Hybridization plays an important role in the evolution of certain groups of organisms, adaptation to their environments, and diversification of their genomes. The evolutionary histories of such groups are reticulate, and methods for reconstructing them are still in their infancy and have limited applicability. We present a maximum likelihood method for inferring reticulate evolutionary histories while accounting simultaneously for incomplete lineage sorting. Additionally, we propose methods for assessing confidence in the amount of reticulation and the topology of the inferred evolutionary history. Our method obtains accurate estimates of reticulate evolutionary histories on simulated datasets. Furthermore, our method provides support for a hypothesis of a reticulate evolutionary history inferred from a set of house mouse (Mus musculus) genomes. As evidence of hybridization in eukaryotic groups accumulates, it is essential to have methods that infer reticulate evolutionary histories. The work we present here allows for such inference and provides a significant step toward putting phylogenetic networks on par with phylogenetic trees as a model of capturing evolutionary relationships. reticulate evolution | incomplete lineage sorting | phylogenetic networks | maximum likelihood P hylogenetic trees have long been a mainstay of biology, providing an interpretive model of the evolution of molecules and characters and a backdrop against which comparative genomics and phenomics are conducted. Nevertheless, some evolutionary events, most notably horizontal gene transfer in prokaryotes and hybridization in eukaryotes, necessitate going beyond trees (1). These events result in reticulate evolutionary histories, which are best modeled by phylogenetic networks (2). The topology of a phylogenetic network is given by a rooted, directed, acyclic graph (rDAG) that is leaf-labeled by a set of taxa ( Fig. 1; more details are provided in Model and SI Appendix). Reticulation events result in genomic regions with local genealogies that are incongruent with the speciation pattern. Several methods and heuristics use this incongruence as a signal for inferring reticulation events and reconstructing phylogenetic networks from local genealogies. These methods, which are surveyed elsewhere (2-4), assume that reticulation events are the sole cause of all incongruence among the gene trees and seek phylogenetic networks to explain all of the incongruence. A serious limitation of these methods is that they would grossly overestimate the amount of reticulation in a dataset when other causes of incongruence are at play. Indeed, several recent studies (5-9) have shown that detecting hybridization in practice can be complicated by the presence of incomplete lineage sorting (ILS) (Fig. 1).Recently, a set of methods was devised to analyze data where reticulation and ILS might both be simultaneously at play (10-15). However, these methods are all applicable to simple scenarios of species evolution and mostly assume a known hypothesis about the topol...

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa.

Biomass hydrolysis extracts, particularly sugars and other useful derivatives, are important products for further conversion to produce biofuels. The past 2 decades have witnessed significant research and development activities using hot-compressed water for the hydrolysis and conversion of cellulose, hemicellulose, and lignocellulosic biomass materials. This paper summarizes the decomposition mechanisms and hydrolysis products of these materials under various conditions in hot-compressed water. Key factors determining hydrolysis behavior in hot-compressed water are also discussed. Comparisons are made between hydrolysis in hot-compressed water and hydrolysis using other technologies, including acid hydrolysis, alkaline hydrolysis, and enzymatic hydrolysis. Advantages, disadvantages, typical operation conditions, products properties, and applicability are summarized. Key research issues on hydrolysis in hot-compressed water are identified, and future research prospects to further improve the technology are discussed.

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