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.     

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.     

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.     

Wind-induced tree sways

Conclusions The question of how the results of investigations on wind-induced tree sways can be used in practice is often posed. First, it must be said that, according to information in the literature, no tree species can survive violent storms (with mean wind speeds over a period of 10 min higher than 30 m/s) without any damage. This threshold value for wind speed is related to the height near the top of a forest stand. Taking the results of the spectral method as a basis for the reduction of storm risk of vital conifers, necessary silvicultural action must be: (1) to influence the amount and frequency distribution of the wind force in such a way that its shere of action becomes more and more unsuitable for tree sways, and (2) to raise the characteristic frequencies of the trees' primary sways because then effective wind force takes on lower and lower values due to narrow-band energy transfer.Numerous silvicultural methods for achieving these objectives, such as cutting off the tops of crowns or chaining trees together, are described in detail by Rottman (1986).     

Forest tree biotechnology

The past year has seen the fruits of biotechnological manipulation of forest trees approach commercial application. Advances in somatic embryogenesis have brought mass clonal propagation of the top commercial trees closer to reality, and efficient gene transfer systems have been developed for a number of conifers and hardwoods. Radical alterations in the quantity and quality of lignin in wood have been shown to be possible in softwoods and hardwoods through identification of naturally occurring mutants, as well as by engineering the lignin biosynthetic pathway with transgenes. The potential environmental and social impacts of the release of transgenic trees have become an increasingly contentious issue that will require more attention if we are to use these technologies to their full advantage.     

Seeded tree alignment

The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. Here we introduce a constrained form of this problem in which a partial mapping of a set of nodes (the "seeds") in one tree to a corresponding set of nodes in the other tree is given, and present efficient algorithms for both ordered and unordered trees. Whereas ordered tree matching based on seeded nodes has applications in pattern matching of RNA structures, unordered tree matching based on seeded nodes has applications in co-speciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which a polynomial-time algorithm is given here.     

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.     

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.     

QuickJoin--fast neighbour-joining tree reconstruction

We have built a tool for fast construction of very large phylogenetic trees. The tool uses heuristics for speeding up the neighbour-joining algorithm-while still constructing the same tree as the original neighbour-joining algorithm-making it possible to construct trees for 8000 species in <10 min on a single desktop PC. In comparison, the same task takes more than 30 min using the QuickTree neighbour-joining implementation.     

Studies on tree legumes

Twenty five species of tree legumes, belonging to genera Acacia, Albizzia, Bauhinia, Colophospermum, Dichrostachys, Leucaena, Peltophorum, Pithecolobium and Prosopis were examined for nodulation under pot culture conditions using unsterilized soil. Out of these, only nineteen tree-legumes nodulated. It was interesting to note that all the three species of Bauhinia and one each of Acacia, Colophospermum and Peltophorum did not nodulate both at Jodhpur and Delhi. Inoculation of tree legumes with their own rhizobial isolates, improved nodulation under sterilized conditions.     

The tree of eukaryotes

Recent advances in resolving the tree of eukaryotes are converging on a model composed of a few large hypothetical 'supergroups', each comprising a diversity of primarily microbial eukaryotes (protists, or protozoa and algae). The process of resolving the tree involves the synthesis of many kinds of data, including single-gene trees, multigene analyses, and other kinds of molecular and structural characters. Here, we review the recent progress in assembling the tree of eukaryotes, describing the major evidence for each supergroup, and where gaps in our knowledge remain. We also consider other factors emerging from phylogenetic analyses and comparative genomics, in particular lateral gene transfer, and whether such factors confound our understanding of the eukaryotic tree.     

Co-divergence and tree topology

Journal of Mathematical Biology - In reconstructing the common evolutionary history of hosts and parasites, the current method of choice is the phylogenetic tree reconciliation. In this model, we...     

生物多样性与林木育种

保护生物多样性在林木育种中必须予以重视。传统的林木育种主要考虑遗传增益。长期育种则以维持育种群体的变异性为主要目的。具有丰富生物多样性的天然森林群体是长期育种的基础。长期育种研究应以物种生物学、群体遗传学和居群生态学等为理论基础。主要研究森林群体的性质及群体的动态变化规律。传统林木育种的研究方向、研究内容及林木育种学的教学内容等都应予以适当的调整和补充。     

Revising the Bantu tree

Phylogenetic methods offer a promising advance for the historical study of language and cultural relationships. Applications to date, however, have been hampered by traditional approaches dependent on unfalsifiable authority statements: in this regard, historical linguistics remains in a similar position to evolutionary biology prior to the cladistic revolution. Influential phylogenetic studies of Bantu languages over the last two decades, which provide the foundation for multiple analyses of Bantu sociocultural histories, are a major case in point. Comparative analyses of basic lexica, instead of directly treating written words, use only numerical symbols that express non-replicable authority opinion about underlying relationships. Building on a previous study of Uto-Aztecan, here we analyse Bantu language relationships with methods deriving from DNA sequence optimization algorithms, treating basic vocabulary as sequences of sounds. This yields finer-grained results that indicate major revisions to the Bantu tree, and enables more robust inferences about the history of Bantu language expansion and/or migration throughout sub-Saharan Africa. “Early-split” versus “late-split” hypotheses for East and West Bantu are tested, and overall results are compared to trees based on numerical reductions of vocabulary data. Reconstruction of language histories is more empirically based and robust than with previous methods.