PATTERNS IN PHYLOGENETIC TREE BALANCE WITH VARIABLE AND EVOLVING SPECIATION RATES

Aspects of phylogenetic tree shape, and in particular tree balance, provide clues to the workings of the macroevolutionary process. I use a simulation approach to explore patterns in tree balance for several models of the evolutionary process under which speciation rates vary through the history of diversifying clades. I demonstrate that when speciation rates depend on an evolving trait of individuals, and are therefore “heritable” along evolutionary lineages, the resulting phylogenies become imbalanced. However, imbalance also results from some (but not all) models of “nonheritable” speciation rate variation. The degree of imbalance increases with the magnitude of speciation rate variation, and then for gradual evolution (but not punctuated equilibria) reaches an asymptote short of the theoretical maximum. Very high levels of rate variation are required to produce imbalance matching that found in real data (estimated phylogenies from the systematic literature). I discuss implications of the simulation results for our understanding of macroevolution.     

SEARCHING FOR EVOLUTIONARY PATTERNS IN THE SHAPE OF A PHYLOGENETIC TREE

If all species in a clade are equally likely to speciate or become extinct, then highly symmetric and highly asymmetric phylogenetic trees are unlikely to result. Variation between species in speciation and extinction rates can cause excessive asymmetry. We developed six non-parametric statistical tests that test for nonrandom patterns of branching in any bifurcating tree. The tests are demonstrated by applying them to two published phylogenies for genera of beetles. Comparison of the power of the six statistics under a simple model of biased speciation suggests which of them may be most useful for detecting nonrandom tree shapes.     

USING PHYLOGENETIC TREES TO STUDY SPECIATION AND EXTINCTION

One tool in the study of the forces that determine species diversity is the null, or simple, model. The fit of predictions to observations, good or bad, leads to a useful paradigm or to knowledge of forces not accounted for, respectively. It is shown how simple models of speciation and extinction lead directly to predictions of the structure of phylogenetic trees. These predictions include both essential attributes of phylogenetic trees: lengths, in the form of internode distances; and topology, in the form of internode links. These models also lead directly to statistical tests which can be used to compare predictions with phylogenetic trees that are estimated from data. Two different models and eight data sets are considered. A model without species extinction consistently yielded predictions closer to observations than did a model that included extinction. It is proposed that it may be useful to think of the diversification of recently formed monophyletic groups as a random speciation process without extinction.     

Geographic range size, life history and rates of diversification in Australian mammals

Abstract What causes species richness to vary among different groups of organisms? Two hypotheses are that large geographical ranges and fast life history either reduce extinction rates or raise speciation rates, elevating a clade's rate of diversification. Here we present a comparative analysis of these hypotheses using data on the phylogenetic relationships, geographical ranges and life history of the terrestrial mammal fauna of Australia. By comparing species richness patterns to null models, we show that species are distributed nonrandomly among genera. Using sister‐clade comparisons to control for clade age, we then find that faster diversification is significantly associated with larger geographical ranges and larger litters, but there is no evidence for an effect of body size or age at first breeding on diversification rates. We believe the most likely explanation for these patterns is that larger litters and geographical ranges increase diversification rates because they buffer species from extinction. We also discuss the possibility that positive effects of litter size and range size on diversification rates result from elevated speciation rates.     

珙桐的生物生态学特性和栽培技术

珙桐是一种残遗种,为我国所特有,只零星分布于长江流域一带湿润亚热带山地,被列为国家一级保护植物。由于它的棕红色头状花序下具有两枚大型的白色苞片,形似白鸽,有中国鸽子树之称,早已成为国外著名的园林观赏树种。我国有不少单位开展引种试验研究,还未得到推广。本文概括地报导了它的地理分布、生物生态学特性和栽培技术,希望能使它在园林绿化事业中占据应有的地位。     

秦岭和黄土高原地区锦鸡儿属的表征,分支和生物地理学的探讨

选用锦鸡儿属在秦岭和秦岭以北的２０余种和５９个形态性状作为分析基础。表征图和分支图共同提示出羽状和掌状叶类群形成两大类。分支图说明了树锦鸡儿Ｃ．ａｒｂｏｒｅｓｃｅｎｓ和柄荚锦鸡儿Ｃ．ｓｔｉｐｉｔａｔａ等为原始类群。沿树锦鸡儿的分布区,本属植物向西和西南方向适应辐射成以温度和降水为主导因子的生态序列：（１）森林种→森林草原种→草原种→荒漠种,森林种→高寒山地种;（２）湿润地带→亚湿润地带→半干旱地带     

