The intraspecific genetic variability of siliceous and calcareous Gentiana species is shaped by contrasting demographic and re-colonization processes

Hybridization and divergent climatic preferences drive divergence of two allopatric Gentiana species on the Qinghai-Tibet Plateau

BACKGROUND AND AIMS

Exploring how species diverge is vital for understanding the drivers of speciation. Factors such as geographical separation and ecological selection, hybridization, polyploidization and shifts in mating system are all major mechanisms of plant speciation, but their contributions to divergence are rarely well understood. Here we test these mechanisms in two plant species, Gentiana lhassica and G. hoae, with the goal of understanding recent allopatric species divergence on the Qinghai-Tibet Plateau (QTP).

METHODS

We performed Bayesian clustering, phylogenetic analysis and estimates of hybridization using 561 302 nuclear genomic single nucleotide polymorphisms (SNPs). We performed redundancy analysis, and identified and annotated species-specific SNPs (ssSNPs) to explore the association between climatic preference and genetic divergence. We also estimated genome sizes using flow cytometry to test for overlooked polyploidy.

KEY RESULTS

Genomic evidence confirms that G. lhassica and G. hoae are closely related but distinct species, while genome size estimates show divergence occurred without polyploidy. Gentiana hoae has significantly higher average FIS values than G. lhassica. Population clustering based on genomic SNPs shows no signature of recent hybridization, but each species is characterized by a distinct history of hybridization with congeners that has shaped genome-wide variation. Gentiana lhassica has captured the chloroplast and experienced introgression with a divergent gentian species, while G. hoae has experienced recurrent hybridization with related taxa. Species distribution modelling suggested range overlap in the Last Interglacial Period, while redundancy analysis showed that precipitation and temperature are the major climatic differences explaining the separation of the species. The species differ by 2993 ssSNPs, with genome annotation showing missense variants in genes involved in stress resistance.

CONCLUSIONS

This study suggests that the distinctiveness of these species on the QTP is driven by a combination of hybridization, geographical isolation, mating system differences and evolution of divergent climatic preferences.

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.

Between allopatry and secondary contact: differentiation and hybridization among three sympatric Gentiana species in the Qinghai-Tibet Plateau

BACKGROUND

Mountains of the world host a significant portion of all terrestrial biodiversity, and the region of the Qinghai-Tibet Plateau (QTP) stands as one of the most remarkable mountain regions on Earth.  Because many explosive radiations occurred there, the QTP is a natural laboratory which is ideal to investigate patterns and processes linked to speciation and diversification. Indeed, understanding how closely related and sympatric species diverged is vital to explore drivers fostering speciation, a topic only rarely investigated in the QTP. By combining genomic and environmental data, we explored the speciation process among three closely related and sympatric species, Gentiana hexaphylla, G. lawrencei and G. veitchiorum in the QTP region.

RESULTS

Combining genome sizes and cytological data, our results showed that G. hexaphylla and G. veitchiorum are diploid, whereas G. lawrencei is tetraploid. Genetic clustering and phylogenetic reconstruction based on genomic SNPs indicated a clear divergence among the three species. Bayesian clustering, migrant, and D-statistic analyses all showed an obvious signature of hybridization among the three species, in particular between G. lawrencei and both G. hexaphylla and G. veitchiorum in almost all populations. Environmental variables related to precipitation and particularly temperature showed significant differences among the three gentians, and in fact a redundancy analysis confirmed that temperature and precipitation were the major climatic factors explaining the genetic differentiation among the three species.

CONCLUSION

Our study suggested that ancient hybridization, polyploidization, geological isolation and the evolution of different climatic preferences were all likely to be involved in the divergence of the three Gentiana species, as may be the case for many other taxa in the QTP region.

Migration patterns of Gentiana crassicaulis , an alpine gentian endemic to the Himalaya–Hengduan Mountains

The Himalaya–Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai–Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological niche models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.

Gentiana clusii Perr.&Song.: Enhanced production of secondary metabolites by in vitro propagation

