The demographic response of a deciduous shrub (the Indigofera bungeana complex, Fabaceae) to the Pleistocene climate changes in East Asia

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

Introduction

Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera.

Methods

Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae.

Results and discussion

The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.

A clue to the evolutionary history of modern East Asian flora: insights from phylogeography and diterpenoid alkaloid distribution pattern of the Spiraea japonica complex

Each subkingdom of East Asian flora (EAF) has a unique evolutionary history, but which has rarely been described based on phylogeographic studies of EAF species. The Spiraea japonica L. complex, which is widespread in East Asia (EA), has received considerable attention because of the presence of diterpenoid alkaloids (DAs). It provides a proxy for understanding the genetic diversity and DA distribution patterns of species under various environmental conditions associated with the geological background in EA. In the present study, the plastome and chloroplast/nuclear DNA of 71 populations belonging to the S. japonica complex and its congeners were sequenced, combined with DA identification, environmental analyses, and ecological niche modelling, to investigate their phylogenetic relationships, genetic and DAs distribution patterns, biogeography, and demographic dynamics. An "ampliative" S. japonica complex was put forward, comprising all species of Sect. Calospira Ser. Japonicae, of which three evolutionary units carrying their respective unique types of DAs were identified and associated with the regionalization of EAF (referring to the Hengduan Mountains, central China, and east China). Moreover, a transition belt in central China with its biogeographic significance was revealed by genetic and DA distribution patterns from the perspective of ecological adaptation. The origin and onset differentiation of the "ampliative" S. japonica complex was estimated in the early Miocene (22.01/19.44 Ma). The formation of Japanese populations (6.75 Ma) was facilitated by the land bridge, which subsequently had a fairly stable demographic history. The populations in east China have undergone a founder effect after the Last Glacial Maximum, which may have been promoted by the expansion potential of polyploidization. Overall, the in-situ origin and diversification of the "ampliative" S. japonica complex since the early Miocene is a vertical section of the formation and development of modern EAF and was shaped by the geological history of each subkingdom.

Genetic Diversity of Oxytropis Species from the Center of the Genus Origin: Insight from Molecular Studies

The genus Oxytropis (Fabaceae) was formed from the ancient species of Astragalus presumably approximately 5.6 Ma ago in Southern Siberia. Our study summarized data on the genetic diversity of 69 populations of 31 Oxytropis species in the center of origin of the genus based on the sequencing of plastid genome markers. Most of the populations (82.6%) are characterized by high gene diversity (0.600–1.000), which indicates a relatively stable state. Phylogenetic relationships between most Oxytropis species remain unresolved. Three genetic complexes and four phyletic lineages have been identified. Some species form weakly differentiated complexes, which is probably caused by their relatively recent divergence and the demography processes, as well as interspecific hybridization and polyploidy characteristic of Oxytropis species.

The nuanced nature of mesic refugia in arid landscapes: a tale of two peas

BACKGROUND AND AIMS

Understanding how genetic diversity is distributed and maintained within species is a central tenet of evolutionary and conservation biology, yet is understudied in arid regions of the globe. In temperate, glaciated environments, high genetic diversity in plant species is frequently found in refugial areas, which are often associated with southern non-glaciated landscapes. In arid, unglaciated environments, landscape features providing mesic conditions are likely to be refugia, although our understanding needs more refinement in these biomes. We test whether refugia and nuclear diversity hotspots occur in high-elevation, topographically complex areas for co-distributed shrubs (Petalostylis labicheoides and Indigofera monophylla; Fabaceae) in the ancient, arid Pilbara bioregion of north-western Australia.

METHODS

We conducted extensive sampling of the Pilbara (>1400 individuals from 62 widespread populations) to detect patterns in nuclear diversity and structure based on 13-16 microsatellite loci. Evidence of historical refugia was investigated based on patterns of diversity in three non-coding chloroplast (cp) sequence regions for approx. 240 individuals per species. Haplotype relationships were defined with median-joining networks and maximum likelihood phylogenetic trees.

KEY RESULTS

We found cpDNA evidence for a high-elevation refugium in P. labicheoides but not for I. monophylla that instead exhibited extraordinary haplotype diversity and evidence for persistence across a widespread area. Nuclear diversity hotspots occurred in, but were not exclusive to, high-elevation locations and extended to adjacent, low-elevation riparian areas in both species.

CONCLUSIONS

Phylogeographic refugia in arid environments may occur in high-elevation areas for some species but not all, and may be influenced by species-specific traits: a mesic montane refugium in P. labicheoides could be related to its preference for growth in water-gaining areas, while a lack of such evidence in I. monophylla could be related to maintenance of cpDNA diversity in a large soil seed bank and dynamic evolutionary history. Mesic environments created by the intersection of topographically complex landscapes with riparian zones can be contemporary reservoirs of genetic diversity in arid landscapes.

