To tree or not to tree

The practice of tracking geographical divergence along a phylogenetic tree has added an evolutionary perspective to biogeographic analysis within single species. In spite of the popularity of phylogeography, there is an emerging problem. Recurrent mutation and recombination both create homoplasy, multiple evolutionary occurrences of the same character that are identical in state but not identical by descent. Homoplasic molecular data are phylogenetically ambiguous. Converting homoplasic molecular data into a tree represents an extrapolation, and there can be myriad candidate trees among which to choose. Derivative biogeographic analyses of 'the tree' are analyses of that extrapolation, and the results depend on the tree chosen. I explore the informational aspects of converting a multicharacter data set into a phylogenetic tree, and then explore what happens when that tree is used for population analysis. Three conclusions follow: (i) some trees are better than others; good trees are true to the data, whereas bad trees are not; (ii) for biogeographic analysis, we should use only good trees, which yield the same biogeographic inference as the phenetic data, but little more; and (iii) the reliable biogeographic inference is inherent in the phenetic data, not the trees.     

Piebaldism in tree shrews

Two types of hair changes occurred in an experimental group of captive tree shrews (Tupaia glis) living on an artificial diet in dark laboratory quarters. The most common variation in the fur consisted of a gradual type of hair loss resulting in a sparse coat and dry skin. The second type of hair change occurred in a female tree shrew in which patches of hair fell out all over the body. White hair regrowth followed exposure to sunlight, with subsequent repigmentation of the bases of the new hairs. Tree shrews suffering from the first type of hair disorder also improved when exposed to sunlight.     

Interspecific variation in tree seedling establishment in canopy gaps in relation to tree density

Abstract. We tested whether interspecific variation in tree seedling establishment in canopy gaps was significantly related to interspecific variation in tree density, for seven deciduous forest tree species (Quercus alba, Hamamelis virginiana, Acer rubrum, Sassafras albidum, Quercus rubra, Prunus serotina, Ostrya virginiana). For each species, seedling establishment was calculated as the difference in seedling density before experimental gap creation versus three years after gap creation. In each of the six experimentally-created gap types (33 % or 66 % removal of tree basal area from 0.01-ha, 0.05-ha or 0.20-ha patches), differences in seedling establishment among species were significantly related to differences in their density in the tree canopy. A regression model with log_e tree density as the independent variable accounted for between 93 % and 98 % of interspecific variation in seedling establishment. Our results provide empirical support for models of tree dynamics in gaps that assume seedling establishment depends on canopy tree density.     

Diverse scaling relationships of tree height and diameter in five tree species

Background: Allometric scaling relationships are important in ecology and forestry. The metabolic scaling theory (MST) predicts a universal invariant scaling relationship for tree growth, relating height and diameter to each other.

Aims: Data on five tree species (Pinus taeda L., Pinus virginiana Mill., Liquidambar styraciflua L., Liriodendron tulipifera L., and Pinus palustris Mill.) were used to test the predictions from MST on the scaling of height–diameter and also diameter growth.

Methods: Data on tree height and diameter for five tree species from both natural forests and plantations were collected to study two types of scaling relationships: tree height–diameter and stem diameter growth. A reduced major axis of regression analysis model type II was used to determine scaling exponents from each species under different environmental conditions.

Results: No universal invariant scaling exponent was found in height–diameter and diameter growth for the five species. The scaling varied across natural forests, plantations and scales (e.g., time and number of measured trees). However, in some situations the scaling exponents failed to show significant difference with the predicted values (e.g., 2/3 or 1).

Conclusions: Diverse scaling exponents were observed for the five tree species with the scaling relationships varying with environmental settings.     

Soil heterogeneity in tree mixtures depends on spatial clustering of tree species

Heterogeneity in soil characteristics promotes and maintains coexistence between a diverse set of species. In forests, trees have species-specific impacts on soil abiotic characteristics and mixing of tree species is being promoted as a tool to ensure high levels of diversity and functioning. Yet, limited knowledge is available on the effect of tree species composition and spatial clustering on heterogeneity in soil characteristics. In this paper we derived heterogeneity of key characteristics of the leaf litterfall, the forest floor and the mineral topsoil (C, N and base cation concentration, C:N ratio and mass) in 53 plots of 7 different tree species compositions. We found that heterogeneity increased from the leaf litterfall, through the forest floor down to the mineral topsoil. Mixing tree species did not lead to an increased heterogeneity in the forest floor and topsoil compared to monocultures. However, we did find that mixed plots where conspecific trees stand in groups are more heterogeneous than plots where species are intimately mixed. Our results imply that heterogeneity in soil characteristics does not necessarily increase with tree diversity, but that within mixed stands the spatial organization of tree species should be considered in relation to the scale at which heterogeneity is desired.     

