Understanding Evolutionary Trees

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

An Anthropogenic Escape Route from the “Gulliver Syndrome” in the West African Savanna

A major challenge for ecologists has long been to develop a model to explain the coexistence of grasses and trees in the savanna. The recent shift in emphasis to non-equilibrium-based theories has resulted in a rethinking of this problem. As resource allocation models have been replaced by demographic ones, the focus has shifted to plant life histories. The tree/grass ratio is now conceptualized as a function of disturbance history. Empirical studies demonstrate that repeat fires trap tree sprouts in perpetual juvenile states. Ecologists suggest natural pathways for juveniles to escape, reach maturity, and maintain tree/grass ratios. This study documents how long-fallow agriculture serves as an anthropogenic pathway. The study compares tree cover on long-fallow and unfarmed savanna plots in southern Mali where burning is annual. Tree height, girth, and species were recorded for 29 quadrats. The results demonstrate a significant difference in the size, number, and species of trees; those on fallow plots were taller, more numerous, and more diverse.

Evidence of gonochorism in a grouper, <Emphasis Type="Italic">Mycteroperca rosacea</Emphasis>, from the Gulf of California,Mexico

The sexual pattern and sexual development of the leopard grouper, Mycteroperca rosacea, were investigated from 483 specimens collected from the Gulf of California, Mexico. Histological and population data indicated a gonochoric sexual pattern. Some juveniles passed through an immature bisexual phase of gonadal development, but no evidence of post-maturational sex change was found. The immature bisexual phase is believed to be associated only with male development. The size distribution and size at sexual maturity were similar for both males and females. In accordance with predictions of the size-advantage model, the gonochoric sexual pattern of M. rosacea is likely influenced by its group-spawning mating system.

Climatic significance of intra-annual bands in the wood of <Emphasis Type="Italic">Nothofagus pumilio</Emphasis> in southern Patagonia

Nothofagus pumilio (Poepp et Endl.) Krasser is the dominant subalpine tree in the southern Andes between 36°S and 55°S. Increment cores from a N. pumilio stand growing near the Ameghino Glacier (50°25S, 73°10W), southern Patagonian Andes, Argentina, contain significant numbers of intra-annual bands (or false rings) which have not been previously described for this species. These samples are used to develop a well-replicated ring-width chronology and a record of intra-annual bands from AD 1760 to 1997. Annual variations in radial growth of N. pumilio at this site are negatively correlated with spring–summer temperatures and positively with spring precipitation. The formation of intra-annual bands appears to be a response to anomalously dry-warm springs followed by wet-warm late summers. Intra-annual bands may occur in up to 95% of the sampled trees in a given year, and the percentage of trees affected was used as an indication of the strength of the forcing event. Narrow rings occurred in the years following intra-annual band formation, reflecting the lagged effect of unfavorable climatic conditions on tree growth during the subsequent growing season. Intra-annual bands occurred more frequently in the twentieth century than the late eighteenth and nineteenth centuries. This contrasting pattern seems to be a response to the combination of a long-term warming trend and a significant decrease in precipitation recorded during the last 100 years in this region of southern South America.

Tree thinking cannot taken for granted: challenges for teaching phylogenetics

Tree thinking is an integral part of modern evolutionary biology, and a necessary precondition for phylogenetics and comparative analyses. Tree thinking has during the 20th century largely replaced group thinking, developmental thinking and anthropocentricism in biology. Unfortunately, however, this does not imply that tree thinking can be taken for granted. The findings reported here indicate that tree thinking is very much an acquired ability which needs extensive training. I tested a sample of undergraduate and graduate students of biology by means of questionnaires. Not a single student was able to correctly interpret a simple tree drawing. Several other findings demonstrate that tree thinking is virtually absent in students unless they are explicitly taught how to read evolutionary trees. Possible causes and implications of this mental bias are discussed. It seems that biological textbooks can be an important source of confusion for students. While group and developmental thinking have disappeared from most textual representations of evolution, they have survived in the evolutionary tree drawings of many textbooks. It is quite common for students to encounter anthropocentric trees and even trees containing stem groups and paraphyla. While these biases originate from the unconscious philosophical assumptions made by authors, the findings suggest that presenting unbiased evolutionary trees in biological publications is not merely a philosophical virtue but has also clear practical implications.

<Emphasis Type="Italic">Berlinia korupensis</Emphasis> (Leguminosae <Emphasis Type="Italic">–</Emphasis> Caesalpinioideae), a new tree species from Cameroon

Summary  The tree species Berlinia korupensis Mackinder & Burgt is described as new. The species is endemic to the southern part of Korup National Park in Cameroon. Seventeen trees have been found so far, the largest being 42 m high and having a trunk diam. of 88 cm. The new species is assessed as Critically Endangered (CR D) under the criteria of IUCN. Two distribution maps are included; one map indicating the single locality in Cameroon near the Nigerian border where the new species was found and another map of the permanent plot where 14 of the 17 trees were recorded. A line drawing is also included, along with colour photographs of the flowers and the trunk.

Pith: a marker of primary growth in Picea abies (L.) Karst.

