Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental Geodynamics

Abstract

One of the two major clades of the endemic American Amaryllidaceae subfam. Amaryllidoideae constitutes the tetraploid-derived (n = 23) Andean-centered tribes, most of which have 46 chromosomes. Despite progress in resolving phylogenetic relationships of the group with plastid and nrDNA, certain subclades were poorly resolved or weakly supported in those previous studies. Sequence capture using anchored hybrid enrichment was employed across 95 species of the clade along with five outgroups and generated sequences of 524 nuclear genes and a partial plastome. Maximum likelihood phylogenetic analyses were conducted on concatenated supermatrices, and coalescent-based species tree analyses were run on the gene trees, followed by hybridization network, age diversification and biogeographic analyses. The four tribes Clinantheae, Eucharideae, Eustephieae, and Hymenocallideae (sister to Clinantheae) are resolved in all analyses with > 90 and mostly 100% support, as are almost all genera within them. Nuclear gene supermatrix and species tree results were largely in concordance; however, some instances of cytonuclear discordance were evident. Hybridization network analysis identified significant reticulation in Clinanthus, Hymenocallis, Stenomesson and the subclade of Eucharideae comprising Eucharis, Caliphruria, and Urceolina. Our data support a previous treatment of the latter as a single genus, Urceolina, with the addition of Eucrosia dodsonii. Biogeographic analysis and penalized likelihood age estimation suggests an origin in the Cauca, Desert and Puna Neotropical bioprovinces for the complex in the mid-Oligocene, with more dispersals than vicariances in its history, but no extinctions. Hymenocallis represents the only instance of long-distance vicariance from the tropical Andean origin of its tribe Hymenocallideae. The absence of extinctions correlates with the lack of diversification rate shifts within the clade. The Eucharideae experienced a sudden lineage radiation ca. 10 Mya. We tie much of the divergences in the Andean-centered lineages to the rise of the Andes, and suggest that the Amotape-Huancabamba Zone functioned as both a corridor (dispersal) and a barrier to migration (vicariance). Several taxonomic changes are made. This is the largest DNA sequence data set to be applied within Amaryllidaceae to date.

Keywords: Andes; Asparagales; anchored hybrid enrichment; biogeography; geophyte; molecular systematics; monocotyledons; phylogenetics.

FIGURE 1

Representative species of the Andean tetraploid clade of the American Amaryllidaceae. (A–C,P,Q) Tribe Clinantheae. (D,E) Tribe Eustephieae. (F–K,O,R) Tribe Eucharideae. (L–N) Tribe Hymenocallideae. (A) Paramongaia milagroantha (Leiva & Meerow) Meerow. (B) Pamianthe ecollis Silverst., Meerow & Sánchez-Taborda. (C). Clinanthus campodensis (Ravenna) Meerow. (D) Pyrolirion tubiflorum L’Hér.) M.Roem. (E) Hieronymiella latifolia (R.E.Fr.) Di Fulvio & Hunz. (F) Rauhia albescens Meerow & Sagást. (G) Urceolina pendula Herb. (H) Eucharis cyaneosperma Meerow. (I) Eucrosia dodsonii Meerow & Dehgan. (J) Stenomesson ecuadorense Meerow, Oleas & L.Jost. (K) Eucrosia bicolor Ker Gawl. (L) Leptochiton helianthus (Ravenna) Gereau & Meerow. (M) Ismene parviflora Meerow & A. Cano. (N) Hymenocallis speciosa (L.f. ex Salisb.) Salisb. (O) Phaedranassa ventricosa Baker. (P) Clinanthus incarnatus (Kunth) Meerow. (Q) Clinanthus variegatus (Ruiz & Pav.) Meerow. (R) Caliphruria subedentata Baker. Photo credits: (A,C,L) Segundo Leiva. (B) Jhon A. Sánchez-Taborda. (D,I–K,N–R) Alan Meerow. (E) John Wood. (F) Abundio Sagástegui. (G,H) Günter Gerlach. (M) Asuncíon Cano. Photos used by permission.

FIGURE 2

Best tree from maximum likelihood analysis of partitioned 524 nuclear gene supermatrix of the Andean tetraploid clade of Amaryllidaceae subfam. Amaryllidoideae, with bootstrap percentages <100 shown above branches (all unmarked branches have 100% BP). The tree is divided into two sections (A,B) for readability; refer to the colored inset (a cartoon of the tree collapsed to the tribal level) as a guide. Colored circles at the nodes in the full tree conform to clade colors in the inset.

FIGURE 3

Local posterior probability (LPP) coalescent species tree from ASTRAL III analysis of gene trees of 526 nuclear genes. LPP scores appear above the branches; bootstrap percentages <100 shown below branches (all unmarked branches have 100% BP). The tree is divided into two sections (A,B) for readability; refer to the colored inset (a cartoon of the tree collapsed to the tribal level) as a guide. Colored circles at the nodes in the full tree conform to clade colors in the inset.

FIGURE 4

Best tree from maximum likelihood analysis of partial plastome sequences across the Andean tetraploid clade of Amaryllidaceae subfam. Amaryllidoideae, with bootstrap percentages <100 shown above branches (all unmarked branches have 100% BP). The tree is divided into two sections (A,B) for readability; refer to the colored inset (a cartoon of the tree collapsed to the tribal level) as a guide. Colored circles at the nodes in the full tree conform to clade colors in the inset.

FIGURE 5

“Tanglegram” created from the best ML 70% taxon coverage nuclear supermatrix (Supplementary Figure 3) and the plastome trees (Figure 4) graphically showing cytonuclear discordance between the two partitions. A = nuclear tree, B = plastome tree.

FIGURE 6

Equal angle 360° hybridization network generated by SplitsTree v. 4.15.1 based on the 99% taxon coverage supermatrix (70 nuclear genes) across the tribe Clinantheae. Numbers above branches are percentages from 300 bootstrap iterations. The entire network is shown in the inset, with subclades (A) and (B) magnified for clarity.

FIGURE 7

Equal angle 360° hybridization network generated by SplitsTree v. 4.15.1 based on the 99% taxon coverage supermatrix (70 nuclear genes) across the tribe Eucharideae, with percentages from 300 bootstrap iterations. The entire network is shown in the inset, with subclades (A) and (B) magnified for clarity. Red arrow indicates possible reticulate origin of the monotypic Plagiolirion.

FIGURE 8

Equal angle 360° hybridization network generated by SplitsTree v. 4.15.1 based on the 99% taxon coverage supermatrix (70 nuclear genes) across the genus Hymenocallis, with percentages from 300 bootstrap iterations. The entire network is shown in the inset, with subclades (A) and (B) magnified for clarity.

FIGURE 9

Relaxed penalized likelihood chronogram of the Andean tetraploid clade using the chronos function of APE with the best 90% taxon coverage supermatrix tree found by RAxML. Arrows indicate calibration nodes used in the analysis. Numbers along branches are millions of years before present. The entire tree is shown in the inset, with subclades (A) and (B) magnified for clarity.

FIGURE 10

Area cladogram generated by Divalike+J analysis with BioGeoBears through RASP 4.2, using the best tree found by maximum likelihood of the 90% taxon coverage supermatrix with RAxML. Areas at any node were limited to three, and only the most likely was mapped onto the tree. Lower case “v” and “d” adjacent to a node = vicariance or dispersal, respectively. The tree is divided into two sections (A,B) for readability; refer to the inset as a guide.