MrEnt: an editor for publication‐quality phylogenetic tree illustrations

We developed MrEnt, a Windows‐based, user‐friendly software that allows the production of complex, high‐resolution, publication‐quality phylogenetic trees in few steps, directly from the analysis output. The program recognizes the standard Nexus tree format and the annotated tree files produced by BEAST and MrBayes. MrEnt combines in a single software a large suite of tree manipulation functions (e.g. handling of multiple trees, tree rotation, character mapping, node collapsing, compression of large clades, handling of time scale and error bars for chronograms) with drawing tools typical of standard graphic editors, including handling of graphic elements and images. The tree illustration can be printed or exported in several standard formats suitable for journal publication, PowerPoint presentation or Web publication.     

PoInTree： A Polar and Interactive Phylogenetic Tree

PoInTree （Polar and Interactive Tree） is an application that allows to build, visualize, and customize phylogenetic trees in a polar, interactive, and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining （N J） algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoInTree, nodes can be dynamically opened and closed and distances between genes are graphically represented. Tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species. The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component （Steema software）.     

Evaluating evolutionary history in the face of high gene tree discordance in Australian Gehyra (Reptilia: Gekkonidae)

Species tree methods have provided improvements for estimating species relationships and the timing of diversification in recent radiations by allowing for gene tree discordance. Although gene tree discordance is often observed, most discordance is attributed to incomplete lineage sorting rather than other biological phenomena, and the causes of discordance are rarely investigated. We use species trees from multi-locus data to estimate the species relationships, evolutionary history and timing of diversification among Australian Gehyra—a group renowned for taxonomic uncertainty and showing a large degree of gene tree discordance. We find support for a recent Asian origin and two major clades: a tropically adapted clade and an arid adapted clade, with some exceptions, but no support for allopatric speciation driven by chromosomal rearrangement in the group. Bayesian concordance analysis revealed high gene tree discordance and comparisons of Robinson–Foulds distances showed that discordance between gene trees was significantly higher than that generated by topological uncertainty within each gene. Analysis of gene tree discordance and incomplete taxon sampling revealed that gene tree discordance was high whether terminal taxon or gene sampling was maximized, indicating discordance is due to biological processes, which may be important in contributing to gene tree discordance in many recently diversified organisms.     

Frequent fires reduce tree growth in northern Australian savannas: implications for tree demography and carbon sequestration

Tropical savannas are typically highly productive yet fire‐prone ecosystems, and it has been suggested that reducing fire frequency in savannas could substantially increase the size of the global carbon sink. However, the long‐term demographic consequences of modifying fire regimes in savannas are difficult to predict, with the effects of fire on many parameters, such as tree growth rates, poorly understood. Over 10 years, we examined the effects of fire frequency on the growth rates (annual increment of diameter at breast height) of 3075 tagged trees, at 137 locations throughout the mesic savannas of Kakadu, Nitmiluk and Litchfield National Parks, in northern Australia. Frequent fires substantially reduced tree growth rates, with the magnitude of the effect markedly increasing with fire severity. The highest observed frequencies of mild, moderate and severe fires (1.0, 0.8 and 0.4 fires yr^?1, respectively) reduced tree growth by 24%, 40% and 66% respectively, relative to unburnt areas. These reductions in tree growth imply reductions in the net primary productivity of trees by between 0.19 t C ha^?1 yr^?1, in the case of mild fires, and 0.51 t C ha^?1 yr^?1, in the case of severe fires. Such reductions are relatively large, given that net biome productivity (carbon sequestration potential) of these savannas is estimated to be just 1–2 t C ha^?1 yr^?1. Our results suggest that current models of savanna tree demography, that do not account for a relationship between severe fire frequency and tree growth rate, are likely to underestimate the long‐term negative effects of frequent severe fires on tree populations. Additionally, the negative impact of frequent severe fires on carbon sequestration rates may have been underestimated; reducing fire frequencies in savannas may increase carbon sequestration to a greater extent than previously thought.     

