Demystifying the age of old olive trees

Iconic to the Mediterranean landscape, the age of monumental olive trees with large trunks and unique silhouettes is often considered several centuries to millennia. Here we combine tree-ring and radiocarbon dating to show that most monumental olive trees may have maximum ages between 300 and 500 years. Our example helps disentangling the tree size-longevity conundrum in a major Mediterranean cultivated tree species and important cultural heritage.     

Priors for the Bayesian star paradox

We show that the Bayesian star paradox, first proved mathematically by Steel and Matsen for a specific class of prior distributions, occurs in a wider context including less regular, possibly discontinuous, prior distributions.     

An empirical test of the midpoint rooting method

The outgroup method is widely used to root phylogenetic trees. An accurate root indication, however, strongly depends on the availability of a proper outgroup. An alternate rooting method is the midpoint rooting (MPR). In this case, the root is set at the midpoint between the two most divergent operational taxonomic units. Although the midpoint rooting algorithm has been extensively used, the efficiency of this method in retrieving the correct root remains untested. In the present study, we empirically tested the success rate of the MPR in obtaining the outgroup root for a given phylogenetic tree. This was carried out by eliminating outgroups in 50 selected data sets from 33 papers and rooting the trees with the midpoint method. We were thus able to compare the root position retrieved by each method. Data sets were separated into three categories with different root consistencies: data sets with a single outgroup taxon (54% success rate for MPR), data sets with multiple outgroup taxa that showed inconsistency in root position (82% success rate), and data sets with multiple outgroup taxa in which root position was consistent (94% success rate). Interestingly, the more consistent the outgroup root is, the more successful MPR appears to be. This is a strong indication that the MPR method is valuable, particularly for cases where a proper outgroup is unavailable.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 669–674.     

Why are rags tied to the sacred trees of the Holy Land?

A field study to survey the custom of tying rags on sacred trees in the northern part of Israel was carried out during 2000–2001. It included 60 interviewees: 24 Druze, 18 Moslem Arabs, 12 Moslem Bedouins and 6 Christian Arab individuals. Tree veneration was found to be quite uncommon among the Bedouins and rare among the Christian Arabs. The results of the present study suggest there are 17 reasons for tying rags on sacred trees. Five reasons, as far as the author is aware, were not previously reported from the literature (i.e., breaking an oath, marking a blessed tree, marking the road to a blessed tree, asking for permission to pick fruit, and setting out rags for needy people). These usages appear to be endemic to Israel and to the Druze. Two customs previously reported from Israel but not corroborated by the present survey are to pacify a tree’s spirit and as a charm for new clothes. Three of the 17 known reasons for tying rags on sacred trees are also known from regions beyond the Middle East (i.e., to transfer illness to the tree, to use a rag as a visiting card, and to pacify the tree’s spirits). And lastly, several customs never reported before from Israel appear to stem from the belief in ancient pagan polytheistic religions (to ensure a good yield, offerings to a tree’s deities/spirits, to pacify the ancestor’s spirits, to commemorate a death, and to pacify a tree’s spirit while picking fruits). Twelve of the reported 17 reasons for hanging rags on sacred trees are known from Israel. These findings elucidate the widespread and variable tree worship traditions that are prevalent today in the region. In spite of a monotheistic ban against ancient pagan beliefs, trees still remain a subject of worship in Israel today, as manifested by the daily tying of rags upon branches.     

Evolution of chorion gene families in Lepidoptera: Characterization of 15 cDNAs from the gypsy moth

Fifteen unique chorion protein-encoding cDNAs from gypsy moth have been completely sequenced. These sequences are encoded by a family of genes, based on pairwise similarity values of 78–100% within a 225-nt region. Pairwise comparisons and maximum parsimony analysis strongly support the existence of two clusters of 11 and four sequences each, called noel and noc2. While noc2 consists of two subclusters, there is little character support for subclusters within noel. The highly localized character-state distribution on the parsimony tree in gypsy moth is reminiscent of that in Bombyx mori, specifically for those chorion families that have been shown to undergo gene conversion. Gene conversion thus becomes a reasonable explanation for the homogeneity of noel sequences and for their distinctness from noc2. The relationship between the two major clusters of chorion sequences in gypsy moth (noel, noc2) and Bombyx mori (Bm , Bm ) has been addressed through mixed-species tree construction. All four groups cluster separately, thus providing no direct evidence of orthologous sequences. However, the occurrence of gene conversion could have eliminated such evidence. The relationship between the chorion gene tree and the species cladogenic event is discussed, as are biases in codon usage, base composition, and nucleotide transformations.Correspondence to: J.C. Regier     