The species of Oxytropis DC. of section Gloeocephala Bunge (Fabaceae) from Northeast Asia: genetic diversity and relationships based on sequencing of the intergenic spacers of cpDNA and ITS nrDNA

Phylogenetic relationships within Oxytropis DC. sect. Gloeocephala Bunge from Northeast Asia were studied using plastid intergenic spacers (psbA-trnH + trnL-trnF + trnS-trnG) and ITS nrDNA. Populations of O. anadyrensis Vass., O. borealis DC., O. middendorffii Trautv., O. trautvetteri Meinsh., and O. vasskovskyi Jurtz. were monomorphic or characterised by a low level of chloroplast genetic diversity (h varied from 0.143 to 0.692, and π from 0.0001 to 0.0005). Presumably, the low genetic diversity was a result of the severe bottlenecks during Pleistocene glaciation-interglacial cycles. Twenty chlorotypes were identified; species studied had no shared chlorotypes. Chlorotypes of O. anadyrensis, O. borealis, and O. middendorffii formed two lineages each, while the chlorotypes of O. trautvetteri and O. vasskovskyi formed one separate lineage each in the phylogenetic network. There were specific diagnostic markers of cpDNA in each lineage, excluding O. vasskovskyi. The presence of a species-specific diagnostic marker in O. trautvetteri and specific markers in two lineages of O. anadyrensis support circumscribing these taxa as independent species. Regarding ITS nrDNA polymorphism, five ribotypes were detected. The differences revealed in plastid and nuclear genomes of Oxytropis sect. Gloeocephala confirmed that the Asian sector of Megaberingia was the main centre of diversification of arctic legumes.

Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

Genetic diversity and its distribution, both within and between populations, may be determined by micro-evolutionary processes, such as the demographic history of populations, natural selection, and gene flow. In plants, indices of genetic diversity (e.g., k, h and π) and structure (e.g., FST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. We also used phylogenetic modeling to assess the relative contribution of relatedness or ecological and reproductive characters to the genetic diversity of plants. We postulated that genetic diversity could be defined not only by microevolutionary factors and life history traits, but also by relatedness, so that species more closely related phylogenetically would have similar genetic diversities. We found a clear tendency for an increase in the number of studies over time, confirming the hypothesis that the advances in the area of molecular genetics have supported the accumulation of data on the genetic diversity of plants. However, we found that the vast majority of these data have been produced by Chinese authors, and refer specifically to populations of Chinese plants. Most of the data on genetic diversity have been obtained for species in the International Union for Conservation of Nature (IUCN) category NE (Not Evaluated), which indicates a relative lack of attention on threatened species. In general, we observed very high FST values in the groups analyzed and, as we focused primarily on species that have not been evaluated by the IUCN, the number of plant species that are threatened with extinction may be much greater than that indicated by the listing of this organization. We also found that the number of haplotypes (k) was influenced by the type of geographic distribution of the plant, while haplotype diversity (h) was affected by the type of flower, and the fixation index (FST), by the type of habitat. The plant species most closely-related phylogenetically have similar levels of genetic diversity. Overall, then, it will important to consider phylogenetic dependence in future studies that evaluate the effects of life-history traits on plant genetic diversity.

Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest

BACKGROUND

Refugial populations in Quaternary glaciations are critical to understanding the evolutionary history and climatic interactions of many extant species. Compared with the well-studied areas of Europe and Northern America, refugia of species in eastern Asia remain largely unknown. Here, we investigated the phylogeographic history of a globally important insect pest, the oriental fruit moth Grapholita molesta, in its native range of China.

RESULTS

Genetic structure analyses unveiled three distinct groups and a set of populations with admixture. Approximate Bayesian Computation (ABC) analyses support range expansion of this moth from southwest groups of Yunnan and Sichuan to northern and eastern China. A set of admixed populations was found around these two ancestral groups. This pattern of genetic structure points to two refugia located in the Yunnan region and Sichuan Basin. The split of the two refugia was dated to 329.2 thousand years ago in the penultimate glacial period. One of the lineages was exclusively found around the Sichuan Basin, indicating the formation of endemic populations in this refugium. Ecological niche model analysis suggested a shrinking distribution from the LIG period to the MID period in the Sichuan lineage but a wide and stable distribution in the other lineage.

CONCLUSIONS

Our results for the first time suggest that Yunnan and Sichuan jointly served as two large-scale refugia in eastern Asia in Quaternary glaciations, helping to maintain genetic diversity overall.