Hollow occurrence and abundance varies with tree characteristics and among species in temperate woodland Eucalyptus

Tree hollows are a critical but diminishing resource for a wide range of fauna around the world. Conservation of these fauna depends on sustainable management of tree species that produce the hollows on which they depend. This study addressed the need for empirical data about intraspecific and interspecific variation in hollow occurrence and abundance in woodland trees in Australia. We measured and performed hollow surveys on 1817 trees of seven species of woodland Eucalyptus in central‐western New South Wales, Australia. Trees were surveyed at 51 one‐hectare sites and about 30% of trees surveyed had multiple stems. Generalized linear mixed models that accounted for nestedness of stems within trees and trees within sites detected a significant amount of variation in hollow occurrence and abundance. Models for individual tree stems of live trees showed hollow probability and abundance increased with diameter at breast height (DBH) and with increasing senescence (form). Stems of Eucalyptus microcarpa Maiden had a higher probability of having hollows than similar DBH stems of Eucalyptus camaldulensis Dehnh., Eucalyptus melliodora A.Cunn. ex Schauer or Eucalyptus populnea ssp. bimbil L.A.S.Johnson & K.D.Hill. Dead stems in live trees were more likely to have hollows than live stems of similar DBH. Each stem in a multi‐stemmed tree had a lower probability of hollow occurrence and lower abundance of hollows than single‐stemmed trees of similar DBH. For stems of dead trees, hollow occurrence and abundance increased with DBH and differed depending on stage of senescence. A comparison of our data with other studies indicates regional variation of hollow abundances within tree species.     

Preference and performance of Lepidoptera varies with tree age in juniper woodlands

1. As trees age, they undergo significant physiological and morphological changes. Nevertheless, tree ontogeny and its impacts on herbivores are often overlooked as determinants of plant–herbivore population dynamics and the strength of plant–herbivore interactions. 2. Juniperus (Cupressaceae) is a dominant, long‐lived conifer that serves as the sole host to a specialised assemblage of caterpillars. Over the past 150 years, several juniper species in western North America have expanded their geographic occupancy at local and regional scales, which has resulted in an increase in the number of immature trees on the landscape. Using assays in the laboratory, the effects of tree ontogeny on caterpillar performance and oviposition preference for two juniper specialist caterpillars, Callophrys gryneus (Lycaenidae) and Glena quinquelinearia (Geometridae), were examined. The study considered whether responses to tree ontogeny were consistent across caterpillar species and juniper host species. 3. Tree age was found to be a reliable predictor of caterpillar performance, with caterpillars developing more quickly and growing larger when fed foliage from young trees. Differences in the phytochemical diversity between foliage from trees of different ages might help to explain observed differences in caterpillar performance. Interestingly, the specialist butterfly, C. gryneus, displayed an oviposition preference for foliage from old‐growth Juniperus osteosperma trees, despite the fact that larvae of this species performed poorly on older trees. 4. It is concluded that young juniper trees are an important resource for the specialised Lepidopteran community and that tree ontogeny is an important component of intraspecific variation, which contributes to the structure of plant–herbivore communities.     

The role of remnant trees in carbon sequestration,vegetation structure and tree diversity of early succession regrowing fallows in eastern Sierra Leone

Remnant tree presence affects forest recovery after slash‐and‐burn agriculture. However, little is known about its effect on above‐ground carbon stocks, especially in Africa. We focused our study on Sierra Leone, part of the Upper Guinean forests, an important centre of endemism threatened by encroachment and forest degradation. We studied 99 (20‐m‐radius) plots aged 2–10 years with and without remnant trees and compared their above‐ground carbon stocks, vegetation structure (stem density, basal area) and tree diversity. Above‐ground carbon stocks, stem density, basal area, species richness and tree diversity increased significantly with fallow age. Remnant tree presence affected significantly tree diversity, species dominance and above‐ground carbon stocks, but not vegetation structure (stem density, basal area). Number of remnant trees and number of species of remnant trees were also important explanatory variables. Although other factors should be considered in future studies, such as the size and dispersal modes of remnant trees, our results highlight that more strategic inclusion of remnant trees is likely to favour carbon stock and forest recovery in old fallows. To our knowledge, this is the first study on early succession regrowing fallows in West Africa.     

