Untangling the contribution of characters to evolutionary relationships: a case study using fossils,morphology, and Genes

Given the importance of phylogenetic trees to understanding common ancestry and evolution, they are a necessary part of the undergraduate biology curriculum. However, a number of common misconceptions, such as reading across branch tips and understanding homoplasy, can pose difficulties in student understanding. Students also may take phylogenetic trees to be fact, instead of hypotheses. Below we outline a case study that we have used in upper-level undergraduate evolution and ichthyology courses that utilizes shark teeth (representing fossils), body characters, and mitochondrial genes. Students construct their own trees using freely available software, and are prompted to compare their trees with a series of questions. Finally, students explore homoplasy, polytomies, and trees as hypotheses during a class discussion period. This case study gives students practice with tree-thinking, as well as demonstrating that tree topology is reliant on which characters and tree-building algorithms are used.     

Winter starch reserves of white oak as a predictor of attack by the twolined chestnut borer,Agrilus bilineatus (Weber) (Coleoptera: Buprestidae)

Summary The twolined chestnut borer, Agrilus bilineatus (Weber) (Coleoptera: Buprestidae), attacks oaks (Quercus spp.) and is associated with extensive mortality of trees in the eastern deciduous forests of North America. We tested the hypothesis that winter starch reserves of oak roots are an indicator of tree vigor and that only trees low in stored starch would be attacked by A. bilineatus. We measured the levels of stored starch in the roots of 200 non-infested healthy white oaks during the dormant season and determined their correlation with A. bilineatus attacks the following spring. There was a significant increase in A. bilineatus captures on sticky traps with a decrease in winter starch reserves. Trees low in stored starch that were also stressed by phloem-girdling attracted 3.7 times as many beetles as did non-girdled trees that were low in starch. However, non-girdled trees that had low winter starch reserves were also attacked. Only oaks that had had extremely low winter root starch reserves (<5mg/g dry weight of root sapwood tissue) were heavily attacked by A. bilineatus and subsequently died. One third of non-girdled low starch trees and 67% of phloem-girdled low starch trees died, whereas none of the trees with root starch >5 mg/g dry wt died. These results indicate that winter starch reserves are a good predictor of A. bilineatus attack.The investigation reported in this paper (No. 87-7-8-118) is in connection with a project of the Kentucky Agricultural Experiment Station and is published with the approval of the Director     

Heterogeneity of phosphorus distribution in a patterned landscape,the Florida Everglades

The biologically mediated transfer of nutrients from one part of a landscape to another may create nutrient gradients or subsidize the productivity at specific locations. If limited, this focused redistribution of the nutrient may create non-random landscape patterns that are unrelated to underlying environmental gradients. The Florida Everglades, USA, is a large freshwater wetland that is patterned with tree islands, elevated areas that support woody vegetation. A survey of 12 tree islands found total soil phosphorus levels 3–114 times greater on the island head than the surrounding marsh, indicating that the Florida Everglades is not a homogeneous oligotrophic system. It was estimated that historically 67% of the phosphorus entering the central Everglades was sequestered on tree islands, which are ~3.8% of the total land area. This internal redistribution of phosphorus onto tree islands due to the establishment of trees may be one reason that marshes have remained oligotrophic and may explain the spatial differentiation of the patterned Everglades landscape.     

Forest decline: Endogenous dynamics,tree defenses,and the elimination of spurious correlation

Two important unresolved problems in pollution impact research are early detection of changes in tree and forest growth and determination of the causes of observed growth declines. Consideration of tree defensive systems can shed light on dieback phenomena. Trees possess both chemical and structural defenses, with both types having both active and passive dimensions. When stress or pollution causes a reduction in vigor, defenses may become ineffective, resulting in insect pest and pathogen attack. This leads to a positive feedback cycle of declining vigor. Level of defenses differs by species, site, and life-stage. Consideration of these factors leads to better statistical methods for correlating pollution dose with tree growth response. It is shown that several recent studies are potentially flawed by inadequate consideration of species type, tree age, or stand density. It is shown that forest growth models can be used to correct for endogenous changes in tree growth rates as long as the trees used to derive parameters for the model were not themselves affected by pollution.     

Tree diversity in sacred groves of the Jaintia hills in Meghalaya, northeast India

Biodiversity of woody species was investigated in Ialong and Raliangsacred groves of the Jaintia hills in Meghalaya, northeast India. These grovesrepresent the climax subtropical broad-leaved forest of the area. A total of 738individuals belonging to 82 species, 59 genera and 39 families was identified ina 0.5 ha plot of the Ialong sacred grove, whereas the same area in theRaliang sacred grove had 469 individuals of 80 species, 62 genera and 41families. About 32% species were common to both groves. Lauraceae, with10–17 species, was the dominant family. The canopy and subcanopy stratawere respectively composed of 28 and 33% of the total tree species in theforest. The number of species as well as stem density were greater for the treesof lower dbh (5–15 cm) class compared to the higher (> 66cm) dbh class. The majority of the species showed a contagiousdistribution pattern and low frequency. The basal area varied from 57.4 to 71.4m² ha^–1. Species richness within theforest varied from 3 to 15 per 100 m² in Ialong and 3 to 12 per 100m² in Raliang. The dominance–distribution curves showed highequitability and low dominance in both groves.     

Tree invasion of a montane meadow complex: temporal trends,spatial patterns,and biotic interactions

Questions: Do spatial and temporal patterns of encroachment of Pinus contorta and Abies grandis in a montane meadow suggest strong biotic controls on the invasion process? Location: Forest–meadow mosaic, 1350 m a.s.l., Cascade Range, Oregon, US. Methods: We combined spatial point pattern analysis, population age structures, and a time‐series of stem maps to quantify spatial and temporal patterns of conifer invasion over a 200‐yr period in three plots totaling 4 ha. Results: Trees established during two broad, but distinct periods (late 1800s, then at much greater density in the mid‐1900s). Recent invasion was not correlated with climatic variation. Abies grandis dominated both periods; P. contorta established at lower density, peaking before A. grandis. Spatially, older (≥90 yr) P. contorta were randomly distributed, but older A. grandis were strongly clumped (0.2‐20 m). Younger (<90 yr) stems were positively associated at small distances (both within and between species), but were spatially displaced from older A. grandis, suggesting a temporal shift from facilitation to competition. Establishment during the 1800s resulted in widely scattered P. contorta and clumps of A. grandis that placed most areas of meadow close to seed sources permitting more rapid invasion during the mid‐1900s. Rapid conversion to forest occurred via colonization of larger meadow openings – first by shade‐intolerant P. contorta, then by shade‐tolerant A. grandis– and by direct infilling of smaller openings by A. grandis. Conclusions: In combination, spatial and temporal patterns of establishment suggest an invasion process shaped by biotic interactions, with facilitation promoting expansion of trees into meadows and competition influencing subsequent forest development. Once invasion is initiated, tree species with different life histories and functional traits can interact synergistically to promote rapid conversion of meadow to forest under a broad range of climatic conditions.     

TWIG: a model to simulate the gravitropic response of a tree axis in the frame of elasticity and viscoelasticity, at intra-annual time scale

Trees are able to maintain or modify the orientation of their axes (trunks or branches) by tropic movements. For axes in which elongation is achieved but cambial growth active, the tropic movements are due to the production of a particular wood, called reaction wood which is prestressed within the growing tree. Several models have been developed to simulate the gravitropic response of axes in trees due to the formation of reaction wood, all within the frame of linear elasticity and considering the wood maturation as instantaneous. The effect viscoelasticity of wood has, to our knowledge, never been considered. The TWIG model presented in this paper aims at simulating the gravitropic movement of a tree axis at the intra-annual scale. In this work we studied both the effect of a non-instantaneous maturation process and of viscoelasticity. For this purpose, we considered the elastic case with maturation considered as an instantaneous process as the reference. The introduction of viscoelasticity in TWIG has been done by coupling TWIG to a model developed for bridges. Indeed from a purely mechanical point of view, bridges and trees are very similar: they are structures which are built in stages, they are made of several materials (composite structures), their materials are prestressed (wood is prestressed during the maturation process as a result of polymerisation of lignin and cellulose to form the secondary cell wall and concrete is prestressed during drying). Simulations gave evidence that the reorientation process of axes can be significantly influenced by the kinetics of maturation. Moreover the model has now to be tested with more experimental data of wood viscoelasticity but it appears that in the range of a relaxation time from 0 to 50 days, viscoelasticity has an important effect on the evolution of tree shape as well as on the values of prestresses.     

Lack of demographic equilibrium indicates natural,large‐scale forest dynamics,not a problematic forest conservation policy – a reply to Brzeziecki et al.

Brzeziecki et al. 2016 (Journal of Vegetation Science 27: 460–467.) describe a decrease in population densities and proportion of younger individuals for several tree species in permanent research plots in the core zone of the Bia?owie?a National Park. They attribute insufficient tree recruitment inter alia to the strict protection. Although the authors performed a thorough analysis of tree population dynamics, the scales of the study mean that their far‐reaching conclusions on the causes and consequences of the lack of demographic equilibrium cannot be supported by the data. The inadequate spatial and temporal scales of the study did not allow for the observation of representative population dynamics. Furthermore, they did not compare the results obtained in the strictly protected area with known demographic dynamics of trees in surrounding managed forests or under other forms of nature conservation. Looking from the wider ecosystem perspective, it is clear that strict protection is not a cause for concern and, instead, that such a near‐natural forest manifests population dynamics at rather larger scales.     

