The shape of mammalian phylogeny: patterns, processes and scales

Abstract

Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'-points at which net diversification rate has changedidentifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of 'rules'. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space.

Detecting shifts in diversity limits from molecular phylogenies: what can we know?

“…Higher d facilitates a more rapid approach to the new equilibrium, but is also associated with larger fluctuations (and more zero-rate intervals) across the rest of tree, eroding any signal of the downshift. Downshifts may be more easily detected when specific traits or conditions have led to a diversity loss in one part of a tree and stasis or gain in another part [44,51]. While periods of low diversification across the tree can be inferred, unambiguously pinpointing clade-wide reductions in M on a reconstructed phylogeny will be difficult.…”

“…Indeed, some of the pulses detected in our empirical trees are probably caused by only a subset of lineages [44,56]. Pinpointing the lineages responsible for diversification pulses requires additional tests incorporating tree topology [44,51]. Our methods are, however, unlikely to perform well if changes are weak or affect different sub-clades in opposite ways.…”

“…It is unlikely that either clade evolved under a single or even two-phase homogeneous diversification process [36,44]; however, we were interested in whether our methods detect anomalous time intervals despite the heterogeneity of process expected within trees of this size. Similarly, it is not problematic that the angiosperm tree has families as tips, as we are testing for diversification pulses deeper in the tree where sampling is effectively complete.…”

“…Our supplementary analyses showed that, when only a subset of lineages responds to the change in M, the pulse is still detectable (electronic supplementary material, S1). Indeed, some of the pulses detected in our empirical trees are probably caused by only a subset of lineages [44,56]. Pinpointing the lineages responsible for diversification pulses requires additional tests incorporating tree topology [44,51].…”

“…We have modelled diversity-dependent cladogenesis using a single M. Although an improvement on densityindependent alternatives, our model is a caricature of the complex interplay between clades and their environments [25,44,56]. A more realistic model may comprise distinct adaptive zones [2], each able to sustain some equilibrium species diversity, and sub-clades diversifying in a diversity-dependent manner within them.…”