The primary growth of trees may be studied either by following their development over time, which is costly and requires long-term monitoring, or by a posteriori growth analyses. Trees in temperate forests show rhythmic growth, which is characterised by morphological or anatomical markers. The study described here focuses on the pith of trees as an internal marker for the retrospective analysis of primary growth. Changes in pith size and density were quantified along a stem of Norway spruce [Picea abies (L.) Karst.] with high spatial resolution. The results showed that pith would appear to be a reliable marker of the annual growth rhythm even in the presence of polycyclism. Annual shoot limits were characterised by reductions in pith size associated, at the same time, with increases in pith density. In addition, pith size may provide information about tree ontogeny. The start of the competition with neighbouring trees was very likely responsible for an overall decrease in pith size. Regarding high frequency variations, pith size appeared to be less sensitive to local environmental fluctuations like climate than other studied variables such as annual shoot length and annual ring width. Finally, X-ray computed tomography proved to be a very promising method for the non-destructive detection of annual shoot limits in stems based on longitudinal changes in pith density, as demonstrated in a log of Norway spruce.

A single operon-encoded form of the acetyl-CoA decarbonylase/synthase multienzyme complex responsible for synthesis and cleavage of acetyl-CoA in <Emphasis Type="Italic">Methanosarcina thermophila</Emphasis>

Methanogens growing on C-1 substrates synthesize 2-carbon acetyl groups in the form of acetyl-CoA for carbon assimilation using the multienzyme complex acetyl-CoA decarbonylase/synthase (ACDS) which contains five different subunits encoded within an operon. In species growing on acetate ACDS also functions to cleave the acetate C-C bond for energy production by methanogenesis. A number of species of Methanosarcina that are capable of growth on either C-1 compounds or acetate contain two separate ACDS operons, and questions have been raised about whether or not these operons play separate roles in acetate synthesis and cleavage. Methanosarcina thermophila genomic DNA was analyzed for the presence of two ACDS operons by PCR amplifications with different primer pairs, restriction enzyme analyses, DNA sequencing and Southern blot analyses. A single ACDS operon was identified and characterized, with no evidence for more than one. MALDI mass spectrometric analyses were carried out on ACDS preparations from methanol- and acetate-grown cells. Peptide fragmentation patterns showed that the same ACDS subunits were present regardless of growth conditions. The evidence indicates that a single form of ACDS is used both for acetate cleavage during growth on acetate and for acetate synthesis during growth on C-1 substrates. Electronic Supplementary Material  Supplementary material is available for this article at

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Two new species of <Emphasis Type="Italic">Mycena</Emphasis> from alpine sites in Norway

Mycena aphanes and Mycena exilis, belonging to section Filipedes and section Polyadelphia, are proposed as new species. They are described and illustrated and compared to other species in the two sections. Mycena aphanes is a strikingly characteristic Mycena with fulvous or yellowish brown colours of both pileus and stipe. Mycena exilis is characterized by its occurrence on fallen Salix leaves, a pale brown pileus, occasionally with a pale pink tinge, narrowly adnate lamellae, four-spored basidia, and the presence of clamp connections.

Leitlinien zur molekulargenetischen Diagnostik: Fragiles-X und Fragiles-X assoziiertes Tremor/Ataxie Syndrom

Ohne Zusammenfassung

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Hierarchical analysis of piecewise affine models of gene regulatory networks

A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions. In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns out to be quite relevant because of the strong discrete structure underlying these equations. Its biological relevance is shown on a 7-dimensional PWA system modeling the gene network responsible for the carbon starvation response in Escherichia coli.

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Individual variability of behavioural responses by Wandering Albatrosses (Diomedea exulans) to human disturbance

Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.

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Ecological and population genetics research imperatives for transgenic trees

Applied research that supplies requisite, albeit incomplete, scientific knowledge is necessary if we are to address the legal, regulatory, and social/ethical issues regarding the use of transgenic trees. The technology for creating these trees has gotten far ahead of research on the ecological and population genetics impacts that may emerge. In this paper, we propose a comprehensive, interdisciplinary scientific approach that combines experimental results with model projections. We believe that much of this work must be completed before social issues can be clarified and resolved. Broad-based failure by those in the forestry-minded scientific community to carry out this interdisciplinary research could lead either to the establishment of transgenic trees with unintended consequences, or to an inability to realize the numerous advantages that this technology may offer.

Will Agroforests Vanish? The Case of Damar Agroforests in Indonesia

Resin producing agroforestry in the Krui area of Sumatra in Indonesia is presented as an environmentally friendly, income generating land-use system which contributes to both development and conservation objectives. We studied the change in household income portfolios in three communities in the Krui area. The studies revealed that in the period 1995–2004 agroforestry remained the main source of income. We predict, however, that due to declining resin productivity per hectare, and rising price and demand for timber, an increasing number of farmers will cut their mature agroforests in the near future. At the same time our data suggests that farmers will continue tree planting activities. In result old agroforests may vanish while new ones will be established.

Progress in understanding the <Emphasis Type="Italic">N-</Emphasis>demethylation of alkaloids by exploiting isotopic techniques

The reaction of N-demethylation plays an important role in the degradation of some alkaloids in a number of organisms. This review presents how our understanding of the N-demethylation of nicotine in plants has been improved through studies in cell cultures of Nicotiana plumbaginifolia and N. glutinosa using a variety of isotopic techniques. The overall aim is to understand how metabolism recycles the alkaloid skeleton, both in terms of the metabolic route(s) exploited and the reaction mechanisms of the enzymes involved. The former has been approached using high-resolution 2-dimensional NMR and GC-MS methods; the latter by determining kinetic isotope effects and modelling the potential reaction steps. It appears that the mechanism for nicotine demethylation in plants is similar to but has significant differences from that described for mammals and Pseudomonas bacteria. These differences are discussed.