Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Abstract

Background: The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes.

Results: We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae.

Conclusions: A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).

Keywords: Divergence time; Diversification; Genome; Juglandaceae; Phylogenomics; Plastome.

Fig. 1

Geographic distribution of modern and fossil members of the Juglandaceae. Lined regions indicate the modern distribution of ten genera belong to the three subfamilies (Juglandoideae, blue line; Engelhardioideae-red line; and Rhoipteleoideae, black line). The map used ArcGIS (version 10.0). The source locations of Juglandaceae fossils used in our analyses are colored dots. blue-Juglandoideae (Juglans, Platycarya, Pterocarya, Cyclocarya, and Carya), red-Engelhardioideae (Oreomunnea, Engelhardia, Alfaroa, and Alfaropsis), and Black- Rhoipteleoideae (Rhoiptelea)

Fig. 2

Variability of the family Juglandaceae represented over the circular map of Juglans regia, and comparison of percentage of variable characters in Juglandaceae plastomes. a Circular map comparing the chloroplast genomes of the genera of the walnut family (the reference chloroplast genome sequence NCBI accession number: KT963008; Hu et al. 2016a). The two inverted repeat regions (IRa and IRb) separate the large (LSC) and small (SSC) single copy regions, respectively. Genes represented by outside rectangles are on the positive strand, genes represented by inside rectangles are on the negative strand. Density of chloroplast SNPs is represented by a heatmap that varies from low (white) to high (dark blue). The circle depicts average SNP density estimated in 350 bp moving windows. Carya = Carya cathayensis, Rhoiptelea = Rhoiptelea chiliantha, Alfaropsis = Alfaropsis roxburghiana, Platycarya = Platycarya strobilacea, Pterocarya = Pterocarya fraxinifolia, Juglans = Juglans ailantifolia. Comparison of percentage of variable characters in Juglandaceae plastomes. b Protein-coding genes (CDS), c Intergenic spacer (IGS) regions. The peaks labeled in blue were highly variable genes or regions

Fig. 3

The Maximum Likelihood (ML) phylogenetic trees of Juglandaceae. Trees are based on a sixty one chloroplast protein-coding genes in the chloroplast, b 16 mtCDS fragement DNA sequence data, and c nuclear SNPs from whole genome resequencing data. For these trees, the PartitionFinder method for the best model combinations (Additional file 1: Table S4) was inferred by RAxML. Numbers at nodes correspond to ML bootstrap percentages (10,000 replicates). The three subfamilies are indicated with red arrows; Rhoipteleoideae (black bar), Engelhardioideae (dark red bar), and Juglandoideae (blue bar). Fruit morphology is shown using one species from each genus; the black solid circles indicate wingless fruits, hollow circles indicate winged fruits. Details for the outgroups (orange bar) are in Additional file 1: Table S1. The triangles indicate taxa with discordance between nuclear and chloroplast phylogeny

Fig. 4

Time-calibrated phylogenetic tree of Juglandaceae based on 61 protein-coding genes (CDS) of chloroplast genomes. Mean divergence times estimated using a relaxed molecular clock model with 6 fossil priors (red stars). Blue bars across nodes indicate 95% HPD intervals around the mean divergence time estimates. Nodes are numbered as ages. The genera and subfamilies of Juglandaceae are shown in the figure and the geological time scale is shown below the tree. A stacked deep-sea benthic foraminiferal oxygen-isotope curve shows the evolution of global climate over the last 65 Mya, as modified from Zachos et al. (2001, 2008) [47, 48]. PETM Palaeocene–Eocene thermal maximum, ETM Eocene thermalmaximum, Pl pliocene. Reprinted by permission from Macmillan Publishers Ltd: Nature (451, 279–283), copyright (2008).