Phylogenomics recovers monophyly and early Tertiary diversification of Dipteronia (Sapindaceae)

Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two 'living fossil' tree species of Dipteronia

'Living fossils', that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Dipteronia sinensis and D. dyeriana, two East Asian Tertiary relict trees. We found large-scale genome reorganizations and identified species-specific genes under positive selection that are likely involved in adaptation. Our demographic analyses suggest that the wider-ranged D. sinensis repeatedly recovered from population bottlenecks over late Tertiary/Quaternary periods of adverse climate conditions, while the population size of the narrow-ranged D. dyeriana steadily decreased since the late Miocene, especially after the Last Glacial Maximum (LGM). We conclude that the efficient purging of deleterious mutations in D. sinensis facilitated its survival and repeated demographic recovery. By contrast, in D. dyeriana, increased genetic drift and reduced selection efficacy, due to recent severe population bottlenecks and a likely preponderance of vegetative propagation, resulted in fixation of strongly deleterious mutations, reduced fitness, and continuous population decline, with likely detrimental consequences for the species' future viability and adaptive potential. Overall, our findings highlight the significant impact of demographic history on levels of accumulation and purging of putatively deleterious mutations that likely determine the long-term survival and extinction risk of Tertiary relict trees.

New insights into the phylogeny and evolution of Podocarpaceae inferred from transcriptomic data

Phylogenies of an increasing number of taxa have been resolved with the development of phylogenomics. However, the intergeneric relationships of Podocarpaceae, the second largest family of conifers comprising 19 genera and approximately 187 species mainly distributed in the Southern Hemisphere, have not been well disentangled in previous studies, even when genome-scale data sets were used. Here we used 993 nuclear orthologous groups (OGs) and 54 chloroplast OGs (genes), which were generated from 47 transcriptomes of Podocarpaceae and its sister group Araucariaceae, to reconstruct the phylogeny of Podocarpaceae. Our study completely resolved the intergeneric relationships of Podocarpaceae represented by all extant genera and revealed that topological conflicts among phylogenetic trees could be attributed to synonymous substitutions. Moreover, we found that two morphological traits, fleshy seed cones and flattened leaves, might be important for Podocarpaceae to adapt to angiosperm-dominated forests and thus could have promoted its species diversification. In addition, our results indicate that Podocarpaceae originated in Gondwana in the late Triassic and both vicariance and dispersal have contributed to its current biogeographic patterns. Our study provides the first robust transcriptome-based phylogeny of Podocarpaceae, an evolutionary framework important for future studies of this family.

Natural Hybrid Origin of the Controversial "Species" Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence

Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold-adapted vine species, Clematis pinnata, which is a rare and taxonomically controversial taxon endemic to northern China. Using field investigations, flow cytometry (FCM), phylogenomic analysis, morphological statistics, and niche modeling, we tested hybrid origin and species status of C. pinnata. The FCM results showed that all the tested species were homoploid (2n = 16). Phylonet and HyDe analyses based on transcriptome data showed the hybrid origins of C. × pinnata from either C. brevicaudata × C. heracleifolia or C. brevicaudata × C. tubulosa. The plastome phylogeny depicted that C. × pinnata in different sampling sites originated by different hybridization events. Morphological analysis showed intermediacy of C. × pinnata between its putative parental species in many qualitative and quantitative characters. Niche modeling results suggested that C. × pinnata had not been adapted to a novel ecological niche independent of its putative parents. These findings demonstrated that plants of C. × pinnata did not formed a self-evolved clade and should not be treated as a species. The present study also suggests that interspecific hybridization is a common mechanism in Clematis to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in Clematis.