Effectiveness of measures requiring and not requiring prior sequence alignment for estimating the dissimilarity of natural sequences

Summary Various measures of sequence dissimilarity have been evaluated by how well the additive least squares estimation of edges (branch lengths) of an unrooted evolutionary tree fit the observed pairwise dissimilarity measures and by how consistent the trees are for different data sets derived from the same set of sequences. This evaluation provided sensitive discrimination among dissimilarity measures and among possible trees. Dissimilarity measures not requiring prior sequence alignment did about as well as did the traditional mismatch counts requiring prior sequence alignment. Application of Jukes-Cantor correction to singlet mismatch counts worsened the results. Measures not requiring alignment had the advantage of being applicable to sequences too different to be critically alignable. Two different measures of pairwise dissimilarity not requiring alignment have been used: (1) multiplet distribution distance (MDD), the square of the Euclidean distance between vectors of the fractions of base singlets (or doublets, or triplets, or…) in the respective sequences, and (2) complements of long words (CLW), the count of bases not occurring in significantly long common words. MDD was applicable to sequences more different than was CLW (noncoding), but the latter often gave better results where both measures were available (coding). MDD results were improved by using longer multiplets and, if the sequences were coding, by using the larger amino acid and codon alphabets rather than the nucleotide alphabet. The additive least squares method could be used to provide a reasonable consensus of different trees for the same set of species (or related genes).     

Exploring gene tree incongruence at the origin of ants and bees (Hymenoptera)

The fact that different phylogenomic data sets can lead to highly supported but inconsistent results suggest that conflict among gene trees in real data sets could be severe. We provide here a detailed exploration of gene tree space to investigate the relationships in Hymenoptera based on data obtained by Johnson et al. (Current Biology, 2013, 23, 2058), in which ants and Apoidea (bees and spheciform wasps) were recovered as sister groups, contradicting previous studies. We found high levels of topological variation among gene trees, several of them disagreeing with previously published hypotheses. To profile the dynamics of emerging support versus conflicting signal in combined analysis of data, we employed a novel method based on the incremental addition of randomized data to coalescence‐based phylogenetic inference. Although the monophyly of Aculeata and of Formicidae were consistently recovered using as little as 6.5% of the 308 available markers, signal for the Formicidae + Apoidea clade prevailed only after more than 50% of the loci were sampled. Still, non‐negligible support for alternative hypotheses remained until all genes were added to the analysis. Our results suggest that phylogenetic conflict is rather pervasive and not scattered as noise across individual gene trees because alternative topologies were recovered not from a specific subset, but from several random combinations of loci. Thus, even though phylogenetic signal recovered from full gene data sets was already dominant in much smaller ensembles, large amounts of data may be indeed necessary to overcome phylogenetic conflict.     

The Bayesian "star paradox" persists for long finite sequences

The "star paradox" in phylogenetics is the tendency for a particular resolved tree to be sometimes strongly supported even when the data is generated by an unresolved ("star") tree. There have been contrary claims as to whether this phenomenon persists when very long sequences are considered. This note settles one aspect of this debate by proving mathematically that the chance that a resolved tree could be strongly supported stays above some strictly positive number, even as the length of the sequences becomes very large.     

The potential of the decay fungus Chondrostereum purpureum in the biocontrol of broadleaved tree species

The ability of the decay fungus Chondrostereum purpureum to grow within birch (Betula pendula and Betula pubescens), aspen (Populus tremula), rowan (Sorbus aucuparia) and willow (Salix caprea) stumps or root systems is unknown, although such information would be crucial in understanding its impact on the vegetative growth of broadleaved trees, their ecology and potential biocontrol. Saplings of these tree species were cut and inoculated with the fungus. After 3 months, 47, 14, 0 and 0% of birch, aspen, rowan and willow stumps, respectively, were dead, and C. purpureum was frequently present within the stumps of all species. In more than half of the birch stumps investigated, the fungus had penetrated into the roots unlike in the other tree species. Our results indicate that C. purpureum can utilize the woody material of birch better than that of other species, and that penetration into the roots is needed to kill the host.     

