What are decision trees?

Decision trees have been applied to problems such as assigning protein function and predicting splice sites. How do these classifiers work, what types of problems can they solve and what are their advantages over alternatives?     

“Only slaves climb trees”

Professional and popular publications have increasingly depicted native peoples of Amazonia as “natural” conservationists or as people with an innate “conservation ethic.” A few classic examples are cited repeatedly to advance this argument with the result that these cases tend to be generalized to all indigenous peoples. This paper explores the premise that many of these systems of resource conservation come from areas of Amazonia where human survival depends on careful management of the subsistence base and not from a culturally imbedded “conservation ethic.” Where resource constraints do not pertain, as in the case of the Yuquí of lowland Bolivia, such patterns are unknown. Finally, the negative consequences of portraying all native peoples as natural conservationists is having some negative consequences in terms of current struggles to obtain indigenous land rights.     

How good are deep phylogenetic trees?

Great interest is given to species emerging early in phylogenetic reconstruction because they are often assumed to represent an ancestor. Recent studies indicate, however, that species branching deep in molecular trees are often fast-evolving ones, misplaced because of the long-branch artefact. The detection of genuinely deep-branching organisms remains an elusive task.     

Why are so many trees hollow?

In many living trees, much of the interior of the trunk can be rotten or even hollowed out. Previously, this has been suggested to be adaptive, with microbial or animal consumption of interior wood producing a rain of nutrients to the soil beneath the tree that allows recycling of those nutrients into new growth via the trees roots. Here I propose an alternative (non-exclusive) explanation: such loss of wood comes at very little cost to the tree and so investment in costly chemical defence of this wood is not economic. I discuss how this theory can be tested empirically.     

Structural trees for proteins containing φ-motifs

In the present study, a novel structural motif of proteins referred to as the phi-motif is considered, and two novel structural trees in which the phi-motif is taken as the root structure have been constructed. The simplest phi-motif is formed by three adjacent beta-strands connected by loops and packed in one beta-sheet so that its overall fold resembles the Greek letter phi. Construction of the structural trees and modeling of folding pathways have shown that all structures of the protein superfamilies can be obtained by stepwise addition of alpha-helices and/or beta-strands to the root phi-motif taking into account a restricted set of rules inferred from known principles of protein structure. The structural trees are a good tool for structure comparison, structural classification of proteins, as well as for searching for all possible protein folds and folding pathways.     

Do trees in urban or ornamental plantings receive more damage by insects than trees in natural forests?

Abstract.

• 1 To determine if trees in urban or ornamental plantings are more susceptible to attack and receive more damage to foliage by herbivores than trees in natural forests, we compared the amount of leaf damage caused by several guilds of insects feeding on seven species of native, broadleaf trees in two geographic locations.
• 2 Total leaf damage did not differ significantly between urban or ornamental and natural forests, although trees in natural forests tended to have slightly higher levels of leaf damage.
• 3 Damage caused by chewing insects was consistently higher on trees in natural forests than in urban or ornamental plantings. All other feeding guilds showed no consistent pattern in levels of damage between the two habitats.
• 4 Total damage levels were highest on canopy trees and lowest on understorey trees.
• 5 These results are inconsistent with the view that trees in urban or ornamental settings are more susceptible to insect attack than trees in natural forests.
• 6 The lower level of foliar damage caused by chewing insects on trees in urban or ornamental plantings may arise because of low rates of dispersal by insects into urban environments, higher levels of plant resistance to insect attack in urban or ornamental plantings, or lower survival rates of herbivorous insects in urban environments.

     

Can exotic pine trees assist in restoration?

Invasive exotic woody species, including conifers escaped from plantations, are usually regarded as serious threats to native biodiversity. Becerra & Montenegro (Applied Vegetation Science, 16, 2013, 2) present an interesting example of invasive Pinus radiata facilitating native woody regeneration in semi‐arid central Chile. However, the positive value of invasive conifers for restoration and conservation will not necessarily apply in all situations.     

Can large unmanaged trees replace ancient pollarded trees as habitats for lichenized fungi,non-lichenized fungi and bryophytes?

