Phylogenetic Diversity by Unknown

Author:Unknown
Language: eng
Format: epub
ISBN: 9783319931456
Publisher: Springer International Publishing

Polytomies and Increases in Tree Length and Phylogenetic Measures of Biodiversity

As a general rule, the tree length of a phylogeny that is ultrametric will increase as polytomies are introduced (Fig. 5.2). Thus, when quantifying a phylogenetic measure of biodiversity that utilizes branch length information (i.e., essentially all of them), we should a priori expect a bias toward overestimating the true level of biodiversity. This general rule may be broken if the taxa in the area being studied are from a portion of the phylogeny that is fully resolved and the portions that are unresolved do not contain taxa in the area. In other words, in special cases where polytomies are nonrandomly distributed on the phylogeny and the taxa in the geographic area of interest are also nonrandomly absent from the region of the phylogeny that has polytomies, then the bias will be mitigated or nonexistent. However, this may be an unlikely scenario as we show here with simulations.

If there is a silver lining to this bias it is that understudied areas of the phylogeny or understudied geographic areas, that therefore likely contain taxa that are in unresolved areas of the phylogeny, will appear to have greater biodiversity when using a phylogenetic measure and may therefore attract more study. This is a far better direction of bias, in our opinion, than underestimating biodiversity in clades or geographic areas that have been traditionally understudied. However, we can imagine that others, perhaps those that study vertebrates with well-resolved phylogenies, would have a different perspective.

One may be tempted to say that a null model may magically make this bias disappear. Previous work has shown this not to be the case (Kress et al. 2009; Swenson 2009). Specifically, unresolved phylogenies tend to increase type I error in null model studies, but the direction of the type I error is not consistent. Specifically, polytomies cause researchers to falsely infer that their observed phylogenetic biodiversity measure is no different from that expected given the species richness when it is in fact significantly higher or lower than expected. In other words, we know polytomies would cause someone to miss extreme or unusual levels of phylogenetic biodiversity, but they would not know if the true values were unusually high or low.

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