Phylogenomics and phylogeography of Menispermum (Menispermaceae)

Abstract

Introduction: Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant families. Menispermum L. (Menispermaceae) consists of three species, M. dauricum DC., M. canadense L., and M. mexicanum Rose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whether M. mexicanum is a distinct species, a variety of M. dauricum, or simply a synonym of M. canadense. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses.

Methods: In this study, we examined phylogenomics and phylogeography of Menispermum across its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships of Menispermum and explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family.

Results and discussion: Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show that Menispermum clusters into two clades with high support values, Clade A (M. dauricum) and Clade B (M. canadense + M. mexicanum). However, M. mexicanum is nested within M. canadense and, as a result, we support that M. mexicanum is a synonym of M. canadense. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (Pi) values > 0.05, including two coding genes (matK, ycf1), four introns (trnK intron, rpl16 intron, rps16 intron, ndhA intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (trnH-psbA, ndhF-rpl32, trnK-rps16, and trnP-psaJ) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.

Keywords: Menispermaceae; disjunct distribution; phylogeny; plastome evolution; systematic.

Figure 1

The distribution/sampling sites of M. canadense (dark green/yellow triangle), M. dauricum (orange/blue dot), and M. mexicanum (light green/red triangle). (A) world map; (B) eastern North America; (C) East Asia. Sample codes are the same as in Table 1 .

Figure 2

Representative plastome maps of the newly sequenced plastomes of Menispermaceae (19 in total). (A) Menispermum; (B) Sinomenium.

Figure 3

Maximum likelihood (ML) and Bayesian inference (BI) phylogeny based on 29 complete plastomes of Menispermaceae, with Ranunculus as outgroup. Numbers at each node represent ML bootstrap support (BS) and BI posterior probability (PP) values, respectively. Hyphens indicate the nodes not found in the strict consensus BI tree. The phylogram on the upper left shows the relative branch lengths. Sample codes are the same as in Table 1 .

Figure 4

Maximum likelihood (ML) and Bayesian inference (BI) phylogeny based on 17 ITS1&ITS2 sequences of Menispermum, with Sinomenium as outgroup. Numbers at each node represent ML bootstrap support (BS) and BI posterior probability (PP) values, respectively. Hyphens indicate the nodes not found in the strict consensus BI tree. The phylogram on the upper left shows the relative branch lengths. Sample codes are the same as in Table 1 .

Figure 5

Haplotype (A) and ribotype (B) networks of Menispermum. C, D, and M represent M. canadense, M. dauricum, and M. mexicanum, respectively. Sample codes are the same as in Table 1 .

Figure 6

Comparison of the LSC/IRb/SSC/IRa junctions among the 12 complete plastomes of Menispermaceae. Sample codes are the same as in Table 1 .

Figure 7

Nucleotide diversity (Pi) values of 12 Menispermaceae plastome sequences.