A synthesis of radial growth patterns preceding tree mortality

Tree mortality is a key factor influencing forest functions and dynamics, but our understanding of the mechanisms leading to mortality and the associated changes in tree growth rates are still limited. We compiled a new pan‐continental tree‐ring width database from sites where both dead and living trees were sampled (2970 dead and 4224 living trees from 190 sites, including 36 species), and compared early and recent growth rates between trees that died and those that survived a given mortality event. We observed a decrease in radial growth before death in ca. 84% of the mortality events. The extent and duration of these reductions were highly variable (1–100 years in 96% of events) due to the complex interactions among study species and the source(s) of mortality. Strong and long‐lasting declines were found for gymnosperms, shade‐ and drought‐tolerant species, and trees that died from competition. Angiosperms and trees that died due to biotic attacks (especially bark‐beetles) typically showed relatively small and short‐term growth reductions. Our analysis did not highlight any universal trade‐off between early growth and tree longevity within a species, although this result may also reflect high variability in sampling design among sites. The intersite and interspecific variability in growth patterns before mortality provides valuable information on the nature of the mortality process, which is consistent with our understanding of the physiological mechanisms leading to mortality. Abrupt changes in growth immediately before death can be associated with generalized hydraulic failure and/or bark‐beetle attack, while long‐term decrease in growth may be associated with a gradual decline in hydraulic performance coupled with depletion in carbon reserves. Our results imply that growth‐based mortality algorithms may be a powerful tool for predicting gymnosperm mortality induced by chronic stress, but not necessarily so for angiosperms and in case of intense drought or bark‐beetle outbreaks.     

Resource availability and disturbance shape maximum tree height across the Amazon

Tall trees are key drivers of ecosystem processes in tropical forest, but the controls on the distribution of the very tallest trees remain poorly understood. The recent discovery of grove of giant trees over 80 meters tall in the Amazon forest requires a reevaluation of current thinking. We used high‐resolution airborne laser surveys to measure canopy height across 282,750 ha of old‐growth and second‐growth forests randomly sampling the entire Brazilian Amazon. We investigated how resources and disturbances shape the maximum height distribution across the Brazilian Amazon through the relations between the occurrence of giant trees and environmental factors. Common drivers of height development are fundamentally different from those influencing the occurrence of giant trees. We found that changes in wind and light availability drive giant tree distribution as much as precipitation and temperature, together shaping the forest structure of the Brazilian Amazon. The location of giant trees should be carefully considered by policymakers when identifying important hot spots for the conservation of biodiversity in the Amazon.     

Roost tree characteristics determine use by the white‐striped freetail bat (Tadarida australis,Chiroptera: Molossidae) in suburban subtropical Brisbane,Australia

Abstract We examined factors affecting roost tree selection by the white‐striped freetail bat Tadarida australis (Chiroptera: Molossidae), a large insectivorous bat in suburban Brisbane, Australia. We compared biophysical characteristics associated with 34 roost trees and 170 control trees of similar diameter, height and tree senescence characters. Roost trees used by the white‐striped freetail bat had significantly higher numbers of hollows in the trunk and branches (P < 0.003) and were more likely to contain a large trunk cavity with an internal diameter of >30 cm (P < 0.001) than control trees. These trees also accommodated more species of hollow‐using fauna (P = 0.005). When comparing roost trees with control trees of similar diameters and heights, roost trees were on average at a later stage of tree senescence (P < 0.001). None of the roost trees were found in the large forest reserves fringing the Brisbane metropolitan area despite these areas being used for foraging by the white‐striped freetail bat. Although all tree locations in this study were in modified landscapes, roost trees tended to be surrounded by groups of trees and undergrowth. Roost trees provide important habitat requirements for hollow‐using fauna in suburban, rural and forested environments.     