On an outbreak of the citrus flat-headed borer,Agrilus auriventris E. Saunders in Nagasaki Prefecture

The process of an outbreak of the citrus flat-headed borer, Agrilus auriventris in Nagasaki Prefecture was described with some ecological considerations on causative factors. This outbreak which showed a typical “Gradation”, initiated around 1958, and terminated in 1963. The peak year was seen in 1961. At first attack by the borer was restricted to old and weak trees, but it was also found in young and healthy trees in the peak year. Some environmental conditions in orchards were examined in relation to the intensity of infestation by the borer. Soil management and drought seemed to have remarkable correlations with the borer's infestations. Probably, this outbreak was caused by the weakening of citrus tree by gummosis and abnormal defoliation, aging of orchard trees, and drought in the summer of 1959∼1960. Interrelation between these causes and processes are shown schematically in Fig. 12.     

Tree species diversity in small, tropical riparian forest fragments in Belize, Central America

Tree species diversity was measured in a network of very small galleryforests within the Mountain Pine Ridge savanna in Belize. Research focussed onforest patches smaller than 1 ha in size (micro-forests) and linearstrips of trees along creeks lacking interior core zones with low understoreylight levels (tree thickets). Twenty-five micro-forests and 51 tree thicketsites were sampled throughout the savanna. A total of 144 morphospecies 5cm dbh (106 in micro-forests and 117 in tree thickets) werefound, which represents 1/5 of the approximately 700 native tree species in Belize.Most (85.3%) of the species encountered are typically found in tropical rainforests and few are restricted to savanna or riparian environments. Speciesaccumulated at a much faster rate in micro-forests than in tree thickets. Onlyone species, the palm Acoelorraphe wrightii, was extremelyabundant, accounting for almost 30% of all stems. Many of the species werepresent in very low densities: 19% of all species found in micro-forests and 42%of those found in tree thickets had on average one or fewer stems per hectare. Alarge proportion of species were also found infrequently across the landscape,being present in only 36% of micro-forests and at 52% of tree thicket sites. Theresults indicate that networks of very small forest patches can contain highnumbers of species and could therefore contribute to the maintenance of regionalbiodiversity.     

Correlation between trunk and branch age in trees as a new parameter in the analysis of tree architecture

A method for characterizing tree form is developed by linear regression of the age of the trunk on the average branch age at different heights. This relationship holds for a wide variety of situations, including both theoretical models and observed tree samples. The intercept of the regression, a, the ‘index of trunk distinctness’, reflects the branching pattern inherent to the species and indicates whether the trunk is erect or not. The slope, b, is termed the ‘crown thickness coefficient’, because it indicates a branching pattern. Tree forms can be classified into nine theoretical groups; three of these are physically impossible. The method was applied to real trees and a and b are shown to be useful tree form characteristics. Possible applications of the method are briefly discussed.     

Short-term changes in tree populations in a tropical evergreen forest at Varagalaiar, Western Ghats, India

Within a 30-ha permanent plot of a tropical evergreen forest in the Anamalais, Indian Western Ghats, all the 13415 trees 30cmgbh (belonging to 153 species) were identified and tagged during 1997–1998. This communication reports the results of tree population changes based on two annual censuses (1999 and 2000) of the plot after the initial census, and compares the results with other tropical forest sites. One species, Ficus beddomei, disappeared from the plot and there was no new addition of species. Of the 96 species that showed changes in their population density, for 12 species recruitment and mortality matched. Tree recruitment (5 treesha^–1year^–1) exceeded mortality (4 treesha^–1year^–1) during the two-year period. Four modes of tree deaths were recorded in our site. The per cent mortality of trees differed between tree size classes during each recensus. The plot tree density increased progressively in the two-year period, indicating that shifts in species composition and density in natural forests, without major catastrophic disturbance, occur slowly.     

Interactions between climate change, competition, dispersal, and disturbances in a tree migration model

Potentially significant shifts in the geographical patterns of vegetation are an expected result of climate change. However, the importance of local processes (e.g., dispersal, competition, or disturbance) has been often ignored in climate change modeling. We develop an individual-based simulation approach to assess how these mechanisms affect migration rate. We simulate the northward progression of a theoretical tree species when climate change makes northern habitat suitable. We test how the rate of progression is affected by (1) competition with a resident species, (2) interactions with disturbance regimes, (3) species dispersal kernel, and (4) the intensity of climate change over time. Results reveal a strong response of species’ expansion rate to the presence of a local competitor, as well as nonlinear effects of disturbance. We discuss these results in light of current knowledge of northern forest dynamics and results found in the climatic research literature.     

