Multilocus phylogeny and phylogenomics of Eriochrysis P. Beauv. (Poaceae–Andropogoneae): Taxonomic implications and evidence of interspecific hybridization

Abstract

Species delimitation is a vital issue concerning evolutionary biology and conservation of biodiversity. However, it is a challenging task for several reasons, including the low interspecies variability of markers currently used in phylogenetic reconstructions and the occurrence of reticulate evolution and polyploidy in many lineages of flowering plants. The first phylogeny of the grass genus Eriochrysis is presented here, focusing on the New World species, in order to examine its relationships to other genera of the subtribe Saccharinae/tribe Andropogoneae and to define the circumscriptions of its taxonomically complicated species. Molecular cloning and sequencing of five regions of four low-copy nuclear genes (apo1, d8, ep2-ex7 and ep2-ex8, kn1) were performed, as well as complete plastome sequencing. Trees were reconstructed using maximum parsimony, maximum likelihood, and Bayesian inference analyses. The present phylogenetic analyses indicate that Eriochrysis is monophyletic and the Old World E. pallida is sister to the New World species. Subtribe Saccharinae is polyphyletic, as is the genus Eulalia. Based on nuclear and plastome sequences plus morphology, we define the circumscriptions of the New World species of Eriochrysis: E. laxa is distinct from E. warmingiana, and E. villosa is distinct from E. cayennensis. Natural hybrids occur between E. laxa and E. villosa. The hybrids are probably tetraploids, based on the number of paralogues in the nuclear gene trees. This is the first record of a polyploid taxon in the genus Eriochrysis. Some incongruities between nuclear genes and plastome analyses were detected and are potentially caused by incomplete lineage sorting and/or ancient hybridization. The set of low-copy nuclear genes used in this study seems to be sufficient to resolve phylogenetic relationships and define the circumscriptions of other species complexes in the grass family and relatives, even in the presence of polyploidy and reticulate evolution. Complete plastome sequencing is also a promising tool for phylogenetic inference.

Phylogenomics of Andropogoneae (Panicoideae: Poaceae) of Mainland Southeast Asia

“…Chrysopogon and Eriochrysis-Both Chrysopogon and Eriochrysis are monophyletic, consistent with previous results SYSTEMATIC BOTANY [Volume 42(Mathews et al 2002;Estep et al 2014;Welker et al 2016). Chrysopogon species fall into two groups, the clade of C. gryllus (L.) Trin.…”

“…Instead A. burmanicus and Parahyparrhenia siamensis are in a clade with Eulalia contorta that is entirely Southeast Asian, but sister to the widespread genus Eriochrysis. Pseudosorghum fasciculare is sister to Eulalia siamensis, and neither is closely related to Eulalia contorta, supporting the polyphyly of Eulalia as noted by other authors (Skendzic et al 2007;Teerawatananon et al 2011;GPWG II 2012;Estep et al 2014;Soreng et al 2015;Welker et al 2016).…”

“…We confirmed the traditional subtribe "Saccharinae" as polyphyletic (Hodkinson et al 2002;Welker et al 2016), with scattered positions of Eulalia, Eulaliopsis, and Pogonatherum. Prior to this study, Teerawatananon et al (2011), GPWG II (2012), Estep et al (2014), and Welker et al (2015Welker et al ( , 2016 also demonstrated that Pogonatherum is linked with subtribe Germainiinae (Germainia and Apocopis).…”

“…The Core Andropogoneae-The core Andropogoneae has been widely accepted and retrieved in all phylogenetic studies to date, including analyses of nuclear genes such as PHYB (Mathews et al 2002), GBSSI (Mason-Gamer et al 1998;Mathews et al 2002), single-copy genes (Estep et al 2014;Welker et al 2015Welker et al , 2016, and ITS (Skendzic et al 2007), chloroplast genes such as ndhF (Giussani et al 2001;Mathews et al 2002) and trnL-F (Teerawatananon et al 2011), and combined data. Two clades are clearly found: 1) the group of Cymbopogon, Dichanthium, Heteropogon, and Themeda and 2) the group of Andropogon, Hyparrhenia, and Schizachyrium.…”

“…Eriochrysis forms a well-supported clade and is sister to a clade of endemic Southeast Asian species. Although all samples of Eriochrysis in the analyses are American, members of the genus Eriochrysis are also distributed in Africa and India (Clayton and Renvoize 1986;Kellogg 2015;Welker and Longhi-Wagner 2012;Welker et al 2016). In future studies, African or Indian Eriochrysis species should be included to determine whether they are more closely related to the Southeast Asian ones and diverge before the American species as suggested by Welker et al (2016).…”