Drought-induced tree death in savanna

Increasing densities of woody plants in savannas has been attributed to both elevated atmospheric CO₂ and reduced burning with grazing management, such that the biome could represent a substantial carbon sink. However, we show that extreme droughts (less than two-thirds expected rainfall over 3 years) occur in the drier half of the savanna biome and can cause substantial tree death. An Australian case study reveals that a net increase in tree cover over five decades of above-average rainfall was offset by sudden tree death during drought. The relationship between woody cover change and rainfall is moderated by competition with growth being facilitated by low woody cover and drought-induced death more likely as the woody component of savanna increases. The results are not supportive of a sustained increase in the woody component of xeric savannas resulting from CO₂ fertilization or land management. Extensive tree death in savanna regions will become a stark consequence of climate change if predictions of increasing severity and frequency of drought are realized.     

Human time in tree rings

‘Human time’ means time in the context of human culture and activities. It is shown how ‘human time’ is biologically archived in and dendrochronologically extracted from tree rings. For illustration, examples in the late medieval Hanseatic city of Lübeck are selected.     

Stardust component in tree rings

Tree-ring series collected from different parts of Arctic (Fennoscandia, Kola Peninsula and Northern Siberia) are investigated by means of the multi-taped method (MTM) of spectral analysis. Results of spectral analysis allow us to select the main periods of solar variability (22-, 30–33- and 80–90-year solar cycles) in Kola and Fennoscandia tree-ring chronologies. Besides it was found that only periodicities of around 20 years are present in Siberian and Stockholm series, respectively. With respect to 11-year periodicity, which is the most prominent one in sunspot number spectrum (Schwabe cycle) it may be said that it hardly appeared in Arctic tree-ring series. Although the 22-year cycles in climatic records are perceivable (it is also evident from our and other results), any physical mechanisms by which a reversal in the solar magnetic field could influence climate are still missing. To our mind, a potential cause of this phenomenon seems to be a variation of stardust flux inside the solar system. The most recent observations in frame of the DUST experiment on board the Ulysses spacecraft have shown that stardust level inside of the solar system was trebled during the recent solar maximum (Landgraf et al., 2003. Penetration of the heliosphere by the interstellar dust stream during solar maximum. Journal Geophysical Research 108, 8030). It is possible that the periodic increase of stardust in the solar system will influence the amount of extraterrestrial material that rains down to the Earth and consequently down to the Earth's atmosphere and may affect climate through alteration of atmospheric transparency and albedo.     

Variation in litter under individual tree crowns: Implications for scattered tree ecosystems

In forest ecosystems litter is usually assessed in terms of the average amount produced by the canopy. In scattered tree ecosystems this approach is problematic because the canopy is discontinuous and the spatial arrangement of litter highly variable. We addressed this problem by quantifying the spatial variation in litter load and litter composition associated with individual trees in a Eucalyptus melliodora – Eucalyptus blakelyi woodland. Litter was sampled under crowns and in grassland adjacent to 10 E. blakelyi and 10 E. melliodora trees ranging in diameter at breast height (dbh) from 14 to 129 cm. A total of 302 L samples were collected from these trees, at distances ranging from 0 to 42 m from main stem. The sampled litter loads ranged from 0.02 to 109.3 t ha^?1 and were significantly higher under tree crowns than in grassland for litter and each component of litter (leaves, bark, fine twigs, coarse twigs). In particular, the mean litter load under tree crowns (12.5 t ha^?1) was an order of magnitude higher than the mean litter load in grassland (1.27 t ha^?1). There was a significant (P = 0.0103) positive relationship between mean litter load under the tree crown and dbh, indicating larger trees produced more litter per unit area of ground than smaller trees. Generalized Linear Modelling produced highly significant (P < 0.0001) models predicting the spatial variation in litter load and litter composition in terms of distance from main stem and dbh. Our models demonstrate gradients in litter load and composition under tree crowns. These gradients were most pronounced for the large trees in our study. The disproportionate input of litter and variety of litter components associated with large trees in our study supports their keystone role in scattered tree ecosystems and highlights the need to maintain these structures in agricultural landscapes.     

