Networks in a Large-Scale Phylogenetic Analysis: Reconstructing Evolutionary History of Asparagales (Lilianae) Based on Four Plastid Genes

Abstract

Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses.

A new family placement for Australian blue squill, Chamaescilla: Xanthorrhoeaceae (Hemerocallidoideae), not Asparagaceae

“…The order is united largely by molecular evidence and a black pigment in their seed coat, with few other morphological characters . Relationships between families in Asparagales are well understood with the sample-rich phylogeny of Chen et al (2013) agreeing with the data-rich phylogeny of Steele et al (2012), although Chen et al (2013) note some level of reticulation at the base of the phylogeny. Nested clade analysis infers Australia as the centre of origin of the order, with many families such as Asparagaceae, Xanthorrhoeaceae, Orchidaceae and several early diverging lineages, such as the endemic Boryaceae and Doryanthaceae, occurring on that continent (Bremer & Janssen 2006).…”

“…Asparagales is the largest monocot order, comprising approximately 50% of monocot species and 10-15% of all flowering plants (Chen et al 2013), including the extremely diverse Orchidaceae, important food species such as Asparagus Linnaeus (1753a: 313) and Allium Linnaeus (1753a: 294), and garden plants like Hemerocallis Linnaeus (1753a: 324), which is also a potential new model organism (Rodriguez-Enriquez & Grant-Downton 2013). The order is united largely by molecular evidence and a black pigment in their seed coat, with few other morphological characters .…”

“…Nested clade analysis infers Australia as the centre of origin of the order, with many families such as Asparagaceae, Xanthorrhoeaceae, Orchidaceae and several early diverging lineages, such as the endemic Boryaceae and Doryanthaceae, occurring on that continent (Bremer & Janssen 2006). Chen et al (2013) included a single sample of Chamaescilla, which their analysis placed in Hemerocallidoideae (Xanthorrhoeaceae) alongside two non-Australian members of the subfamily. This novel family placement was not commented on by Chen et al (2013).…”

“…Chen et al (2013) included a single sample of Chamaescilla, which their analysis placed in Hemerocallidoideae (Xanthorrhoeaceae) alongside two non-Australian members of the subfamily. This novel family placement was not commented on by Chen et al (2013). An unpublished analysis of the Lomandroideae (Sirisena 2010) also shows Chamaescilla sitting outside the rest of the subfamily, but that phylogenetic position might be an artefact of the enforced placement of Asparagus as an outgroup.…”

“…In order to test the phylogenetic position of Chamaescilla we added partial sequences of the four genes (atpB, matK, ndhF, rbcL) used by Chen et al (2013) for a new collection of C. corymbosa, and an rbcL sequence for the unplaced genus Hodgsoniola Mueller (1861: 176). Sequences retrieved from GenBank were used to add the remaining genera of Hemerocallidoideae and Lomandroideae to confirm the new familial position of Chamaescilla and determine relationships between genera in those subfamilies.…”