A phylogenetic tree is an illustration depicting the hypothesized degrees of evolutionary relationship amongst a selected set of taxa (singular = taxon). The taxa are typically species, but can also be higher-level Linnaean groupings like genera or families. Alternatively, some phylogenetic trees depict relationships among individuals within a species (e.g., from geographically isolated populations). Regardless of their rank, the taxa depicted in a phylogenetic tree are often called terminal taxa , because they occur at the tips of the tree. They are sometimes referred to as “terminals” or “leaves.”
Cross-scale management strategies for optimal control of trees invading from source plantations
Biological invasion by non-native tree species can transform landscapes, and as a consequence, has received growing attention from researchers and managers alike. This problem is driven primarily by the naturalisation and invasion of tree species escaping from cultivation or forestry plantations. Furthermore, these invasions can be strongly influenced by the land-use matrix of the surrounding region, specific management of the source populations, and environmental conditions that influence seed dispersal or habitat quality for the invader. A major unresolved challenge for managing tree invasions in landscapes is how management should be deployed to contain or slow the spread of invading populations from one or more sources (e.g. plantations). We develop a spatial simulation model to test: (1) how to best prioritise the control of invasive tree populations spatially to slow or contain the biological invader when habitat quality varies in the landscape, and (2) how to allocate control.
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The effect of environmental heterogeneity on spatial spread of invasive species has received little attention in the literature. Altering landscape heterogeneity may be a suitable strategy to control invaders in man-made landscapes. We use a population-based, spatially realistic matrix model to explore mechanisms underlying the observed invasion patterns of an alien tree species, Prunus serotina Ehrh., in a heterogeneous managed forest. By altering several parameters in the simulation, we test for various hypotheses regarding the role of several mechanisms on invasion dynamics, including spatial heterogeneity, seed dispersers, site of first introduction, large-scale natural disturbances, and forest management. We observe that landscape heterogeneity makes the invasion highly directional resulting from two mechanisms: (1) irregular jumps, which occur rarely via long-distance dispersers and create new founder populations in distant suitable areas, and (2) regular, continuous diffusion toward adjacent cells via short- and mid-distance vectors. At the landscape scale, spatial heterogeneity increases the invasion speed but decreases the final invasion extent. Hence, natural disturbances (such as severe storms) appear to facilitate invasion spread, while forest management can have contrasting effects such as decreasing invasibility at the stand scale by increasing the proportion of light interception at the canopy level. The site of initial introduction influences the invasion process but without altering the final outcome. Our model represents the real landscape and incorporates the range of dispersal modes, making it a powerful tool to explore the interactions between environmental heterogeneity and invasion dynamics, as well as for managing plant invaders.
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Diversity and Distributions
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Journal of Applied …
1. Designing practical rules for controlling invasive species is a challenging task for managers, particularly when species are long-lived, have complex life cycles and high dispersal capacities. Previous findings derived from plant matrix population analyses suggest that effective control of long-lived invaders may be achieved by focusing on killing adult plants. However, the cost-effectiveness of managing different life stages has not been evaluated. 2. We illustrate the benefits of integrating matrix population models with decision theory to undertake this evaluation, using empirical data from the largest infestation of mesquite (Leguminosae: Prosopis spp) within Australia. We include in our model the mesquite life cycle, different dispersal rates and control actions that target individuals at different life stages with varying costs, depending on the intensity of control effort. We then use stochastic dynamic programming to derive cost-effective control strategies that minimize the cost of controlling the core infestation locally below a density threshold and the future cost of control arising from infestation of adjacent areas via seed dispersal. 3. Through sensitivity analysis, we show that four robust management rules guide the allocation of resources between mesquite life stages for this infestation: (i) When there is no seed dispersal, no action is required until density of adults exceeds the control threshold and then only control of adults is needed; (ii) when there is seed dispersal, control strategy is dependent on knowledge of the density of adults and large juveniles (LJ) and broad categories of dispersal rates only; (iii) if density of adults is higher than density of LJ, controlling adults is most cost-effective; (iv) alternatively, if density of LJ is equal or higher than density of adults, management efforts should be spread between adults, large and to a lesser extent small juveniles, but never saplings. 4. Synthesis and applications. In this study, we show that simple rules can be found for managing invasive plants with complex life cycles and high dispersal rates when population models are combined with decision theory. In the case of our mesquite population, focussing effort on controlling adults is not always the most cost-effective way to meet our management objective.