Diverging growth and resilience of Pinus tabulaeformis and Pinus massoniana to droughts in north-south transition zone,central China

Climate transition zone is a sensitive area of climate change and ecological transition where forests are vulnerable to climate extremes. Extreme droughts are increasing in frequency and magnitude under climate change, resulting in structure and function changes of forest ecosystems. Here, to analyze climate-growth relationships and quantify tree resilience to extreme droughts, we developed six tree-ring-width chronologies from P. tabulaeformis and P. massoniana sampling sites in Mt. Jigong region, Central China. The results indicated that all chronologies from the two species had good consistency, precipitation in current April and mean temperature in current August or mean minimum temperature from current August to October were the main limiting factors of the two tree species growth, but the responses of P. massoniana ring-width to climatic factors was more complex than that of P. tabulaeformis. The results also showed that tree growth of 1999–2005 was the lowest growing period during 1979–2018, and P. massoniana grew better than P. tabulaeformis before 2005 and vice versa after 2005. Comparing low growth years of trees, we identified to study tree growth resilience. The calculations from 1988, 1999–2005 and 2011 drought years indicated that P. tabulaeformis had more increased resilience to extreme droughts than that of P. massoniana, and the two species had stronger ecological recovery and resilience under global warming and non-extreme drought conditions in the recent 40 years. These results have implications for predicting tree resilience and identifying tree species in heterogeneous forest landscapes vulnerable to future climate change in climatic transition zone.     

Tree structure,regeneration and survival of seedlings and sprouts in highmontane forests of the Garhwal Himalayas,India

The tree structure of some timberline and sub-alpine forests of the Garhwal Himalayas was studied with reference to the regeneration status and survival of tree seedlings and sprouts. Nine tree and shrub species were chosen. The dominating tree species wereAbies pindrow andQuercus semicarpifolia. Sprouts were found to have a higher survival rate than seedlings, but both suffered from winter conditions. Girth class measurements showed that trees between 1.6 and 2.5 m were best represented.     

Population dynamics of the swallowtail butterfly,Papilio xuthus L., in a deforested area

The long-term population dynamics of the swallowtail butterfly, Papilio xuthus, were studied by means of life table analysis in a deforested area, where the host tree, Zanthoxylum ailanthoides, was growing. The number of eggs laid on host trees in the deforested area decreases as secondary succession progresses. When the trees were classified into three groups, i. e. tall, medium and short, according to their height relative to the surrounding vegetation, less eggs were laid on tall than on short host trees. Life tables for the natural populations in each generation were developed on the basis of mean values for 6 years. Eggs and larvae in early stages were attacked chiefly by small- and middle-sized predators, such as ants, spiders, bugs and orthopterids, while later stage larvae were attacked chiefly by birds or Polistes wasps. An inchneumonid wasp was the most important mortality factor in the pupal stage. Key-factor analysis was tested on the life table data of each immature stage. The late larval stage was a key stage, and most mortality factors were considered to operate independently. The test for density dependency did not show any tendencies. The analysis of variance in two-way classifications was carried out for the difference of survival rate among the tree groups. It was suggested that tall host trees were unsuitable for P. xuthus. The construction of life tables for artificially inoculated populations on large host trees showed that high physiological death rate were characteristic of such trees in comparison with natural populations on smaller trees. The characteristics of the population dynamics of P. xuthus in the deforested area are compared among some kinds of the habitat, and the interrelationship between P. xuthus and its host plant are discussed.     

弄岗北热带喀斯特季节性雨林15 hm2动态监测样地树木死亡特征分析

以广西弄岗北热带喀斯特季节性雨林15 hm²森林动态监测样地为对象，结合2011年和2016年两次调查数据，分析5年间样地树木死亡个体的数量、径级结构和空间格局特征等。结果显示：2011年至2016年，样地有86.5%的树种出现了个体死亡的现象，死亡个体占个体总数的14.4%；死亡个体的聚集程度随空间尺度的增大而逐渐减弱；小径级个体死亡与周边邻体和环境的关联性较大；竞争是影响弄岗北热带喀斯特季节性云林树木死亡的主要因素。综合来看，北热带喀斯特季节性雨林内树木死亡并非是一个完全随机的过程，而是树木本身特征和生物与非生物环境共同作用的结果。