Voltammetric Electrochemical Sensor for Phylogenetic Study in Acer Linn

Acer Linn. is a highly divergent species morphology in the maple family (Aceraceae). It is one of the genera facing a very difficult taxonomic situation. The phylogeny of the genus and the taxonomic system under the genus remain unclear. The use of electrochemical fingerprints for plant phylogenetic study is an emerging application in biosensors. In this work, leaves of 18 species of Acer Linn. with an exo-taxa were selected for electrochemical fingerprint recording. Two different conditions were used for improving the data abundance. The fingerprint of all species showed a series of oxidation peaks. These peaks can be ascribed to the oxidation of flavonols, phenolic acids, procyanidins, alkaloids, and pigments in plant tissue. These electrochemical fingerprints can be used for the identification of plant species. We also performed a phylogenetic study with data from electrochemical fingerprinting. The phylogenetic tree of Acer is divided into three main clades. The result is in full agreement with A. shangszeense var. anfuense, A. pictum subsp. mono, A. amplum, A. truncatum, and A. miaotaiense, belonging to the subsection Platanoidea. A. nikoense and A. griseum were clustered together in the dendrogram. Another group that fits the traditional classification results is in the subsection Integrifolia.

Phylogenetic relationships and molecular evolution of woody forest tree family Aceraceae based on plastid phylogenomics and nuclear gene variations

The forest tree family Aceraceae is widespread in the northern hemisphere and it has ecological and economic importance. However, the phylogenetic relationships and classifications within the family are still controversial due to transitional intraspecific morphological characteristics and introgression hybridization among species. In this study, we determined the evolutionary relationships and molecular evolution of Aceraceae based on plastid phylogenomics and two nuclear gene variations. Phylogenetic analysis based on the plastid genomes suggested that Aceraceae species can be divided into two larger sub-clades corresponding to the two genera Acer and Dipteronia. Conjoint analysis of the plastid and nuclear gene sequences supported the classification with two genera in the family. Molecular dating showed that the two genera diverged 60.2 million years ago, which is generally consistently with previously reported results. Divergence hotspots and positively selected genes identified in the plastid genomes could be useful genetic resources in Aceraceae.

Evolutionary history of endangered and relict tree species Dipteronia sinensis in response to geological and climatic events in the Qinling Mountains and adjacent areas

Geological and climatic events are considered to profoundly affect the evolution and lineage divergence of plant species. However, the evolutionary histories of tree species that have responded to past geological and climate oscillations in central China's mountainous areas remain mostly unknown. In this study, we assessed the evolutionary history of the endangered and relict tree species Dipteronia sinensis in the Qinling Mountains (QM) and adjacent areas in East Asia based on variations in the complete chloroplast genomes (cpDNA) and reduced-genomic scale single nucleotide polymorphisms (SNPs). Population structure and phylogenetic analysis based on the cpDNA variations suggested that D. sinensis could be divided into two intraspecific genetic lineages in the eastern and western sides of the QM (EQM and WQM, respectively) in East Asia. Molecular dating suggested that the intraspecific divergence of D. sinensis occurred approximately 39.2 million years ago during the later Paleogene. It was significantly correlated with the orogeny of the QM, where the formation of this significant geographic barrier in the region may have led to the divergence of independent lineages. Bayesian clustering and demographic analysis showed that intraspecific gene flow was restricted between the EQM and WQM lineages. Isolation-with-migration analysis indicated that the two genetic lineages experienced significant demographic expansions after the Pleistocene ice ages. However, the genetic admixture was determined in some populations between the two lineages by the large scale of SNP variations due to DNA incompatibility, the large significant population size, and rapid gene flow of nuclear DNA markers. Our results suggest that two different conservation and management units should be constructed for D. sinensis in the EQM and WQM areas. These findings provide novel insights into the unprecedented effects of tectonic changes and climatic oscillations on lineage divergence and plant population evolution in the QM and adjacent areas in East Asia.