Clades, clans, and reciprocal monophyly under neutral evolutionary models

The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions concerning the probability that pre-specified groups of taxa form monophyletic groups (clades) in the tree. We extend earlier work to derive exact formulae for the probability of finding one or more groups of taxa as clades in a rooted tree, or as ‘clans’ in an unrooted tree. Our findings are relevant for calculating the statistical significance of observed monophyly and reciprocal monophyly in phylogenetics.     

Xylem hydraulic safety and construction costs determine tropical tree growth

Faster growth in tropical trees is usually associated with higher mortality rates, but the mechanisms underlying this relationship are poorly understood. In this study, we investigate how tree growth patterns are linked with environmental conditions and hydraulic traits, by monitoring the cambial growth of 9 tropical cloud forest tree species coupled with numerical simulations using an optimization model. We find that fast‐growing trees have lower xylem safety margins than slow‐growing trees and this pattern is not necessarily linked to differences in stomatal behaviour or environmental conditions when growth occurs. Instead, fast‐growing trees have xylem vessels that are more vulnerable to cavitation and lower density wood. We propose the growth ‐ xylem vulnerability trade‐off represents a wood hydraulic economics spectrum similar to the classic leaf economic spectrum, and show through numerical simulations that this trade‐off can emerge from the coordination between growth rates, wood density, and xylem vulnerability to cavitation. Our results suggest that vulnerability to hydraulic failure might be related with the growth‐mortality trade‐off in tropical trees, determining important life history differences. These findings are important in furthering our understanding of xylem hydraulic functioning and its implications on plant carbon economy.     

芍药属牡丹组基于形态学证据的系统发育关系分析

对芍药属牡丹组Paeonia L.sect.Moutan DC.（全部野生种）40个居群进行了基于形态学证据的系统学分析,试图建立组内种间的系统发育关系。利用PAUP （4.0）计算机程序分别构建了建立在25个形态学性状基础上的所有研究类群的距离树（UPGMA、NJ）和最大简约树（MP）。所得树的拓扑结构基本一致,差异只发生在距离树和简约树之间,在由形态和细胞学关系都很近的5个种（牡丹P.suffruticosa、矮牡丹P.jishanensis、卵叶牡丹P.qiui、紫斑牡丹P.rockii和凤丹P.o     

A holistic approach to determine tree structural complexity based on laser scanning data and fractal analysis

The three‐dimensional forest structure affects many ecosystem functions and services provided by forests. As forests are made of trees it seems reasonable to approach their structure by investigating individual tree structure. Based on three‐dimensional point clouds from laser scanning, a newly developed holistic approach is presented that enables to calculate the box dimension as a measure of structural complexity of individual trees using fractal analysis. It was found that the box dimension of trees was significantly different among the tested species, among trees belonging to the same species but exposed to different growing conditions (at gap vs. forest interior) or to different kinds of competition (intraspecific vs. interspecific). Furthermore, it was shown that the box dimension is positively related to the trees’ growth rate. The box dimension was identified as an easy to calculate measure that integrates the effect of several external drivers of tree structure, such as competition strength and type, while simultaneously providing information on structure‐related properties, like tree growth.     

Tree recruitment of European tree species at their current upper elevational limits in the Swiss Alps

Aim The physical and physiological mechanisms that determine tree‐line position are reasonably well understood, but explanations for tree species‐specific upper elevational limits below the tree line are still lacking. In addition, once these uppermost positions have been identified, questions arise over whether they reflect past expansion events or active ongoing recruitment or even upslope migration. The aims of this study were: (1) to assess current tree recruitment near the cold‐temperature limit of 10 major European tree species in the Swiss Alps, and (2) to rank species by the extent that their seedlings and saplings exceed the elevational limit of adult trees, possibly reflecting effects of the recent climate warming. Location Western and eastern Alps of Switzerland. Methods For each species, occurrences were recorded along six elevational transects according to three size classes from seedlings to adult trees in 25‐m‐elevation steps above and below their regional upper elevational limit. Two methods were used to compare upper elevational limits between seedlings, saplings and adults within species. First, we focused on the uppermost occurrence observed in each life stage for a given species within each studied region; and second, we predicted their upper distribution range using polynomial models fitted to presence/absence data. Results Species exhibited a clear ranking in their elevational limit. Regional differences in species limits (western versus eastern Swiss Alps) could largely be attributed to regional differences in temperature. Observed and predicted limits of each life stage showed that all species were represented by young individuals in the vicinity of the limit of adult trees. Moreover, tree recruitment of both seedlings and saplings was detected and predicted significantly beyond adult tree limits in most of the species. Across regions, seedlings and saplings were on average found at elevations 73 m higher than adult trees. Main conclusions Under current conditions, neither seed dispersal nor seedling establishment constitutes a serious limitation of recruitment at the upper elevational limits of major European trees. The recruits found beyond the adult limits demonstrate the potential for an upward migration of trees in the Alps in response to ongoing climate warming.     

PhyloDraw: a phylogenetic tree drawing system

SUMMARY: PhyloDraw is a unified viewing tool for phylogenetic trees. PhyloDraw supports various kinds of multi-alignment formats (Dialign2, Clustal-W, Phylip format, NEXUS, MEGA, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cladogram, slanted cladogram, phylogram, unrooted tree, and radial tree. By using several control parameters, users can easily and interactively manipulate the shape of phylogenetic trees. This program can export the final tree layout to BMP (bitmap image format) and PostScript. AVAILABILITY: http://pearl.cs.pusan.ac.kr/phylodraw/ CONTACT: jhchoi@pearl.cs.pusan.ac.kr     

Historical biogeography of Australian Rhamnaceae, tribe Pomaderreae

Aim To discover the pattern of relationships of areas of endemism for Australian genera in the plant family Rhamnaceae tribe Pomaderreae for comparison with other taxa and interpretation of biogeographical history. Location Australian mainland, Tasmania and New Zealand. Methods A molecular phylogeny and geographic distribution of species within four clades of Pomaderreae are used as a basis for recognition of areas of endemism and analysis of area relationships using paralogy‐free subtrees. The taxon phylogeny is the strict consensus tree from a parsimony analysis of 54 taxa, in four clades, and sequence data for the internal transcribed spacer regions of ribosomal DNA (ITS1‐5.8S‐ITS2) and the plastid DNA region trnL‐F. Results The biogeographical analysis identified five subtrees, which, after parsimony analysis, resulted in a minimal tree with 100% consistency and seven resolved nodes. Three sets of area relationships were identified: the areas of Arnhem and Kimberley in tropical north Australia are related based on the phylogeny of taxa within Cryptandra; the moister South‐west of Western Australia, its sister area the coastal Geraldton Sandplains, the semi‐arid Interzone region and arid Western Desert are related, based on taxa within Cryptandra, Spyridium, Trymalium and Pomaderris; and the eastern regions of Queensland, McPherson‐Macleay, south‐eastern New South Wales (NSW), Victoria, southern Australia, Tasmania and New Zealand are related based on Cryptandra, Pomaderris and Spyridium. Tasmania and NSW are related based entirely on Cryptandra, but the position of New Zealand relative to the other south‐eastern Australian regions is unresolved. Main conclusions The method of paralogy‐free subtrees identified a general pattern of geographic area relationships based on Australian Pomaderreae. The widespread distribution of clades, the high level of endemicity and the age of fossils for the family, suggest that the Pomaderreae are an old group among the Australian flora. Their biogeographical history may date to the early Palaeogene with subsequent changes through to the Pleistocene.     

