Every five years, Mike Steel puts predictions up on his webpage of five directions in phylogenetics that will grow in the next five years.
His predictions for the period 2011-2016:
- Development of network‐based methods to display ‘evolution as it happened’ including reticulation (LGT, endosymbiosis, hybrid species etc) up to the limits of what can be discerned from extant data.
- Phylogenetic approaches for handling patchy taxon coverage and analyzing large numbers of short reads from next generation sequencing.
- Phylogenetic approaches to early life using non‐stationary models and protein structural constraints
- Statistical approaches for analyzing non‐aligned sequence data.
- More realistic models of speciation and extinction that better describe the shape of ‘real’ phylogenies.
I can say that people are certainly doing #2, but it seems to me that most folks are just running classical approaches to datasets that are a high percent gap.
A lot of these touch on topics that I don't know anything about, such as early life.