两种光照下木质藤本和树木幼苗的生理生态学特征

对比研究生长在两种光照环境（4％和35％）下的7种热带木质藤本和5种常见的雨林冠层树种幼苗叶片的光合能力、色素含量和形态解剖特征。结果表明：（1）与树木相比,低光下木质藤本光合能力（Pmax）较弱,光强升高,木质藤本光合能力提高86．4％,树木提高61．5％,且木质藤本具有更高的光合能力。其光合作用光补偿点（LCP）和饱和点（LSP）较高。（2）木质藤本和树木正午光化学效率（Fv／Fm）下降,非光化学耗散（NPQ）升高。相同处理条件下,木质藤本光化学效率高于树木,正午光系统Ⅱ受到光抑制的程度较小。（3）光强升高,木质藤本和树木单位叶面积叶绿素含量减少。木质藤本比树木单位面积均具有更高的叶绿素a、叶绿素b、叶绿素总量和类胡萝卜素含量,以及更高的叶绿素a／b的比值。（4）与研究树木相比,木质藤本具有更大的叶片厚度,并且具有更大的比叶面积（SLA）,反映出其较低的叶片密度。     

Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life

Summary The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family 1) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family 11) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotesin distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree. Offprint requests to: B. Labedan     

Phylogenetic structure and biogeography of the Pacific Rim clade of Sphagnum subgen. Subsecunda: haploid and allodiploid taxa

Although it is an uncommon distribution in seed plants, many bryophytes occur around the Pacific Rim of north‐western North America and eastern Asia. This work focuses on a clade of peatmosses (Sphagnum) that is distributed around the Pacific Rim region, with some individual species found across the total range. The goals were to infer divergent phylogenetic relationships among haploid species in the clade, assess parentage of allopolyploid taxa, and evaluate alternative hypotheses about inter‐ and intraspecific geographical range evolution. Multiple data sets and analyses resolved an ‘Alaska’ clade, distributed across western North America, eastern China and Japan, and an ‘Asia’ clade that includes western Chinese, Thai, Korean, eastern Chinese and Japanese lineages. Allopolyploids have arisen at least four times in the Pacific Rim clade of Sphagnum subgen. Subsecunda; it appears that all allopolyploid origins involved closely related haploid parental taxa. Biogeographical inferences were impacted by topological uncertainty and especially by the biogeographical model utilized to reconstruct ancestral areas. Most analyses converge on the conclusion that the ancestor to this clade of Pacific Rim Sphagnum species was widespread from Alaska south to eastern Asia, but a northern origin for the Alaska subclade was supported by one of the two biogeographical models we employed, under which it was robust to phylogenetic uncertainty.     

Morphology of the Respiratory Trees in the Holothurians Apostichopus japonicus and Cucumaria japonica

The morphology of the respiratory trees in the holothurians Apostichopus japonicus and Cucumaria japonica was studied using histochemical and electron microscopic techniques. The epithelium of the respiratory tree cavity in A. japonicus consists of columnar cells about 17–20 m high. In C. japonica, this epithelium is composed of two cell types: bulbous cells embedded in the connective tissue layer and secretory cells; cells are 1–12 m high. A characteristic feature of cells of the respiratory tree cavity epithelium in these species is the presence of numerous phagosomes and coated vesicles in the apical cytoplasm. The cell surface has many microvilli and a single cilium. Cells of the coelomic epithelium contain vacuoles in the apical part and myofibrils in the basal region; the thickness of this epithelium in A. japonicus and C. japonica is 9–16 and 10–30 m, respectively. Based on the different structure of the respiratory trees and the absence of hemocytes in A. japonicus, it is suggested that the holothurian species studied have different routes of oxygen transport from the environment to the internal organs.     

