I have been studying for molecular characterization of tree species (specifically Tectona grandis L. f.). Phylograph is a visual result of such finding which is acquaint to all taxonomist, ecologist and geneticist . An insight on the above subject is as following:
Phylo genetic diversity (PD) is a measure of the genetic diversity contained within different branches of a phylogenetic tree and is useful when deciding which species or populations to conserve in order to retain maximum levels of genetic diversity and hence evolutionary potential.PD can also inform about how much unique genetic diversity a taxonomic unit (or subset of taxonomic units) contains and therefore how evolutionarily distinct that unit is. To calculate PD you construct a phylogenetic tree that depicts the evolutionary relationships among taxonomic units. PD for a given sub-set of taxonomic units is then the “minimum length of all phylogenetic branches required to span a given set of taxa on the phylogenetic tree” (Faith 1992). The larger the value of PD the greater the level of diversity captured. PD can be applied to different taxonomic groupings (populations, species, orders, etc.) and can be used in conjunction with measures of extinction risk or threat level to set conservation priorities for both taxonomic units and geographic areas. PD aims to identify for conservation those taxa with maximum underlying genetic diversity and taxonomic distinctness. Because PD can be applied at different taxonomic levels it avoids the issue of what defines a unit as a species or population.
Central to calculating PD is the construction of a phylogenetic tree which depicts the evolutionary relationships between taxonomic units based on the number of genetic differences between them. Within the tree the branches are the segments connecting different nodes. The nodes represent either real taxonomic units in the tree or hypothesised ancestors of extant taxonomic units. For the purpose of PD calculation the tree is rooted with a species known to be a common ancestor of all other taxonomic units in the tree.
To calculate PD for a subset of the taxonomic units ‘s’ within the tree (this can range from one taxonomic group through to the whole tree), first calculate the minimum spanning path (MSP). The MSP is ‘the smallest assemblage of branches within the whole phylogeny such that for any two members of ‘s’, a path along the phylogeny connecting the two can be found that only uses branches within the assemblage’.
Once the MSP has been determined then PD for the taxonomic subset can be calculated by summing the lengths of all the branches within the MSP. This calculation can be done manually in simple trees, but for trees of greater complexity a matrix can be constructed containing pair-wise branch distances between taxonomic groups, implemented in the software Phylogenetic Diversity Analyzer (PDA; Minh et al. 2006).
Using PD to set priorities
PD is intended to facilitate the assessment of biodiversity, in combination with other metrics and considerations when deciding which species out of a subset to focus conservation efforts on or when planning the location and scale of reserves (see Moritz et al. 2000)
For example, for a network of protected areas that contains a particular subset of taxonomic units, the increase in PD that is obtained when adding an additional taxonomic unit (‘x’) to the network can be calculated. This is termed calculating the gain in PD (G; Faith 1992).
G = 0.5 (Dx,i + Dx,j – Di,j)
Where Dij is the pairwise distance between taxa ‘i’ and ‘j’, and ‘x’ represents the new taxonomic unit. The taxonomic units that would contribute the most to increasing diversity within the protected area are the ones which maximise G.
EDGE: Incorporating Extinction Risk
PD provides a useful relative metric of diversity among taxonomic lineages , but other factors are also important, such as extinction risk. Threats from anthropogenic causes can be taken into account qualitatively, for example by comparing the geographic distribution of taxonomic units with anthropogenic threats in those areas. However a recent quantitative approach has been developed that combines Evolutionary Distinctiveness (ED – a derivative of PD) with the IUCNs red list classification (Referred to as EDGE; Isaac et al. 2007).
ED divides total PD amongst all members within the taxonomic subset by applying a value to each branch that is equal to its length divided by the number of nodes which the branch gives rise to. Thus ED takes into account the uniqueness of lineage s, giving priority to those with the highest levels of uniqueness. For example, a species with few close relatives that has been evolving independently for millions of years will have a high ED (such as the aardvark or various taxa in Madagascar) whereas a species that has radiated recently and has many close relatives will have a low ED.
To incorporate extinction risk and calculate EDGE:
EDGE = ln(1 + ED) + GE * ln(2)
Where GE = Rank based on IUCN red list classification.
EDGE can be calculated in the software package ‘Tuatara’ (Maddison & Mooers 2007).
PD values are comparable within a given study, based on the methods used to produce the full phylogeny. However, comparisons between studies may not be possible if the methodology differs. Further, the strength of inference depends on the accuracy of the phylogeny, which is only an approximation of an evolutionary history, and dependent on the data included and the methods applied.
It is appropriate to compute PD based on the use of more than one marker type. This is because the stochastic nature of evolution means that a single locus is not necessarily representative of the evolutionary history (and therefore the genetic diversity) of a whole population or species.
The central aim of PD is to conserve as much evolutionary uniqueness as possible, however it is calculated using neutral markers (DNA not involved in selection /adaptation) and therefore may not reflect the full extent of evolutionary potential within a species/population (for more information please see the pages on Genetic Diversity and adaptive potential ).
PD (and its derivatives) is a useful measure that can be applied to conserving genetic diversity within taxonomic units when conservation resources are finite and must be prioritised. Because PD takes into account extinct ancestors of the units in question and the relationships amongst extant units, it allows us to select sets of units which maximise the evolutionary potential contained within an ecosystem. PD should be combined with external factors such as geographic distribution, anthropogenic threats and extinction risk to consider the broader threat level for setting conservation priorities.
Relevant management topics:
- Assessing extinction risk
- Genetic tools for ecosystem management
- Measuring biodiversity using genetic tools
- Monitoring the genetic consequences of threats to populations
Faith D (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation. 61, 1-10.
Isaac NJB, Turvey ST, Collen B, Waterman C, Baillie JEM (2007) Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE. 2(3):e296
Maddison WP, Mooers AO (2007). Tuatara: Conservation priority in a phylogenetic context. Version 1.0. http://mesquiteproject.org/packages/tuatara
Minh BQ, Klaere S, von Haeseler A (2006) Phylogenetic diversity within seconds. Systematics Biology. 55, 769-773.
Moritz C, Patton JL, Schneider CJ, Smith TB (2000) Diversification of rainforest faunas: an integrative molecular approach. Annual Review of Ecology & Systematics. 31, 533-563.
The topic is open for discussion!