A tree of tree frogs around the Black Sea

Speciation, the process by which one species evolves into two or more, is a major focus of ongoing debate, particularly regarding the geographic context in which it occurs. Geographic models of speciation tend to fall into discrete categories, typically referred to as allopatric, parapatric and sympatric speciation, according to whether two groups evolve reproductive isolation while geographically isolated, differentiated but connected by gene flow, or completely co‐occurring. Yet molecular studies indicate that full development of reproductive isolation can take very long compared with the timescale at which climatic oscillations occur, such that the geographic context of differentiating forms might change often during the long process to full species. Studies of genetic relationships across the ranges of organisms with low‐dispersal distances have the potential to reveal these complex histories. In a particularly elegant example in this issue, Dufresnes et al. ( 2016 ) use genetic variation and ecological niche modelling to show that a ring of populations of the eastern tree frog (Hyla orientalis) surrounding the Black Sea had a complex history of geographic differentiation. Alternating phases of geographic fragmentation and phases of gene flow between neighbouring populations have produced a pattern of gradual genetic change connecting the western, southern and eastern sides of the ring, with the northwestern and northeastern forms being most differentiated. In the north, a population in Crimea appears to have been produced through mixture of the two extreme forms. The overall genetic relationships are reminiscent of those found in ring species, which have been used as prime demonstrations of the process of speciation. The difference, however, is that the terminal forms appear to have mixed rather than be reproductively isolated, although more research is needed to infer whether there might be some reproductive isolation on the northern side of the ring.     

Human time in tree rings

‘Human time’ means time in the context of human culture and activities. It is shown how ‘human time’ is biologically archived in and dendrochronologically extracted from tree rings. For illustration, examples in the late medieval Hanseatic city of Lübeck are selected.     

Microbes in tree swallow semen

A frequently hypothesized but poorly studied cost of multiple mating in birds is that exposure to pathogenic sexually transmitted microbes (STM's) can lower reproductive success. Conversely, female birds may benefit from high frequencies of copulation and multiple copulation partners if they receive cloacal inoculations of beneficial STM's that can either protect them against future encounters with pathogens and/or serve as therapy against present infection. We examined the semen of 30 male tree swallows (Tachycineta bicolor) in 1998 to determine the presence and prevalence of potential pathogenic and beneficial STM's. Semen was collected directly from males after applying gentle pressure to the cloaca and we used standard microbiological techniques to identify microbes. We found that 19 of 30 samples contained one or more types of microbes. In these 19 positive samples, we isolated both pathogenic and beneficial microbes from 11, only pathogenic microbes from seven, and only beneficial microbes from one. This variation among males suggests that females would benefit from considering a particular male's potential as a donor of either pathogenic or beneficial STM's as a criterion for mate choice. There were few significant differences between males with pathogen-infected semen and those without pathogens in their semen in measures of size, morphology, and ectoparasite score and feather damage. Likewise, there were few significant differences between males with beneficial Lactobacilli spp. in their semen and those without Lactobacilli spp. in their semen in measures of size, morphology, and ectoparasite score and feather damage. We were unable to determine if there was a relationship between microbe presence and prevalence on reproductive performance.     

Effect of density control on tree growth at ecological tree planting sites in Japan

The effect of density control of tree growth on revegetation sites planted by the ecological tree planting (ETP) method, one of the most common woodland creation methods devised in the 1970s in Japan, is analyzed. The ETP method is performed with the expectation of natural establishment of woodlands by planting saplings of native tree species composing potential natural vegetation in high density. The results show that the general growth condition of such woodlands is not inferior. Often, however, it is suggested that transition of the composition of the woodlands does not progress exactly along the transition expected, because of the characteristics of ETP sites, that is, even-aged forest despite the planting concept consisting of several tree species. Occasionally, expected natural selection does not occur. In such circumstances this is interpreted as suggesting that artificial density control, for example thinning, is necessary. A thinning trial was conducted on the ETP woodland in Himeji, Hyogo, Japan during the fourth year after planting, and tree growth was investigated in the third, seventh, and ninth years after thinning. The results show thinning has the potentiality to bring about substantial change in the establishment of multiple layered woodlands. When natural selection cannot be expected on ETP woodland, application of thinning as part of the management plan is important to establish ecological woodland with much ecological function.     

树木年龄和断面积对加拿大北方林树木死亡率的影响

以加拿大北部的杨树(Populus spp.)、斑克松(Pinus banksiana)、黑云杉(Picea mariana)为对象,采用长期定位试验,对134块固定样地的活立木及枯死木进行调查,并运用线性回归的方法研究树木年龄、断面积和林分类型对3种树木死亡率的影响.结果表明:随着树龄和断面积的增加,林木的死亡率呈上升趋势.杨树在斑克松林中的死亡率较高,而在黑云杉林中死亡率较低.在黑云杉林中,树龄是影响斑克松死亡率的主要因子;而在杨树林中,断面积是影响斑克松死亡率的重要因子;不同林分类型中树龄对黑云杉死亡率的影响显著.树种组成对树种的死亡率有显著影响;树木年龄、断面积和林分类型之间的交互效应对各树种的死亡率均有显著影响;不同林分类型中同一树种的死亡状况有明显差异.     

