Revisiting the Darwinian shortfall in biodiversity conservation

Among the seven shortfalls of biodiversity knowledge, the one that makes direct reference to phylogenetic information is the Darwinian shortfall, which embraces three components: “(1) the lack of fully resolved phylogenies for most groups of organisms; (2) the limited knowledge of branch lengths and difficulties in absolute time calibrations; and (3) unknown evolutionary models linking those phylogenies to ecological traits and the life-history variation” (Diniz-Filho et al. in Trends Ecol Evol 28:689–694, 2013). In order to overcome them, Diniz-Filho et al. (Trends Ecol Evol 28:689–694, 2013) emphasized the need to know the problems relative to phylogeny reconstruction, but they did not provide a clear comprehension of these problems. In the present article, I aim to comment on these problems in the context of the five epistemic stages of phylogenetic analysis. These are: (1) taxon sampling; (2) evidence; (3) homology assessment; (4) optimization methods; and (5) hypotheses formulation. A brief review of these stages is necessary to comprehend how complex is the use of phylogenetic hypotheses in ecology and conservation. I also provide additional and balanced solutions in an attempt to overcome the evolutionary shortfall.