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The Professional Geographer
The Relatedness of Taxa
Remember that phylogenetic trees depict degrees of relationship among taxa. On a phylogenetic tree, more closely related terminal taxa are connected by shallower nodes (i.e., nodes nearer to the tips of the tree) and more distantly related terminal taxa are connected by deeper nodes (i.e., nodes nearer to the base of the tree).
Examine the figure above. In that figure, Taxon B and Taxon C are more closely related to one another that either is to Taxon A. We know this because Taxon B and Taxon C share a shallower node (the blue node) than then node that either shares with Taxon A (the yellow node). Another way of putting this observation is that Taxon B and Taxon C share a node (the blue node) that neither shares with Taxon A. Taking a broader view, we also know that Taxa A, B, and C are more closely related to each other than they are to Taxa D, E, F, G, and H. This is because Taxa A, B, and C share the yellow node in common, which does not link to Taxa D, E, F, G, or H. Taxa A, B, and C are linked to Taxa D, E, F, G, and H by a deeper node (the red node).
Branches may be rotated about nodes without any change in the hypothesized relationships depicted on a tree diagram. Convince yourself that the three trees below depict the exact same set of relationships among Taxa A-H. In each case, the only change that has been made is that branches and the terminal taxa connected to them have been rotated around nodes. Remember, the degree of relationship amongst various combinations of terminal taxa is indicated by the relative depth of the nodes that connect them.
Tree A. Image by Jonathan R. Hendricks (Creative Commons Attribution-Sharealike 4.0 International License).
Tree B. Image by Jonathan R. Hendricks (Creative Commons Attribution-Sharealike 4.0 International License).
Tree C. Image by Jonathan R. Hendricks (Creative Commons Attribution-Sharealike 4.0 International License).
The graphic style of phylogenetic trees varies. For example, the tree shown below depicts the exact same pattern of relationships among Taxa A–H as the three trees shown above.
A bracket-style phylogenetic tree. Image by Jonathan R. Hendricks (Creative Commons Attribution-Sharealike 4.0 International License).
Increasingly, it is common to see circle-shaped phylogenetic trees such as the one shown below. Circular trees are often used to illustrate relationships among members of major groups of extant organisms, and these trees may have many terminal taxa. Circular trees can be read in the same way as the trees shown above, because the relative depth of the nodes indicates the degree of relatedness among terminals.
A circle-shaped phylogenetic tree that depicts relationships among the major groups of living organisms (blue = bacteria; green = Archaea; pink = eukaryotes). This tree was created by Ivica Letunic and was retraced by Mariana Ruiz Villarreal (public domain).
Clades and Sister Groups
A clade (from the Greek klados = branch) is a group that includes an ancestor (node) and all of its descendants (all shallower nodes and terminal taxa that descend from that node) on a phylogenetic tree. If you pick a node on a phylogenetic tree, you can easily draw a circle around the clade that it defines, as in the tree below. While many clades have no formal names, some important clades are named in formal classification schemes (for more on clades and classification, see this later section).
A phylogenetic tree that illustrates the concept of clades. Note that clades are not mutually exclusive, but are nested within one another. Image by Jonathan R. Hendricks (Creative Commons Attribution-Sharealike 4.0 International license).
Clades are not mutually exclusive, but rather form nested sets on a tree. Thus, any given taxon can belong to many clades. For example, in the tree above, Taxon B belongs to three clades, a clade defined by Node 1, a more inclusive clade defined by Node 2, and an even more inclusive clade defined by Node 7. Taxon E belongs to four clades defined by Nodes 3, 5, 6, and 7, respectively. Try to figure out how many clades Taxon A and Taxon H belong to, and determine which nodes define each clade.