山西稀有濒危树种的新发现

本文发表了槐属一新种即:窄叶槐(Sophora angustifoliolaQ.Q.Liu et H.Y.Ye,sp.nov);油松一新变型即:密枝油松(Pinustabulaeformis Carr.f.densa Q.Q.Liu et H.Y.Ye,f.nov);侧柏一新变型即:垂枝侧柏(Platycladus orientalis(L.)Franco f.pendula Q.Q.Liu.et H.Y.Ye,f.nov.); 灰楸一新变型即:白花灰楸(Catalpafargesii Bur.f.alba Q.Q.liu et H.Y.Ye,f.nov);山西省槐属一新分布即:五色槐(Sophora iaponica L.var.violacea Carr.)。     

THE INTERFACE BETWEEN PHYLOGENETICS AND POPULATION GENETICS: INVESTIGATING GENE TREES,SPECIES TREES,AND POPULATION DYNAMICS IN THE PHYLLOPHAGA FRATERNA SPECIES GROUP

This study uses traditional and contemporary phylogenetic and population genetic analyses to assess the causes of discordance (i.e., lineage sorting and introgression) among mitochondrial and nuclear gene trees for a clade of eastern North American scarab beetles (fraterna species group, genus Phyllophaga). I estimated gene trees using individual and combined analysis of one mitochondrial and two nuclear loci in MrBayes , and inferred a species tree using a hierarchical coalescent approach based on all loci in the program Best . Because hybridization violates the assumptions of Best , I tested for introgression by comparing species monophyly between the mitochondrial and nuclear gene trees based on the prediction that cytoplasmic genomes introgress more readily than nuclear genomes. Haplotype exclusivity was identified using Bayesian tests of monophyly and the genealogical sorting index. I used the results of the phylogenetic analyses and monophyly tests to develop an explicit hypothesis of introgression that could be tested in the program IMa. Results from these analyses provided evidence for introgression across clades within the fraterna group. The tiered analytical approach used in this study demonstrated how the use of multiple methods can identify when assumptions are violated and methods are prone to yield misleading results.     

PHASE III OF WRIGHT'S SHIFTING BALANCE PROCESS AND THE VARIANCE AMONG DEMES IN MIGRATION RATE

Interdemic selection by the differential migration of individuals out from demes of high fitness and into demes of low fitness (Phase III) is one of the most controversial aspects of Wright's Shifting Balance Theory. I derive a relationship between Phase III migration and the interdemic selection differential, S, and show its potential effect on F_ST. The relationship reveals a diversifying effect of interdemic selection by Phase III migration on the genetic structure of a metapopulation. Using experimental metapopulations, I explored the effect of Phase III migration on F_ST by comparing the genetic variance among demes for two different patterns of migration: (1) island model migration and (2) Wright's Phase III migration. Although mean migration rates were the same, I found that the variance among demes in migration rate was significantly higher with Phase III than with island model migration. As a result, F_ST for the frequency of a neutral marker locus was higher with Phase III than it was with island model migration. By increasing F_ST, Phase III enhanced the genetic differentiation among demes for traits not subject to interdemic selection. This feature makes Wright's process different from individual selection which, by reducing effective population size, decreases the genetic variance within demes for all other traits. I discussed this finding in relation to the efficacy of Phase III and random migration for effecting peak shifts, and the contribution of genes with indirect effects to among‐deme variation.     

A chloroplast genealogy of hordeum (poaceae): Long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference

To analyze reasons for inconclusive results of earlier chloroplast phylogenies in the grass genus Hordeum, we established a genealogy of chloroplast haplotypes by sequencing the trnL-trnF region in 875 individuals, covering all 31 species of the genus. Although the outcomes of phenetic and parsimony analyses of 88 haplotypes were ambiguous, a network approach showed that in Hordeum ancient chloroplast types co-occur with their descendants. Moreover, we found up to 18 different chloroplast haplotypes within a single species and up to 6 species sharing single haplotypes. Persisting polymorphisms together with incomplete lineage sorting occurred preferentially in the rapidly speciating New World taxa of the genus, where ancient chloroplast types have survived for at least 4 Myr. Lineages-through-time plots and a high number of missing chloroplast haplotypes indicated far-reaching extinction of chloroplast lineages in Europe and particularly the Mediterranean. Survival of these lineages in East Asia and North America resulted in chloroplast relationships that markedly differed from nuclear estimations of species relationships. Thus, even for the deepest splits in the genus, reaching back more than 9 Myr, no safe phylogenetic inference from chloroplast data is possible in Hordeum. The chloroplast genealogy, however, revealed biogeographic patterns and indicated processes involved in speciation in Hordeum. We conclude that the described phenomena are not restricted to Hordeum and that the knowledge of the chloroplast relationships within a genus is indispensable to prevent misinterpretation of phylogeographic data within single species.     

TESTING MITOCHONDRIAL CAPTURE AND DEEP COALESCENCE IN AMAZONIAN CICHLID FISHES (CICHLIDAE: CICHLA)

Hybridization and introgression have important consequences in evolution, such as increasing the genetic diversity and adaptive potential of a species. One of their most conspicuous footprints is discordance among gene trees or between genes and phenotypes. However, most studies that report introgression fail to disprove the null hypothesis that genetic incongruence may result from stochastic sorting of ancestral allelic polymorphisms. In the case of ancient introgression, these two processes may be especially difficult to distinguish topologically, but they make different predictions about the patterns of coalescence among loci. Here we apply three methods, molecular dating, multispecies coalescent models, and gene tree simulation under coalescence, to compare these two hypotheses that explain the polyphyletic mtDNA of the butterfly peacock bass, Cichla orinocensis. In comparison with a species tree based on 20 unlinked nuclear loci, we determined that mtDNA divergences were too recent to be explained by ancestral polymorphism. Similarly, coalescent species tree branches were significantly shorter when putative introgressed mtDNA was incorporated, and simulations showed the mtDNA topology to be unlikely under lineage sorting only. We conclude that introgression approximately 1.5 million years ago resulted in capture by C. orinocensis of an mtDNA lineage ancestral to the modern subspecies C. oc. monoculus.     

DIVERSIFICATION AND GENE FLOW IN NASCENT LINEAGES OF ISLAND AND MAINLAND NORTH AMERICAN TREE SQUIRRELS (TAMIASCIURUS)

Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data, we examined diversification, isolation, and hybridization in two sibling species of tree squirrels (Tamiasciurus douglasii and Tamiasciurus hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the Late Pleistocene. The island population is phylogenetically nested within T. hudsonicus according to our nuclear analysis but within T. douglasii according to mitochondrial DNA. This conflict is more likely due to historical hybridization than to incomplete lineage sorting, and it appears that bidirectional gene flow occurred between the island population and both species on the mainland. This interpretation of our genetic analyses is consistent with our bioclimatic modeling, which demonstrates that both species were able to occupy this region throughout the Late Pleistocene. The divergence of the island population 40,000 years ago suggests that tree squirrels persisted in a refugium on Vancouver Island at the last glacial maximum, 20,000 years ago. Our observations demonstrate how Pleistocene climate change and habitat shifts have created incipient divergence in the presence of gene flow.     

西双版纳茶林及橡胶林区鸟类调查

1983年5—7月,作者对云南省西双版纳的勐海、勐养和勐腊三个地区的茶林和橡胶林区的鸟类区系组成情况进行了调查,其结果若与开发前（郑作新、郑宝赉,1961,1962;A.И.伊万诺夫,1961）的记录对照,在季节时间上有所不同,但该地区的热带雨林和季雨林被开垦种植为茶林、橡胶林及其它经济作物之后,反映出各林区现在的繁殖鸟种类减少很多,鸟类区系组成情况有显著的变化。     

基于线粒体Cyt b基因和CO I基因序列研究豹蛱蝶亚科(鳞翅目,蛱蝶科)10属间的系统发生关系

测定了国产豹蛱蝶亚科10属共10个代表种的Cyt 6基因和CO Ⅰ基因的部分序列.结合从GenBank中获得的3个种类CO Ⅰ基因的同源序列,以锯眼蝶亚科2个物种为外群,通过遗传分析软件对CO Ⅰ、Cyt b独立基因序列和联合基因序列以及编码的氨基酸序列进行了比较分析,同时用邻接法(NJ)、最大简约法(MP)、最大似然法(ML)和贝叶斯法(BI)重建分子系统树,分析了该亚科10个属之间的系统发生关系.结果显示:1)联合基因序列的A+T平均含量为71.90h,具A、T偏倚性,其编码的357个氨基酸中没有半胱氨酸,变异率为11.5%;2)豹蛱蝶亚族为单系群;3)青豹蛱蝶属和豹蛱蝶属间、黄襟蛱蝶属和珐蛱蝶属间具有较近的亲缘关系;4)支持将文蛱蝶属、襟蛱蝶属和珐蛱蝶属从豹蛱蝶亚科中分离出来.     