Chronic water stress reduces tree growth and the carbon sink of deciduous hardwood forests

Predicted decreases in water availability across the temperate forest biome have the potential to offset gains in carbon (C) uptake from phenology trends, rising atmospheric CO₂, and nitrogen deposition. While it is well established that severe droughts reduce the C sink of forests by inducing tree mortality, the impacts of mild but chronic water stress on forest phenology and physiology are largely unknown. We quantified the C consequences of chronic water stress using a 13‐year record of tree growth (n = 200 trees), soil moisture, and ecosystem C balance at the Morgan–Monroe State Forest (MMSF) in Indiana, and a regional 11‐year record of tree growth (n > 300 000 trees) and water availability for the 20 most dominant deciduous broadleaf tree species across the eastern and midwestern USA. We show that despite ~26 more days of C assimilation by trees at the MMSF, increasing water stress decreased the number of days of wood production by ~42 days over the same period, reducing the annual accrual of C in woody biomass by 41%. Across the deciduous forest region, water stress induced similar declines in tree growth, particularly for water‐demanding ‘mesophytic’ tree species. Given the current replacement of water‐stress adapted ‘xerophytic’ tree species by mesophytic tree species, we estimate that chronic water stress has the potential to decrease the C sink of deciduous forests by up to 17% (0.04 Pg C yr^?1) in the coming decades. This reduction in the C sink due to mesophication and chronic water stress is equivalent to an additional 1–3 days of global C emissions from fossil fuel burning each year. Collectively, our results indicate that regional declines in water availability may offset the growth‐enhancing effects of other global changes and reduce the extent to which forests ameliorate climate warming.     

Everglades tree island restoration: testing a simple tree planting technique patterned after a natural process

Tree islands in the Everglades are critical landscape features, but anthropogenic modification of the Everglades during the past century has led to the degradation and loss of many of the tree islands that originally dotted the Everglades landscape. Many of the tree islands have lost elevation and the majority of their woody species such that they are now covered with emergent plants such as sawgrass (Cladium jamaicense). A simple, cost‐effective tree planting technique is needed for restoring degraded Everglades tree islands. We patterned our design after a natural Everglades process that creates floating islands, which promotes tree survival and growth in both flooded and dry conditions and may lead to the development of fixed islands. Commercial peat bags were tested as a means to provide the medium for the growth and establishment of potted tree saplings native to Everglades tree islands. Three tree species (Annona glabra, Ficus aurea, and Acer rubrum) and five treatments were evaluated. The results indicate that the preferred deployed peat‐bag configuration should provide the greatest additional elevation to minimize inundation and be planted with a single Everglades tree island species sapling, with a single commercial tree fertilizer spike inserted for nutrients. Although most plants survived and many thrived for the two‐year period of this study, determining whether the trees planted using this technique can become established will require longer‐term studies and extensive field tests.     

Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia

Recent phylogenetic analyses of a large dataset for mammalian families (169 taxa, 26 loci) portray contrasting results. Supermatrix (concatenation) methods support a generally robust tree with only a few inconsistently resolved polytomies, whereas MP‐EST coalescence analysis of the same dataset yields a weakly supported tree that conflicts with many traditionally recognized clades. Here, we evaluate this discrepancy via improved coalescence analyses with reference to the rich history of phylogenetic studies on mammals. This integration clearly demonstrates that both supermatrix and coalescence analyses of just 26 loci yield a congruent, well‐supported phylogenetic hypothesis for Mammalia. Discrepancies between published studies are explained by implementation of overly simple DNA substitution models, inadequate tree‐search routines and limitations of the MP‐EST method. We develop a simple measure, partitioned coalescence support (PCS), which summarizes the distribution of support and conflict among gene trees for a given clade. Extremely high PCS scores for outlier gene trees at two nodes in the mammalian tree indicate a troubling bias in the MP‐EST method. We conclude that in this age of phylogenomics, a solid understanding of systematics fundamentals, choice of valid methodology and a broad knowledge of a clade's taxonomic history are still required to yield coherent phylogenetic inferences.