Linking multiple-level tree traits with biomass accumulation in native tree species used for reforestation in Panama

To improve establishment yield and carbon accumulation during reforestation, analyses of species adaptations to local environments are needed. Here we measured, at the individual scale, links between biomass accumulation and multiple-level tree traits: biomass partitioning, crown morphology and leaf physiology. The study was carried out on one- and three-year-old individuals of five tropical tree species assigned to pioneer (P) or non-pioneer (NP) functional groups. Among the species, Cedrela odorata, Luehea seemannii and Hura crepitans showed the greatest biomass accumulation. On our seasonally dry site, species performance during the first year was dependent on a greater investment in above-ground foraging, while performance after three years was mainly related to water relations. However, large biomass accumulations were not simply associated with an efficient water use but also with contrasting water uses, based on inter-specific relationships. Generally, greater carbon isotope discrimination (Δ_leaf) was related to greater allocation to roots. Species with high Δ_leaf generally showed high leaf potential nitrogen use efficiency (PNUE), suggesting that lower water use efficiency (WUE) increases the efficiency of photosynthetically active N. Also, PNUE was negatively correlated to leaf mass per area (LMA), implying that photosynthetically active N is diluted as total leaf mass increases. Finally, no distinction in measured traits, including biomass accumulation, was observed between the two functional groups.     

Differences in tree and shrub establishment due to tree guard type in a temperate upland pasture

Success of establishing native trees in cool temperate environments depends on the ability of seedlings to withstand subzero temperatures and recurrent frosts. This study compared the survival and growth of five tree and shrub species with two guard types at three landscape positions in an upland pasture. Seedlings were planted between December 2013 and March 2014. Half of the seedlings were planted in tall Corflute^® guards (60 cm high), and the remaining seedlings were interplanted in milk cartons (30 cm). Seedling survival and height were measured in November 2014. Hourly temperature readings were recorded between March and November 2014. Seedling height for all species was greater in tall guards than milk cartons at all landscape positions, possibly at least partly due to etiolation. However, seedlings in tall guards survived better than seedlings in milk cartons at mid‐ and upper‐slope positions. Higher temperatures may have benefited seedling performance by prolonging the growing season as average maximum temperature was significantly higher inside tall guards than milk cartons and ambient conditions at all landscape positions. Average daily temperature was significantly higher in tall guards compared to milk cartons and ambient conditions at the upper‐slope site only. There were no significant differences in average minimum temperature between guard types at all landscape positions.     

谈系统发生树建立的分子标准

随着进化生物学以及生物信息学的发展 ,研究不同物种间进化关系的方法也有了新的进展。其中分子进化方法使得系统发生树的建立更加简便和精确。几种系统发生树的建树方法及相关分子标准目前比较流行。。     

Maximum tree: a consistent estimator of the species tree

We propose a model based approach to use multiple gene trees to estimate the species tree. The coalescent process requires that gene divergences occur earlier than species divergences when there is any polymorphism in the ancestral species. Under this scenario, speciation times are restricted to be smaller than the corresponding gene split times. The maximum tree (MT) is the tree with the largest possible speciation times in the space of species trees restricted by available gene trees. If all populations have the same population size, the MT is the maximum likelihood estimate of the species tree. It can be shown the MT is a consistent estimator of the species tree even when the MT is built upon the estimates of the true gene trees if the gene tree estimates are statistically consistent. The MT converges in probability to the true species tree at an exponential rate.     

High tree alpha-diversity in Amazonian Ecuador

In a 1 ha square plot of terra firme forest at 260 m elevation in Amazonian Ecuador, all trees with diameter at breast height (dbh) 5 cm were studied. There were 1561 individuals, 473 species, 187 genera and 54 families. Of these, 693 individuals, 307 species, 138 genera and 46 families had a dbh 10 cm. This is the highest number of tree species ever recorded for a tropical rain forest sample of this size. In both dbh classes, the most species-rich families were: Fabaceae sensu lato (including Mimosaceae and Caesalpiniaceae), Lauraceae and Sapotaceae; the most species-rich genera, were Pouteria, Inga and Protium. The vertical space was partitioned among species: 166 species were found only in the 5–10 dbh cm class and were mostly sub-canopy treelets, and 307 species with dbh 10 cm were mostly large canopy trees.