Phylogenomics, co-evolution of ecological niche and morphology, and historical biogeography of buckeyes, horsechestnuts, and their relatives (Hippocastaneae, Sapindaceae) and the value of RAD-Seq for deep evolutionary inferences back to the Late Cretaceous

Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species - influences of host identity, environment, phylogeny, and geographic isolation

Introduction

The well-known eastern Asian (EA) and eastern North American (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or lineages isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these lineages. Here we compared foliar endophytic fungi and bacteria-archaea (FEF and FEB) in 17 EA-ENA disjunct species or clade pairs from genera representing conifers and 10 orders of five major groups of angiosperms and 23 species of Cornus from EA and North America.

Methods

Metagenomic sequencing of fungal ITS and bacterial-archaeal 16S rDNA was used to capture the foliar endophytic communities. Alpha and beta diversity of fungi and bacteria were compared at multiple scales and dimensions to gain insights into the relative roles of historical geographic isolation, host identity, phylogeny, and environment from samples at different sites in shaping endophytic diversity patterns.

Results

We found that beta diversity of endophytes varied greatly among plant individuals within species and between species among genera at the same sampling site, and among three sampling sites, but little variation between region-of-origin of all plant species (EA vs ENA) and between EA-ENA disjunct counterparts within genera. Various numbers of indicator fungal species differing in abundance were identified for each plant genus and Cornus species. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance of plants was detected among the disjunct genera but not among species of Cornus. However, significant correlations between beta diversities at different taxonomic scales of endophytes and phylogenetic distances of Cornus species were observed.

Discussion

Our results suggest important roles of host identity and environment (sampling sites), and a likely minor role of phylogenetic divergence and historical biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera and Cornus. The results lead to a hypothesis that the sister taxa in EA and ENA likely differ in FEF and FEB when growing in native habitats due to differences in local environments, which may potentially drive allopatric divergence of the functional features of species.

An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data

PREMISE

A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group.

METHODS

We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis.

RESULTS

A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode.

CONCLUSIONS

Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names.

The Chromosome-level genome of Aesculus wilsonii provides new insights into terpenoid biosynthesis and Aesculus evolution

Aesculus L. (buckeye and horse chestnut) are woody plant species with important horticultural and medicinal values. Aesculus seeds are widely used as biomedicine and cosmetic ingredients due to their saponins. We report a chromosomal-scale genome of Aesculus wilsonii. Sequences amounting to a total of 579.01 Mb were assembled into 20 chromosomes. More than half of the genome (54.46%) were annotated as repetitive sequences, and 46,914 protein-coding genes were predicted. In addition to the widespread gamma event with core eudicots, a unique whole-genome duplication (WGD) event (17.69 Mya) occurred in Aesculus after buckeye differentiated from longan. Due to WGD events and tandem duplications, the related synthetic genes of triterpene saponins unique to Aesculus increased significantly. Combined with transcriptome characterization, the study preliminarily resolved the biosynthetic pathway of triterpenoid saponins like aescin in A. wilsonii genome. Analyses of the resequencing of 104 buckeye accessions revealed clear relationship between the geographic distribution and genetic differentiation of buckeye trees in China. We found that the buckeye species found in southern Shaanxi is A. wilsonii rather than A. chinensis. Population dynamics analysis further suggests that the population size and evolution of existing buckeye species have been influenced by climate fluctuations during the Pleistocene and recent domestication events. The genome of A. wilsonii and population genomics of Aesculus provide a resource for future research on Hippocastanaceae. These findings will contribute to the utilization and diversity protection of Aesculus.

Comparative Metabolomics of Reproductive Organs in the Genus Aesculus (Sapindaceae) Reveals That Immature Fruits Are a Key Organ of Procyanidin Accumulation and Bioactivity

Fruit from A. hippocastanum L. are used commercially for chronic venous insufficiency (CVI). The isomeric mixture of pentacyclic triterpenoid saponins (β-aescin) exert anti-inflammatory effects. Hence, research has focused on β-aescin, yet the diversity, accumulation, and bioactivity of organ-specific secondary metabolites represent missed pharmacological opportunities. To this end, we applied an untargeted metabolomics approach by liquid chromatography—tandem mass spectrometry (LC–MS/MS) to the chemical profiles of flowers, immature fruits, and pedicels from 40 specimens across 18 species of Aesculus. Principal component analysis (PCA), orthogonal partial least squares (OPLS-DA), and molecular networking revealed stronger chemical differences between plant organs, than between species. Flowers are rich in glycosylated flavonoids, pedicels in organic acids and flavonoid aglycones, and immature fruits in monomeric flavan-3-ols and procyanidins. Although a high diversity of flavonoids and procyanidins was observed, the relative amounts differed by plant organ. Fruit extracts demonstrated the strongest antifungal (Saccharomyces cerevisiae) and antioxidant activity, likely from the procyanidins. Overall, secondary metabolite profiles are organ-specific, and fruits accumulate antifungal and antioxidant compounds. Due to the chemical similarity between species, similar effects may be achieved between species. This creates incentives for further exploration of the entire genus, in bioprospecting for potential therapeutic leads.

Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

Foundational hypotheses addressing plant-insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude 1H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other's state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.

A New Pipeline for Removing Paralogs in Target Enrichment Data

Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of data sets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene data sets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study. [Angiosperms353; Castanea; divergence time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.]

Phylotranscriptomics reveals the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution

The disjunct distribution between East Asia and North America is one of the best established biogeographic patterns. A robust phylogeny is fundamental for understanding the biogeographic histories of taxa with this distribution pattern. Tsuga (hemlock) is a genus of Pinaceae with a typical intercontinental disjunct distribution in East Asia and eastern and western North America, and its phylogeny has not been completely reconstructed in previous studies. In this study, we reconstructed a highly resolved phylogeny of Tsuga using 881 nuclear genes, 60 chloroplast genes and 23 mitochondrial genes and explored its biogeographic and reticulate evolutionary history. The results of phylogenetic analysis, molecular dating and ancestral area reconstruction indicate that Tsuga very likely originated from North America in the late Oligocene and dispersed from America to East Asia via the Bering Land Bridge during the middle Miocene. In particular, we found complex reticulate evolutionary pattern among the East Asian hemlock species. T. sieboldii possibly originated from hybridization with the ancestor of T. chinensis from mainland China and T. forrestii as the paternal donor and the ancestor of T. diversifolia and T. ulleungensis as the maternal donor. T. chinensis (Taiwan) could have originated by hybridization together with T. sieboldii and then evolved independently after dispersal to the Taiwan Island, subsequently experiencing mitochondrial DNA introgression with T. chinensis from mainland China. Moreover, our study found that T. chinensis from western China is more closely related to T. forrestii than to T. chinensis from eastern China. The nonmonophyletic T. chinensis needs taxonomic reconsideration.

Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny

Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. Calibration of a Bayesian phylogeny with fossil evidence produced divergence time estimates for the clade consistent with a late Oligocene origin in North America, followed by a period of elevated diversification between 12 and 5 Mya. Comparison of the ddRADseq phylogenies with a phylogeny based on Sanger-sequenced chloroplast DNA revealed five instances of pronounced discordance, illustrating the potential for chloroplast introgression, chloroplast transfer, or incomplete lineage sorting to influence organellar phylogeny. Our results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence.

Chloroplast Phylogenomics Reveals the Intercontinental Biogeographic History of the Liquorice Genus (Leguminosae: Glycyrrhiza)

The liquorice genus, Glycyrrhiza L. (Leguminosae), is a medicinal herb with great economic importance and an intriguing intercontinental disjunct distribution in Eurasia, North Africa, the Americas, and Australia. Glycyrrhiza, along with Glycyrrhizopsis Boiss. and Meristotropis Fisch. & C.A.Mey., comprise Glycyrrhiza s.l. Here we reconstructed the phylogenetic relationships and biogeographic history in Glycyrrhiza s.l. using sequence data of whole chloroplast genomes. We found that Glycyrrhiza s.l. is sister to the tribe Wisterieae and is divided into four main clades. Clade I, corresponds to Glycyrrhizopsis and is sister to Glycyrrhiza sensu Meng. Meristotropis is embedded within Glycyrrhiza sensu Meng, and these two genera together form Clades II-IV. Based on biogeographic analyses and divergence time dating, Glycyrrhiza s.l. originated during the late Eocene and its most recent common ancestor (MRCA) was distributed in the interior of Eurasia and the circum-Mediterranean region. A vicariance event, which was possibly a response to the uplifting of the Turkish-Iranian Plateau, may have driven the divergence between Glycyrrhiza sensu Meng and Glycyrrhizopsis in the Middle Miocene. The third and fourth main uplift events of the Qinghai-Tibetan Plateau may have led to rapid evolutionary diversification within Glycyrrhiza sensu Meng. Subsequently, the MRCA of Clade II might have migrated to North America (G. lepidota) via the Bering land bridge during the early Pliocene, and reached temperate South America (G. astragalina) by long-distance dispersal (LDD). Within Clade III, the ancestor of G. acanthocarpa arrived at southern Australia through LDD after the late Pliocene, whereas all other species (the SPEY clade) migrated to the interior of Eurasia and the Mediterranean region in the early Pleistocene. The MRCA of Clade IV was restricted in the interior of Eurasia, but its descendants have become widespread in temperate regions of the Old World Northern Hemisphere during the last million years.