orders have had conflicting results. While studies using nuclear DNA sequences tend to support traditional taxonomic views, also supported by morphological data [(paleognaths (galloanseres (all other birds)))], with songbirds forming a clade within Neoaves (all other birds), analyses with complete mtDNA genomes have resulted in topologies that place songbirds as one of the earliest-diverging avian lineages. Considering that over half of the extant bird species are songbirds, these different results have very different implications for our understanding of avian evolution. We analyzed data sets comprising nearly 4 kb of mitochondrial DNA (mtDNA) (complete 12S, ND1, ND2, and cytochrome b) plus 600 bp of the nuclear gene c-mos for 15 birds that were chosen to represent all major avian clades and to minimize potential long-branch attraction problems; we used a partition-specific maximum likelihood approach. Our results show congruence with respect to the ingroup among phylogenies obtained with mtDNA and the nuclear gene c-mos, separately or combined. The data sets support a traditional avian taxonomy, with paleognaths (ratites and tinamous) occupying a basal position and with songbirds more derived and forming a monophyletic group. We also show that, for mtDNA studies, turtles may be a better outgroup for birds than crocodilians because of their slower rate of sequence evolution.     

世界蓑藓属植物分布式样及其系统演化和生物地理学意义

蓑藓属（Macromitrium）是苔藓植物分类、生态学研究及生物多样性保护的重要类群。以“Index Muscorum”中的14个藓类植物地理分布单位为分析区域,基于标本信息和相关文献,在分类修订的基础上,统计了世界蓑藓属274种植物在14个地理单位的分布数据,基于这些数据,应用聚类分析和除趋势对应分析法,分别得到了14个地理单位的聚类图和三维空间图,直观展示了世界蓑藓属植物的地理分布格局。发现蓑藓属植物区系在东亚（As2）、大洋洲（Oc）、南亚和东南亚（As3,As4）、非洲（Afr2,Afr3,Afr4）、中美洲-南美洲（Am2,Am3,Am4,Am5）、澳洲（Austr1,Austr2）存在区域分化。热带亚洲和热带美洲是世界蓑藓属植物的多样化中心。除长柄蓑藓（M.microstomum（Hook.&Grev.）Schwägr.）在14个地理单位均有分布外,大部分种类分布限于少数或仅一个地理单位。蓑藓属植物在东亚、热带亚洲、热带美洲和澳洲不仅种类存在明显分化,而且形态性状也有区域特点。根据蓑藓属植物的现代分布式样,探讨了其系统演化和生物地理学意义。     

Log Transformation Improves Dating of Phylogenies

Phylogenetic trees inferred from sequence data often have branch lengths measured in the expected number of substitutions and therefore, do not have divergence times estimated. These trees give an incomplete view of evolutionary histories since many applications of phylogenies require time trees. Many methods have been developed to convert the inferred branch lengths from substitution unit to time unit using calibration points, but none is universally accepted as they are challenged in both scalability and accuracy under complex models. Here, we introduce a new method that formulates dating as a nonconvex optimization problem where the variance of log-transformed rate multipliers is minimized across the tree. On simulated and real data, we show that our method, wLogDate, is often more accurate than alternatives and is more robust to various model assumptions.     

Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin

One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΔΔG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution.     

永瓣藤的地理分布及其种群空间格局

应用Ｇｒｅｉｇ－Ｓｍｉｔｈ邻接格子取样法,研究了我国珍稀植物永瓣藤（ＭｏｎｉｍｏｐｅｔａｌｕｎｃｈｉｎｅｎｓｅＲｅｈｄ）,的地理分布和种群空间格局及其形成机制,分析了其克隆生长格局和生态适应对策,研究结果表明,永瓣藤的分布区域狭窄,其种群空间格局为集群型,克隆生长格避为游击式稀疏形式样式,这与其生物学特性和种群生态适应的对策密切相关。     

Congruence of Morphological and Molecular Phylogenies

When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant for the molecular partition. Because the level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be underestimated by congruence within partitions. Thus comparisons between morphological and molecular trees are particularly useful for detecting this incongruence (spurious or otherwise). Molecular trees have higher average congruence than morphological trees, but the difference is not significant, and both within- and between-partition incongruence is much lower than expected by chance alone. Our results suggest that both molecular and morphological trees are, in general, useful approximations of a common underlying phylogeny and thus, when molecules and morphology clash, molecular phylogenies should not be considered more reliable a priori.     

