Phylogenomic approaches to deciphering the tree of life

Abstract

Phylogenomics comprises an interdisciplinary field of comparative biology that uses genomic data to produce phylogenetic relationships among organisms (Philippe et al., 2005; Chan & Ragan, 2013). The term “phylogenomics” was initially applied to studies on gene functions (Eisen, 1998) but subsequently has been widely used to infer the tree of life (Philippe et al., 2004, 2005; Pennisi, 2008; Zou et al., 2008; Dos Reis et al., 2012; Liu et al., 2015a, 2015b). With the advent and rapid development of next-generation sequencing (NGS), phylogenomics has gained more popularity in the last few years and is now being employed by many members of the evolutionary and systematics community (Lemmon & Lemmon, 2013; Wen et al., 2015, 2013; Jarvis et al., 2014; Weitemier et al., 2014; Wickett et al., 2014; Zeng et al., 2014). This special issue features a range of papers on the utility and analytical methods of phylogenomic data in systematics. Zimmer & Wen (2015) provide an overview of the major next-gen approaches used for nuclear gene data production applied to plant phylogenetics, as a follow-up sister paper published by the authors in 2012 (Zimmer & Wen, 2012). In the current paper, Zimmer & Wen (2015) review the most commonly used NGS methods for accessing nuclear genes and discuss many NGS case studies. With the availability of genome-scale sequence data for phylogenetic studies, it is challenging to develop probabilistic models to account for heterogeneity of phylogenomic data. Liu et al. (2015a) evaluate the performance of coalescent-based methods for estimating species trees from genome-scale sequence data, and investigate the effects of deep coalescence and mutation on the performance of species tree estimation methods. The coalescent-based methods were found to perform well in estimating species trees for a large number of genes, regardless of the degree of deep coalescence and mutation, with the performance of the coalescent methods negatively correlated with the lengths of internal branches of the species tree. Major phylogenomic approaches include whole genome sequencing, transcriptome sequencing, Exon-Primed Intron-Crossing sequencing (EPIC), targeted enrichment (or sequence capture), Restriction–site Associated DNA (RAD) sequencing, and genome skimming (Zimmer & Wen, 2015). This special issue includes four papers as case studies applying these phylogenomic methods to decipher the tree of life. Mandel et al. (2015) elucidate complex relationships in the largest plant family Compositae (Asteraceae or sunflowers) using targeted capture of low-copy sequences. Ma et al. (2015) use transcriptome sequence data to resolve relationships in the birch family (Betulaceae) and explore the efficacy of low-copy-gene-based approaches and mapping-based approaches for phylogenetic reconstruction. Gostel et al. (2015) explore the development of a set of 91 nuclear markers using microfluidic PCR, which bypasses the costly library preparation step in the myrrh plant genus Commiphora Jacq. (Burseraceae). Qi et al. (2015) conduct phylogenetic analyses of extant populations of Fothergilla L. (Hamamelidaceae) using RAD-tags from genotyping by sequencing (GBS) to understand evolutionary relationships and origins of polyploid species in the genus. Chloroplast phylogenomics is a cost-effective approach that is contributing greatly to the plant tree of life. Lu et al. (2015) explore the phylogenetic utility of large chloroplast gene datasets in resolving difficult deep nodes in ferns. Schwarz et al. (2015) report sequences of 13 new plastid genomes of legumes spanning all three subfamilies and explore chloroplast genome evolution across the legume family. Genome and transcriptome sequences offer new opportunities for studying the homology of important plant characters. Zhang et al. (2015) examine the homology of the leaf-opposed tendril, a likely morphological key innovation for the grape family Vitaceae, to the plant's inflorescence. Using data from the grape genome and transcriptome sequences, they obtained gene sequences of four key floral meristem genes, i.e., FUL, AP1, FT and LEAFY orthologs for 15 Vitaceae species and the outgroup Leea guineensis. Possible mechanisms on the evolution of tendrils were proposed for Vitaceae based on the combined evidence from genealogies and expression patterns of these four genes. With the major technical advances in next-generation sequencing, it has become feasible for the plant systematics community to use a phylogenomic approach to decipher the tree of life and reconstruct the evolutionary history of important taxonomic characters. Phylogenomics nevertheless faces major challenges of data heterogeneity (Jeffroy et al., 2006; Lemmon & Lemmon, 2013; Liu et al., 2015a), issues related to gene orthology (Yang & Smith, 2014), and bioinformatics needs for massive dataset analyses. This special issue showcases the utility of different types of NGS data for phylogenomics in addressing systematic and evolutionary questions and presents discussions on the analytical methods and challenges. We hope that the set of papers in this special issue will stimulate the application of phylogenomics to plant systematics in the coming years. Jun Wen 1, Jianquan Liu 2,3, Song Ge 4, Qiu-Yun (Jenny) Xiang 5, and Elizabeth A. Zimmer 1 1Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA 2State Key Laboratory of Grassland and Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, China 3MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu 610064, China 4State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China 5Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA