REVERSIBILITY IN EVOLUTION: A MAXIMUM LIKELIHOOD APPROACH TO CHARACTER GAIN/LOSS BIAS IN PHYLOGENIES

A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology

Directional evolution has played an important role in shaping the morphological, ecological, and molecular diversity of life. However, standard substitution models assume stationarity of the evolutionary process over the time scale examined, thus impeding the study of directionality. Here we explore a simple, nonstationary model of evolution for discrete data, which assumes that the state frequencies at the root differ from the equilibrium frequencies of the homogeneous evolutionary process along the rest of the tree (i.e., the process is nonstationary, nonreversible, but homogeneous). Within this framework, we develop a Bayesian approach for testing directional versus stationary evolution using a reversible-jump algorithm. Simulations show that when only data from extant taxa are available, the success in inferring directionality is strongly dependent on the evolutionary rate, the shape of the tree, the relative branch lengths, and the number of taxa. Given suitable evolutionary rates (0.1-0.5 expected substitutions between root and tips), accounting for directionality improves tree inference and often allows correct rooting of the tree without the use of an outgroup. As an empirical test, we apply our method to study directional evolution in hymenopteran morphology. We focus on three character systems: wing veins, muscles, and sclerites. We find strong support for a trend toward loss of wing veins and muscles, while stationarity cannot be ruled out for sclerites. Adding fossil and time information in a total-evidence dating approach, we show that accounting for directionality results in more precise estimates not only of the ancestral state at the root of the tree, but also of the divergence times. Our model relaxes the assumption of stationarity and reversibility by adding a minimum of additional parameters, and is thus well suited to studying the nature of the evolutionary process in data sets of limited size, such as morphology and ecology.

An integrative test of the dead-end hypothesis of selfing evolution in Triticeae (Poaceae)

Self-fertilization is hypothesized to be an evolutionary dead end because reversion to outcrossing can rarely happen, and selfing lineages are thought to rapidly become extinct because of limited potential for adaptation and/or accumulation of deleterious mutations. We tested these two assumptions by combining morphological characters and molecular-evolution analyses in a tribe of hermaphroditic grasses (Triticeae). First, we determined the mating system of the 19 studied species. Then, we sequenced 27 protein-coding loci and compared base composition and substitution patterns between selfers and outcrossers. We found that the evolution of the mating system is best described by a model including outcrossing-to-selfing transitions only. At the molecular level, we showed that regions of low recombination exhibit signatures of relaxed selection. However, we did not detect any evidence of accumulation of nonsynonymous substitutions in selfers compared to outcrossers. Additionally, we tested for the potential deleterious effects of GC-biased gene conversion in outcrossing species. We found that recombination and not the mating system affected substitution patterns and base composition. We suggest that, in Triticeae, although recombination patterns have remained stable, selfing lineages are of recent origin and inbreeding may have persisted for insufficient time for differences between the two mating systems to evolve.

The Ancestral Distance Test: What Relatedness can Reveal about Correlated Evolution in Large Lineages with Missing Character Data and Incomplete Phylogenies

The ancestral distance test is introduced to detect correlated evolution between two binary traits in large phylogenies that may lack resolved subclades, branch lengths, and/or comparative data. We define the ancestral distance as the time separating a randomly sampled taxon from its most recent ancestor (MRA) with extant descendants that have an independent trait. The sampled taxon either has (target sample) or lacks (nontarget sample) a dependent trait. Modeled as a Markov process, we show that the distribution of ancestral distances for the target sample is identical to that of the nontarget sample when characters are uncorrelated, whereas ancestral distances are smaller on average for the target sample when characters are correlated. Simulations suggest that the ancestral distance can be estimated using the time, total branch length, taxonomic rank, or number of speciation events between a sampled taxon and the MRA. These results are shown to be robust to deviations from Markov assumptions. A Monte Carlo technique estimates P-values when fully resolved phylogenies with branch lengths are available, and we evaluate the Monte Carlo approach using a data set with known correlation. Measures of relatedness were found to provide a robust means to test hypotheses of correlated character evolution.

Ancient polymorphism reveals unidirectional breeding system shifts

Loss of complex characters is thought to be irreversible (Dollo's law). However, hypotheses of irreversible evolution are remarkably difficult to test, especially when character transitions are frequent. In such cases, inference of ancestral states, in the absence of fossil evidence, is uncertain and represents the single greatest constraint for reconstructing the evolutionary history of characters. Breeding system character transitions are of particular interest because they affect the amount and distribution of genetic variation within species. Transitions from obligate outcrossing to partial or predominant self-fertilization are thought to represent one of the most common trends in flowering plants. We use the unique molecular genetic properties (manifested as deep persistent polymorphisms) of the locus that enforces outcrossing to demonstrate that its loss is irreversible in the plant family Solanaceae. We argue that current phylogenetic methods of reconstruction are potentially inadequate in cases where ancestral state information is inferred by using only the phylogeny and the distribution of character states in extant taxa. This study shows in a statistical framework that a particular character transition is irreversible, consistent with Dollo's law.

The origin and maintenance of nuclear endosperms: viewing development through a phylogenetic lens

The endosperm develops in fertilized ovules of angiosperms following fertilization of the central cell and nuclei in the female gametophyte. Endosperms differ in whether, and which, nuclear divisions are followed by cellular divisions; the variants are classified as cellular, nuclear or helobial. Functional correlates of this variation are little understood. Phylogenetic methods provide a powerful means of exploring taxonomic variation and phylogenetic patterns, to frame questions regarding biological processes. Data on endosperms across angiosperms were analysed in a phylogenetic context in order to determine homologies and detect biases in the direction of evolutionary transitions. Analyses confirm that neither all nuclear nor all helobial endosperms are homologous, raise the possibility that cellular development is a reversal in some derived angiosperms (e.g. asterids) and show that a statistically significant bias towards evolution of nuclear endosperms (and against reversals) prevails in angiosperms as a whole. This bias suggests strong selective advantages to having nuclear endosperm, developmental constraints to reversals or both. Homologies suggest that the microtubular cycle and cellularization pattern characteristic of reproductive cells across land plants may have been independently co-opted during multiple origins of nuclear endosperms, but information on cellular endosperms is essential to investigate further.

Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach

G. Ledyard Stebbins suggested that self-fertilization (selfing) may be an evolutionary dead end because it may result in the loss of genetic diversity and consequently preclude adaptation to changing environments. While the basic premise of selfing as a dead end is widely accepted, there have been few rigorous evaluations of the hypothesis. We examine the foundations of the dead-end hypothesis by considering theoretical advances in the study of mating-system evolution. We discuss theories predicting the irreversibility of self-fertilization and the extinction of selfing lineages through the loss of adaptive potential and genetic degradation. In the second portion of the review, focusing on the irreversibility of selfing, we summarize the contribution of phylogenetic studies of mating-system evolution to determine if evolutionary history supports this well-established hypothesis. Most studies are in accord with the hypothesis; no single study unequivocally demonstrates the transition from highly selfing to outcrossing lineages. Finally, we discuss the problems encountered when phylogenetic studies rely on reconstruction of ancestral mating systems. To avoid some of these problems, we applied likelihood ratio tests of irreversibility of mating-system evolution to several data sets and found that current data sets are probably too small for this test.

A phylogenetic analysis of the Gruiformes (Aves) based on morphological characters, with an emphasis on the rails (Rallidae)

The order Gruiformes, for which even familial composition remains controversial, is perhaps the least well understood avian order from a phylogenetic perspective. The history of the systematics of the order is presented, and the ecological and biogeographic characteristics of its members are summarized. Using cladistic techniques, phylogenetic relationships among fossil and modern genera of the Gruiformes were estimated based on 381 primarily osteological characters; relationships among modern species of Grues (Psophiidae, Aramidae, Gruidae, Heliornithidae and Rallidae) were assessed based on these characters augmented by 189 characters of the definitive integument. A strict consensus tree for 20,000 shortest trees compiled for the matrix of gruiform genera (length = 967, CI = 0.517) revealed a number of nodes common to the solution set, many of which were robust to bootstrapping and had substantial support (Bremer) indices. Robust nodes included those supporting: a sister relationship between the Pedionomidae and Turnicidae; monophyly of the Gruiformes exclusive of the Pedionomidae and Turnicidae; a sister relationship between the Cariamidae and Phorusrhacoidea; a sister relationship between a clade comprisingEurypygaandMesselornisand one comprisingRhynochetosandAptornis; monophyly of the Grues (Psophiidae, Aramidae, Gruidae, Heliornithidae and Rallidae); monophyly of a clade (Gruoidea) comprising (in order of increasingly close relationship)Psophia,Aramus,Balearicaand other Gruidae, with monophyly of each member in this series confirmed; a sister relationship between the Heliornithidae and Rallidae; and monophyly of the Rallidae exclusive ofHimantornis. Autapomorphic divergence was comparatively high forPedionomus,Eurypyga,Psophia,HimantornisandFulica; extreme autapomorphy, much of which is unique for the order, characterized the extinct, flightlessAptornis.

In the species–level analysis of modern Grues, special efforts were made to limit the analytical impacts of homoplasy related to flightlessness in a number of rallid lineages. A strict consensus tree of 20,000 shortest trees compiled (length = 1232, CI = 0.463) confirmed the interfamilial relationships resolved in the ordinal analysis and established a number of other, variably supported groups within the Rallidae. Groupings within the Rallidae included: monophyly of Rallidae exclusive ofHimantornisand a clade comprisingPorphyrio(includingNotornis) andPorphyrula; a poorly resolved, basal group of genera includingGymnocrex,Habroptila,Eulabeornis,Aramides,CanirallusandMentocrex; an intermediate grade comprisingAnurolimnas,Amaurolimnas, andRougetius; monophyly of two major subdivisions of remaining rallids, one comprisingRallina(paraphyletic),Rallicula, andSarothrura, and the other comprising the apparently paraphyletic ‘long–billed’ rails (e.g.Pardirallus,Cyanolimnas,Rallus,GallirallusandCabalusand a variably resolved clade comprising ‘crakes’ (e.g.Atlantisia,LaterallusandPorzana, waterhens (Amaurornis), moorhens (Gallinulaand allied genera) and coots (Fulica). Relationships among ‘crakes’ remain poorly resolved;Laterallusmay be paraphyletic, andPorzanais evidently polyphyletic and poses substantial challenges for reconciliation with current taxonomy. Relationships among the species of waterhens, moorhens and coots, however, were comparatively well resolved, and exhaustive, fine–scale analyses of several genera (Grus,Porphyrio,Aramides,Rallus,LaterallusandFulica) and species complexes (Porphyrio porphyrio–group,Gallirallus philippensis–group andFulica americana–group) revealed additional topological likelihoods. Many nodes shared by a majority of the shortest trees under equal weighting were common to all shortest trees found following one or two iterations of successive weighting of characters. Provisional placements of selected subfossil rallids (e.g.Diaphorapteryx,AphanapteryxandCapellirallus) were based on separate heuristic searches using the strict consensus tree for modern rallids as a backbone constraint.

These analyses were considered with respect to assessments of robustness, homoplasy related to flightlessness, challenges and importance of fossils in cladistic analysis, previously published studies and biogeography, and an annotated phylogenetic classification of the Gruiformes is proposed.