The conservation value of paddock trees for birds in a variegated landscape in southern New South Wales. 1. Species composition and site occupancy patterns

The use of paddock trees by birds was assessed in a grazinglandscape in southern New South Wales, Australia. Seventy paddock treesites were surveyed for 20 min each in the morning, and 36sites were surveyed again at midday in March 2000. During this time, thepresence and abundance of birds was recorded. Several site and landscapevariables were measured at each site. These included tree species, atree size index, a measure of the crown cover density around the site,and proximity to the nearest woodland patch. During formal surveys, 31bird species, including several woodland species, were observed usingpaddock trees. Data from bird surveys in woodland patches that wereobtained in a separate study in November 1999 were used to comparewhether there was a relationship between the abundance of a given birdspecies in woodland patches and paddock trees. Many birds commonlydetected in woodland patches were also common in paddock trees. However,some birds with special habitat requirements were absent from paddocktrees although they were common in woodland patches. Site occupancypatterns were modelled for several guilds of birds using logisticregression. Foliage-foraging birds were more likely to occupy clumps oftrees and sites with a high tree size index. Nectarivores appeared to bemore likely to be detected at sites more than 200 m fromwoodland, although this result was marginally non-significant(P = 0.08). The probability of detecting granivoreswas higher at sites with a low tree size index. Open country specieswere most likely to occupy large trees and sites that were located morethan 200 m from the nearest woodland patch. The value ofpaddock trees may have been underestimated in the past because a widevariety of bird species use paddock trees on a regular basis. Ensuringthe continued survival of paddock trees should be an important aspect offuture conservation and revegetation efforts.     

三种阔叶树雌雄异株木材结构的比较

在光学显微镜下较详细地比较了重阳木、大叶刺篱木和红毛丹,雌雄异株木材的结构。结果表明：同一种树木两性间木材结构总体上是很相似的,但有的定量特征差异显著甚至极显著。３个种的树木中,雌株木纤维壁腔比值较雄株的大,而分膈纤维和纤维管胞数量较小。雌株木材结构特点可能表明其木材具较强的机械支持能力,利用于果实的支持 。     

Asymptotic height as a predictor of growth and allometric characteristics in malaysian rain forest trees

The growth and physiological characteristics of canopy trees are expected to differ systematically from those of understory trees on the basis of size-dependent aspects of biomechanics, resource availability, and life history. Although such differences have previously been noted, there has been relatively little effort to quantify these in terms of interspecific allometric relationships. Asymptotic maximal height (H_max) is advocated as a measure of the size of dicotyledonous woody plants for this purpose. Height diameter (H–D) relationships in 38 species within six genera of Malaysian rain forest trees are well described by an asymptotic model, and thus provide a basis for estimating H_max using static observational data. Three important aspects of tree growth strategies are shown to be predictable on the basis of these values: average tree growth rates are positively related to H_max, while wood density and the initial allometric slope of (species-specific) H–D relationships are negatively related to H_max. These patterns may be explained by an association of low light levels with slow growth and high density wood in understory species; the latter property may in turn allow for relatively high allometric slopes of H–D relationships in saplings of small-statured species. Analyses that control for phylogenetic differences provide evidence that such interspecific allometric patterns are the product of convergent evolution. These results are consistent with the idea that much ecological variation within species-rich taxa of southeast Asian rain forest trees is related to differentiation along a vertical axis of tree size.     

中国橡胶树气候适宜度分布特征研究

选取气温、降水、光照、风速四个气象要素,应用气候适宜度方法对中国橡胶树的气候适宜性进行定量评价.结果表明:中国橡胶树的气候适宜度指数均低于0.8,平均值为0.43,变化趋势普遍在±0.05(10a)-1之间,海南岛的大部分地区为橡胶树气候适宜区,广东,广西和福建南部以及云南南部的部分地区为较适宜区;降水适宜度均值为0....     