中国温带、亚热带和热带森林45个常见树种细根直径变异

 细根在发挥植物功能以及生态系统碳和养分循环过程中起着重要作用。为了解我国不同森林生态系统细根直径变化规律, 提供建立根系模型的基础, 该文研究了我国温带、亚热带和热带45个常见树种1～5级根直径的变异以及直径与根序的关系。结果表明: 1)在所有树种中, 1级根直径最细, 5级根直径最粗, 直径随根序的增加而增加。此外, 同一根序的直径在不同树种间变异较大, 在不同生态系统中, 各树种1级根的总体平均直径呈现温带<亚热带<热带的格局。2)不同生态系统树种同一根序平均直径变异程度不同, 各个根序都是温带最小, 亚热带次之, 热带最大。3)细根内部各个根序的平均直径变异的52%由根序解释, 33%由树种解释, 生态系统类型和生活型分别解释7%和2%。不同系统不同树种直径的变异说明无法用统一的直径级来研究根的功能, 也无法用统一的根序和直径间的关系来建立根系形态模型。今后的研究需要进一步认识根序和直径在不同树种中如何与根的功能相联系。     

适度高温下亚热带阔叶树种叶片的光合速率和吸收光能的分配

 利用光合作用测定系统（Li-COR 6400和叶室荧光仪）,测定了亚热带阔叶树种的光合速率和荧光参数,分析了38 ℃适度高温对叶片光合作用 和吸收光能分配的影响。测试树种包括华南亚热带地区常见的阳生性树种木荷（Schima superba）、耐荫树种黄果厚壳桂（Cryptocarya concinna）和中生性树种红锥（Castanopsis hystrix）。适度高温处理均引起 所有树种的光合能力下降,而且木荷和红锥下降的程度比黄果 厚壳桂明显。与25 ℃的对照温度相比,适度高温处理的木荷叶片用于光化学反应所消耗的光能下降,红锥和黄果厚壳桂也有相似的反应,表明 适度高温限制叶片用于光化学反应的吸收光能。无论哪个树种,38 ℃适度高温处理的植物,叶片总吸收光能中额外多余的那部分和处于非活化 状态PSⅡ所吸收的那部分光能都增加,而且黄果厚壳桂比木荷和红锥显著,因此,亚热带阔叶森林的树种对适度高温的响应因种类而异。研究 结果意味着将来气候变化导致温度的上升对演替后期树种黄果厚壳桂的光合过程的限制比演替早期的树种木荷和中生性树种红锥会更严重。     

HOST PLANT UTILIZATION,HOST RANGE OSCILLATIONS AND DIVERSIFICATION IN NYMPHALID BUTTERFLIES: A PHYLOGENETIC INVESTIGATION

It has been suggested that phenotypic plasticity is a major factor in the diversification of life, and that variation in host range in phytophagous insects is a good model for investigating this claim. We explore the use of angiosperm plants as hosts for nymphalid butterflies, and in particular the evidence for past oscillations in host range and how they are linked to host shifts and to diversification. At the level of orders of plants, a relatively simple pattern of host use and host shifts emerges, despite the 100 million years of history of the family Nymphalidae. We review the evidence that these host shifts and the accompanying diversifications were associated with transient polyphagous stages, as suggested by the “oscillation hypothesis.” In addition, we investigate all currently polyphagous nymphalid species and demonstrate that the state of polyphagy is rare, has a weak phylogenetic signal, and a very apical distribution in the phylogeny; we argue that these are signs of its transient nature. We contrast our results with data from the bark beetles Dendroctonus, in which a more specialized host use is instead the apical state. We conclude that plasticity in host use is likely to have contributed to diversification in nymphalid butterflies.