Molecular evolution of chloroplast genomes in Monsteroideae (Araceae)

This study provides broad insight into the chloroplast genomes of the subfamily Monsteroideae. The identified polymorphic regions may be suitable for designing unique and robust molecular markers for phylogenetic inference. Monsteroideae is the third largest subfamily (comprises 369 species) and one of the early diverging lineages of the monocot plant family Araceae. The phylogeny of this important subfamily is not well resolved at the species level due to scarcity of genomic resources and suitable molecular markers. Here, we report annotated chloroplast genome sequences of four Monsteroideae species: Spathiphyllum patulinervum, Stenospermation multiovulatum, Monstera adansonii, and Rhaphidophora amplissima. The quadripartite chloroplast genomes (size range 163,335-164,751 bp) consist of a pair of inverted repeats (25,270-25,931 bp), separating a small single copy region (21,448-22,346 bp) from a large single copy region (89,714-91,841 bp). The genomes contain 114 unique genes, including four rRNA genes, 80 protein-coding genes, and 30 tRNA genes. Gene features, amino acid frequencies, codon usage, GC contents, oligonucleotide repeats, and inverted repeats dynamics exhibit similarities among the four genomes. Higher rate of synonymous substitutions was observed as compared to non-synonymous substitutions in 76 protein-coding genes. Positive selection was observed in seven protein-coding genes, including psbK, ndhK, ndhD, rbcL, accD, rps8, and ycf2. Our included species of Araceae showed the monophyly in Monsteroideae and other subfamilies. We report 30 suitable polymorphic regions. The polymorphic regions identified here might be suitable for designing unique and robust markers for inferring the phylogeny and phylogeography among closely related species within the genus Spathiphyllum and among distantly related species within the subfamily Monsteroideae. The chloroplast genomes presented here are a valuable contribution towards understanding the molecular evolutionary dynamics in the family Araceae.

Characterization of the complete chloroplast genome of sugar maple (Acer saccharum)

Acer saccharum is one ecologically and economically important tree species cultivated widely across the world. In this study we generated the complete chloroplast (cp) genome of A. saccharum via genome-skimming method. The assembled genome is 155,684 base-pairs (bp) in size, with one large single copy region of 85,393 bp and one small single copy region of 18,033 bp separated by two inverted repeats of 26,129 bp. The genome contains a total of 133 genes, including 85 protein-coding genes, 8 rRNAs and 40 tRNAs. Furthermore, phylogenomic estimation strongly supported A. saccharum as a distinct lineage within the monophyletic Acer.

A multi-locus phylogeny for the Neotropical Anomospermeae (Menispermaceae): Implications for taxonomy and biogeography

Neotropical rainforests cover about half of the world's tropical rainforests and house most of the biodiversity available on Earth. Australasia has been suggested as a potential source for Neotropical diversity. However, it remains unclear whether megathermal lineages could indeed have migrated to South America though Antarctica. The Neotropical Anomospermeae (Menispermaceae) consists of large, canopy lianas and is entirely restricted to tropical lowland rainforests. The sister relationship identified between this group and its Australasian ally represents an excellent model to test hypotheses regarding past connections between those landmasses. In this study, we used six chloroplast and two nuclear DNA markers to reconstruct phylogenetic relationships within the Neotropical Anomospermeae (Menispermaceae). The phylogeny of this group was then used as basis to reconstruct its biogeographical history. The phylogenetic framework reconstructed here strongly supports the monophyly of the Neotropical Anomospermeae and recovers the species of Anomospermum in three different clades: (i) Anomospermum sect. Anomospermum plus Orthomene; (ii) Anomospermum grandifolium and A. solimoesanum (Anomospermum sect. Elissarrhena); and (iii) Anomospermum bolivianum (Anomospermum sect. Elissarrhena). Each of these clades is recognized as a different genus and the necessary taxonomic changes are proposed. Furthermore, the Neotropical Anomospermeae seems to have split from its Australasian sister-group at c. 62 Ma. Ancestral area reconstructions support an Australasian origin for the Neotropical Anomospermeae, providing additional support for the hypothesis that Australasia is a source of Neotropical diversity, with megathermal lineages having dispersed via Antarctica. The Neotropical Anomospermeae differentiated in the late Eocene and subsequently diversified rapidly into seven lineages, suggesting that Neotropical lowland rainforests resembling modern rainforests physiognomically and structurally might not have developed until the late Eocene. The Neotropical Anomospermeae exemplifies the contributions of Australasian migration to Neotropical diversity.