Management of ancient trees constitutes a major dilemma in the conservation of associated biodiversity. While traditional methods are often advocated, such practices may incur considerable costs and their effects have rarely been scientifically evaluated. We compared the communities of lichenized fungi, non-lichenized fungi, and bryophytes among equal number of coarse previously pollarded and unmanaged trees (n = 340). On 400 Ulmus glabra and 280 Fraxinus excelsior trees at 62 sites in Norway, we found 209 lichenized fungi, 128 non-lichenized fungi, and 115 bryophytes. Pollarded trees were richer in microhabitats than unmanaged trees and had significantly higher richness of bryophytes (ash) and non-lichenized fungi (ash and elm), the latter increasing with the availability of dead wood, cavities and coarse bark structure in pollarded trees. Further, the average total number of red-listed species, and red-listed lichenized fungi separately, were significantly higher on pollarded versus unmanaged trees, with diversity related to trunk circumference, depth of bark fissures and number of cavities. Our results underline the importance of microhabitats associated with old trees, but we cannot establish with certainty the importance of pollarding per se. Since we did not find any negative effect of canopy cover for community diversity, we assume that old trees with rich epiphytic communities can develop without management intervention. The high share (37 out of 49) of red-listed species occurring on unmanaged trees, and the fact that 11 red-listed species were found exclusively on unmanaged trees, may further indicate that unmanaged trees can with time replace the ancient pollarded trees as habitats for rich cryptogamic communities.     

Old trees, new trees--is there any progress?

The amount of comparative data for phylogenetic analyses is constantly increasing. Data come from different directions such as morphology, molecular genetics, developmental biology and paleontology. With the increasing diversity of data and of analytical tools, the number of competing hypotheses on phylogenetic relationships rises, too. The choice of the phylogenetic tree as a basis for the interpretation of new data is important, because different trees will support different evolutionary interpretations of the data investigated. I argue here that, although many problematic aspects exist, there are several phylogenetic relationships that are supported by the majority of analyses and may be regarded as something like a robust backbone. This accounts, for example, for the monophyly of Metazoa, Bilateria, Deuterostomia, Protostomia (= Gastroneuralia), Gnathifera, Spiralia, Trochozoa and Arthropoda and probably also for the branching order of diploblastic taxa (“Porifera”, Trichoplax adhaerens, Cnidaria and Ctenophora). Along this “backbone”, there are several problematic regions, where either monophyly is questionable and/or where taxa “rotate” in narrow regions of the tree. This is illustrated exemplified by the probable paraphyly of Porifera and the phylogenetic relationships of basal spiralian taxa. Two problems span wider regions of the tree: the position of Arthropoda either as the sister taxon of Annelida (= Articulata) or of Cycloneuralia (= Ecdysozoa) and the position of tentaculate taxa either as sister taxa of Deuterostomia (= Radialia) or within the taxon Spiralia. The backbone makes it possible to develop a basic understanding of the evolution of genes, molecules and structures in metazoan animals.     

Do most human populations descend from phylogenetic trees?

Molecular biologists and some population geneticists have recently claimed to be able to reconstruct modern human populations remote history by means of phylogenetic trees. Many objections to this method are discussed in the present paper. The most important are

1. Inter-populations migrations are likely to have been important, even in the remote past. So the “treeness” of this evolution is disputable.
2. There is no reason to believe that actual molecular phylogenies would be convergent between different molecules and would therefore represent populations history.

The various kind of genetic data, their relations to other data and the limits of their possible use in the analysis of our past are then discussed, together with the ideological background of the most common theories and of their publication. It is very likely that the history of different populations was heterogeneous. Small and isolated hunter-gatherers frequently evolving close to a phylogenetic model, while dense and increasing populations, since the Neolithic, were closer to a dynamic network model, structured by isolation by distance. In any case, our present knowledge is obviously insufficient to reconstruct our genetic past, especially on the long term, and we can only hope that the development of the HUGO Genome Diversity project is going to yield the significant information presently lacking.     

Carved trees in grazed forests in boreal Sweden—analysis of remaining trees, interpretation of past land-use and implications for conservation

Culturally modified trees (CMTs) provide unique insights into traditional knowledge and uses of the forest ecosystems. In close relation to pre-industrial livestock herding in central Sweden, it was a custom to carve text and symbols on trees and use them as notice boards in the forest. The main aim of this study was to document and analyse remaining carved trees in a managed forest landscape of 160 km². The same area was surveyed twice, once in 1986 and once in 2003. 488 carved trees were documented and classified into legible themes that were interpreted in the light of past herding practices. Name was the most common theme, found in 85% of the carvings. Most of the carvings were made in the period from the 1750s until the early 1900s. The custom of carving on trees was closely related to important grazing areas and the need to establish rights to them. The main losses of carved trees nowadays are due to their natural death and decay as most of the carved trees are located in areas that are not targeted for management. A primary recommendation for preservation is therefore to continue documentation of the trees because of the noticeable deterioration in readability of the carvings.