Sister taxa or sister groups are pairs of terminal taxa and/or clades that branch from a common node and are often considered closely related. Pairs of sister terminal taxa in the figure above include: B and C, E and F, and G and H. The clade defined by Node 3 (Node 3 + Taxon E + Taxon F) is sister to the clade defined by Node 4 (Node 4 + Taxon G + Taxon H). Terminal taxon A is sister to the clade defined by Node 1 (Node 1 + Taxon B + Taxon C). Try to find more sister pairs on the tree above.
The Meaning of Branch Lengths
Two things are implicitly occurring along the branches of a phylogenetic tree. The first is the passage of time. Deeper nodes are older than the shallower nodes to which the are connected. Thus, deeper nodes indicate both more distant relationships among the terminal taxa that they connect, as well a greater age for the most recent common ancestor of those taxa. The second thing is evolutionary modification, or the accumulation of hereditary genetic and/or structural changes along branches. While these changes are often not shown (mapped) directly on the branches, it is these inferred changes that underpin the construction and interpretation of a phylogenetic tree. When systematists talk about ” branch lengths ,” they are typically referring to the number of these changes.
So, does the length of the branches as depicted on a phylogenetic tree (in other words, the length of the branches on an actual diagram showing a hypothesis of evolutionary relationships) mean anything? The answer is: it depends.
Time and number of evolutionary changes may have no direct relationship to the relative lengths of branches as depicted on a tree. Many such trees are cladograms, or branching diagrams made using clastic methods, which have their roots in the work of Willi Hennig. (Note: The term ” cladogram ” is sometimes applied to any type of phylogenetic tree.) Often, diagrams that are drawn for general informational purposes to depict a consensus hypothesis of relationships amongst a group of taxa (for example, in a textbook) also do not have branches scaled to time or to number of evolutionary changes. In this type of diagram, the taxa will either be aligned at the branch tips or all branches will be about the same length (meaning that the taxa are not aligned).
A phylogenetic tree in which the branches are not scaled to time or evolutionary change. This diagram is a cladogram. From: Turner et al. (2017) PLoS ONE 12(2): e0169885. Used in accordance with Creative Commons Attribution 4.0 International (CC BY 4.0) License.
In other cases, branches on a tree are scaled so that they reflect the amount of evolutionary change (in other words, the number of modifications in characteristics) that has occurred. In this type of diagram, branch lengths will differ and taxa will not be aligned at the branch tips. Sometimes this type of tree is called a phylogram.
Example of a phylogenetic tree with branches scaled to depict number of evolutionary changes (a phylogram). Notice the the branch lengths on the diagram differ and the taxa are not aligned. From: Zapata et al. (2015) PLoS ONE 10(10): e0139068. Used in accordance with Creative Commons 0 1.0 Universal, Public Domain Dedication (CC0 1.0).
Trees may also have branch lengths that are scaled to time, making the relationship between relative node depth and time explicit. Typically, a time scale (relative and/or numerical) will be included beside the tree to indicate the timing of branching events. If a tree is explicitly scaled to time, it can be called a chronogram; such trees are also sometimes called ” time trees ” (also time-trees or timetrees). If all taxa in a chronogram are extant (living), they will be aligned at the present.
Example of a phylogenetic tree with branches scaled to depict time (a chronogram). The gray bars at the nodes are error bars. From: Zhang et al. (2013) PLoS ONE 8(7): e70449. Used in Accordance with Creative Commons Attribution (CC BY) License.
Sometimes, extinct taxa may be included as terminals on a phylogenetic tree. If such a tree has branches scaled to time, extinct taxa will not be aligned at the present time. Rather, the branch tips for extinct taxa will end at the levels in time at which they went extinct, as shown below.
Examples of cladograms scaled to time and including extinct taxa as terminals. From: Wright and Stigall (2013) PLoS ONE 8(7): e68353. Used in Accordance with Creative Commons Attribution (CC BY) License.
