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Biology subjects

Freyman, W.

Publications and source records attributed to Freyman, W..

2 recordsLinked to original sources
bioRxiv2017

Inferring the evolutionary reduction of corm lobation in Isoëtes using Bayesian model-averaged ancestral state reconstruction

Inferring the evolution of characters in Isoetes has been problematic, as these plants are morphologically conservative and yet highly variable and homoplasious within that conserved base morphology. However, molecular phylogenies have given us a valuable tool to test hypothesis of character evolution within the genus. One such hypothesis is that extant Isoetes have undergone a morphological reduction from larger arborescent lycophyte ancestors. In this work we examine the reduction in lobe numbers on the underground trunk, or corm, over evolutionary time. Using reversible-jump MCMC and Bayesian inference, our results support the hypothesis of a directional reduction in lobe number in Isoetes, with the best-supported model of character evolution being one of irreversible reduction. Furthermore, the most probable ancestral corm lobe number of extant Isoetes is three, and a reduction to two lobes has occurred at least six times. From our results, we can infer that corm lobation, like many other traits in Isoetes, shows a degree of homoplasy, yet also shows ongoing evolutionary reduction.

evolutionary biology↗
bioRxiv2017

Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible lineages

A major goal of evolutionary biology is to identify key evolutionary transitions that correspond with shifts in speciation and extinction rates. Stochastic character mapping has become the primary method used to infer the timing, nature, and number of character state transitions along the branches of a phylogeny. The method is widely employed for standard substitution models of character evolution. However, current approaches cannot be used for models that specifically test the association of character state transitions with shifts in diversification rates such as state-dependent speciation and extinction (SSE) models. Here we introduce a new stochastic character mapping algorithm that overcomes these limitations, and apply it to study mating system evolution over a time-calibrated phylogeny of the plant family Onagraceae. Utilizing a hidden state SSE model we tested the association of the loss of self-incompatibility with shifts in diversification rates. We found that self-compatible lineages have higher extinction rates and lower net-diversification rates compared to self-incompatible lineages. Furthermore, these results provide empirical evidence for the \"senescing\" diversification rates predicted in highly selfing lineages: our mapped character histories show that the loss of self-incompatibility is followed by a short-term spike in speciation rates, which declines after a time lag of several million years resulting in negative net-diversification. Lineages that have long been self-compatible, such as Fuchsia and Clarkia, are in a previously unrecognized and ongoing evolutionary decline. Our results demonstrate that stochastic character mapping of SSE models is a powerful tool for examining the timing and nature of both character state transitions and shifts in diversification rates over the phylogeny.

evolutionary biology↗