Big‐sized trees overrule remaining trees' attributes and species richness as determinants of aboveground biomass in tropical forests

Large‐diameter, tall‐stature, and big‐crown trees are the main stand structures of forests, generally contributing a large fraction of aboveground biomass, and hence play an important role in climate change mitigation strategies. Here, we hypothesized that the effects of large‐diameter, tall‐stature, and big‐crown trees overrule the effects of species richness and remaining trees attributes on aboveground biomass in tropical forests (i.e., we term the “big‐sized trees hypothesis”). Specifically, we assessed the importance of: (a) the “top 1% big‐sized trees effect” relative to species richness; (b) the “99% remaining trees effect” relative to species richness; and (c) the “top 1% big‐sized trees effect” relative to the “99% remaining trees effect” and species richness on aboveground biomass. Using environmental factor and forest inventory datasets from 712 tropical forest plots in Hainan Island of southern China, we tested several structural equation models for disentangling the relative effects of big‐sized trees, remaining trees attributes, and species richness on aboveground biomass, while considering for the full (indirect effects only) and partial (direct and indirect effects) mediation effects of climatic and soil conditions, as well as interactions between species richness and trees attributes. We found that top 1% big‐sized trees attributes strongly increased aboveground biomass (i.e., explained 55%–70% of the accounted variation) compared to species richness (2%–18%) and 99% remaining trees attributes (6%–10%). In addition, species richness increased aboveground biomass indirectly via increasing big‐sized trees but via decreasing remaining trees. Hence, we show that the “big‐sized trees effect” overrides the effects of remaining trees attributes and species richness on aboveground biomass in tropical forests. This study also indicates that big‐sized trees may be more susceptible to atmospheric drought. We argue that the effects of big‐sized trees on species richness and aboveground biomass should be tested for better understanding of the ecological mechanisms underlying forest functioning.     

Spring Sap of Trees

In the spring, sap in perennial plants becomes available after winter dormancy. As is well known, substances including minerals and organic nutrients are transported from storage compartments in roots and stems to growth regions. For this solute distribution, xylem as well as phloem are used and probably also the cambial region and the ray system. In the present study, a puncture method has been used to record sap availability in six north European tree species during the spring. Attempts were made to withdraw sap from the trees at points 0.5 m, 1.3 m and 3.0 m above ground with “phloem needles” (constructed according to Hammel 1968), and a syringe. Sap could be withdrawn for the longest period for the sycamore (71 days). Birch (47 days) gave an intermediate period, beech (12 days), oak (12 days) and alder (13 days) gave short periods, and sap could not be withdrawn from ash. Effects of two environmental factors, temperature and light intensity on sap availability were examined. Temperature dependence of sap availability, already observed in the genus Acer, was confirmed in sycamore maple (Acer pseudoplatanus). There also seemed to be a correlation between sap availability and light intensity. Analysis of sugar in the tree sap revealed that sucrose was the only sugar in the sap of sycamore but hexoses (glucose and fructose) were preponderant in the sap of the other trees. The pH of sycamore sap (pH 6.9–5.4) fell as the season advanced. However, the pH-values of sap from the other trees did not vary significantly.     

Restoring hardwood trees to lake riparian areas using three planting treatments

Lake riparian areas provide wildlife habitat for a wide variety of species. Residential development throughout such lakeshore areas of the United States has increased exponentially in recent decades. Awareness of the vulnerability and importance of lakeshore ecosystems has increased concurrently. Lakeshore habitat restoration projects have been implemented to mitigate some of the negative impacts of human shoreline development, and containerized (CT) trees are frequently one of the highest costs associated with such restoration projects. As an alternative, we tested the effectiveness of using dormant bare‐root (BR) trees in restoration projects along two lakeshores in northern Wisconsin, U.S.A. In addition, we experimented using BR stock that was incorporated into gravel medium at a local nursery and planted later in the summer months. We monitored growth and survival of four native tree species in these three planting treatments over a 3–4‐year period. CT red maple (Acer rubra), paper birch (Betula paperifera), and northern red oak (Quercus rubra) increased in size significantly faster than BR and/or gravel culture (GC) counterparts, whereas CT showy mountain ash (Sorbus decora) growth rates were similar to those of BR and GC stock. Mortality was generally low, but for those species/planting treatments with higher mortality (paper birch and red oak), CT trees were more likely to survive than BR or GC trees. Our results show that the success of deciduous BR and/or GC tree stock relative to CT trees is species dependent, and for some species, CT trees' higher growth rates and survivorship could offset their higher costs.