Phylogenies of Flying Squirrels (Pteromyinae)

The phylogeny of flying squirrels was assessed, based on analyses of 80 morphological characters. Three published hypotheses were tested with constraint trees and compared with trees based on heuristic searches, all using PAUP*. Analyses were conducted on unordered data, on ordered data (Wagner), and on ordered data using Dollo parsimony. Compared with trees based on heuristic searches, the McKenna (1962) constraint trees were consistently the longest, requiring 8–11 more steps. The Mein (1970) constraint trees were shorter, requiring five to seven steps more than the unconstrained trees, and the Thorington and Darrow (2000) constraint trees were shorter yet, zero to one step longer than the corresponding unconstrained tree. In each of the constraint trees, some of the constrained nodes had poor character support. The heuristic trees provided best character support for three groups, but they did not resolve the basal trichotomy between a Glaucomys group of six genera, a Petaurista group of four genera, and a Trogopterus group of four genera. The inclusion of the small northern Eurasian flying squirrel, Pteromys, in the Petaurista group of giant South Asian flying squirrels is an unexpected hypothesis. Another novel hypothesis is the inclusion of the genus Aeromys, large animals from the Sunda Shelf, with the Trogopterus group of smaller "complex-toothed flying squirrels" from mainland Malaysia and southeast Asia. We explore the implications of this study for future analysis of molecular data and for past and future interpretations of the fossil record.     

中国湿润半湿润地区啮类动物的分布格局

系统收集并整理了我国湿润半湿润地区啮类动物的地理分布资料,基于GIS技术,通过生境分析,确定了每个物种的分布范围,采用6470 km2的等面积栅格作为地理分布单元,系统研究我国湿润半湿润地区啮类动物地理分布规律.我国湿润半湿润地区有啮类动物156种,隶属于2目、12科、62属,占我国啮类动物总数的71.23%.地理单元的物种丰富度分析结果表明,云南西部到四川中部的横断山区、陕西秦岭和甘肃南部山地的啮类动物丰富度较高;河北省东南部、山东、河南、江苏、安徽的长江以北地区及长江三角洲、湖南和湖北的沿江地区以及四川盆地等地物种丰富度较低.地理单元有无物种分布的层次聚类分析结果表明,我国湿润半湿润地区分为三大区域:东部季风区的南北两区(以长江下游-秦岭一线分界),以及青藏高原的半湿润区.     

浙闽樱桃地理分布模拟及气候限制因子分析

为了解浙闽樱桃(Cerasus schneideriana)地理分布特征及与气候限制因子之间的关系,基于DIVA-GIS平台获取实际地理分布点的气候资料,利用BIOCLIM模型预测当下适生区范围以及预测其未来潜在分布。结果表明,浙闽樱桃实际分布区覆盖浙江、福建、安徽、江西、广西及湖南6省,浙闽交界的山区是自然分布的核心区,浙皖交界是其分布的北界。未来气候变化情境(CCM3)下,浙闽樱桃的潜在分布区概率将增大,且有北扩的趋势。主成分分析(PCA)表明,年降水量(bio12)、最湿季降雨量(bio16)、最暖季降雨量(bio18)、温度季节变化方差(bio4)是影响浙闽樱桃当下适生区的气候限制因子,频率直方图进一步确定他们的适宜范围分别为1503~2003 mm、604~951 mm、528~791 mm和601~872(标准差*100)。ROC曲线检验表明BIOCLIM对浙闽樱桃分布预测的精度很高(AUC=0.998),结果是可信的。因此,浙闽樱桃适合生长在我国北亚热带温暖湿润区,水热因子是造成其分布格局的主导气候限制因子。