Shoot and root in vitro culture of endemic European species Gentiana clusii was established for the first time. The effects of different concentrations of benzyl adenine (BA), 6-phurphurylaminopurine (KIN), indole-3-butyric acid (IBA) and naphthalene acetic acid (NAA) on shoot propagation and rooting of G. clusii were investigated. The optimal in vitro conditions for shoot propagation and long-term maintenance were achieved using woody plant medium (WPM) supplemented with 0.5 mg l^-1 KIN, and subsequent application of IBA at 0.5 mg l^-1 significantly improved rooting of these shoots. Root culture was established from excised root tips cultured in ½ MS liquid media with increasing concentrations of IBA (0.1-1.0 mg l^-1). A high root growth rate and considerable biomass yield were obtained by addition of 1.0 mg l^-1 IBA. HPLC analysis revealed that in vitro culture considerably promoted the production of secondary metabolites in G. clusii. The selected protocol for shoot propagation (WPM + 0.5 mg l^-1 KIN) increased the content of sweroside, gentiopicrin and norswertianin-1-O-primeveroside (N-1-P) for more than 2-fold compared with the wild plants. IBA promoted N-1-P and norswertianin production in root cultures; their contents were enhanced 6.4- and 18.6-fold, respectively, compared with the wild plants. The extract of these roots displayed the highest antioxidant capacity (IC₅₀ = 66.57 μg ml^-1). The established shoot and root propagation protocols facilitate in vitro conservation of G. clusii, and provides a promising tool for the large scale production of valuable secoiridoids and xanthones.

Geological and Climatic Factors Affect the Population Genetic Connectivity in Mirabilis himalaica (Nyctaginaceae): Insight From Phylogeography and Dispersal Corridors in the Himalaya-Hengduan Biodiversity Hotspot

The genetic architecture within a species in the Himalaya-Hengduan Mountains (HHM) region was considered as the consolidated consequence of historical orogenesis and climatic oscillations. The visualization of dispersal corridors as the function of population genetic connectivity became crucial to elucidate the spatiotemporal dynamics of organisms. However, geodiversity and physical barriers created by paleo geo-climatic events acted vigorously to impact notable alterations in the phylogeographic pattern and dispersal corridors. Therefore, to achieve detailed phylogeography, locate dispersal corridors and estimate genetic connectivity, we integrated phylogeography with species distribution modelling and least cost path of Mirabilis himalaica (Edgew.) Heimerl in the HHM. We amplified four cpDNA regions (petL-psbE, rps16-trnK, rps16 intron, trnS-trnG), and a low copy nuclear gene (G3pdh) from 241 individuals of 29 populations. SAMOVA, genealogical relationships, and phylogenetic analysis revealed four spatially structured phylogroups for M. himalaica with the onset of diversification in late Pliocene (c. 3.64 Ma). No recent demographic growth was supported by results of neutrality tests, mismatch distribution analysis and Bayesian skyline plot. Paleo-distribution modelling revealed the range dynamics of M. himalaica to be highly sensitive to geo-climatic change with limited long-distance dispersal ability and potential evolutionary adaptation. Furthermore, river drainage systems, valleys and mountain gorges were identified as the corridors for population genetic connectivity among the populations. It is concluded that recent intense mountain uplift and subsequent climatic alterations including monsoonal changes since Pliocene or early Pleistocene formulated fragmented habitats and diverse ecology that governed the habitat connectivity, evolutionary and demographic history of M. himalaica. The integrative genetic and geospatial method would bring new implications for the evolutionary process and conservation priority of HHM endemic species.

Mountains as Evolutionary Arenas: Patterns, Emerging Approaches, Paradigm Shifts, and Their Implications for Plant Phylogeographic Research in the Tibeto-Himalayan Region

Recently, the "mountain-geobiodiversity hypothesis" (MGH) was proposed as a key concept for explaining the high levels of biodiversity found in mountain systems of the Tibeto-Himalayan region (THR), which comprises the Qinghai-Tibetan Plateau, the Himalayas, and the biodiversity hotspot known as the "Mountains of Southwest China" (Hengduan Mountains region). In addition to the MGH, which covers the entire life span of a mountain system, a complementary concept, the so-called "flickering connectivity system" (FCS), was recently proposed for the period of the Quaternary. The FCS focuses on connectivity dynamics in alpine ecosystems caused by the drastic climatic changes during the past ca. 2.6 million years, emphasizing that range fragmentation and allopatric speciation are not the sole factors for accelerated evolution of species richness and endemism in mountains. I here provide a review of the current state of knowledge concerning geological uplift, Quaternary glaciation, and the main phylogeographic patterns ("contraction/recolonization," "platform refugia/local expansion," and "microrefugia") of seed plant species in the THR. In addition, I make specific suggestions as to which factors future avenues of phylogeographic research should take into account based on the fundamentals presented by the MGH and FCS, and associated complementary paradigm shifts.

Species delimitation in the East Asian species of the relict tree genus Zelkova (Ulmaceae): A complex history of diversification and admixture among species

Zelkova species, trees of the elm family (Ulmaceae), are part of the Cenozoic relict flora. In western Eurasia, the genus comprises three species that are restricted to disjunct areas (Z. sicula on Sicily, Z. abelicea on Crete and Z. carpinifolia in Transcaucasia). The situation is different in East Asia, where three species (Z. serrata, Z. schneideriana and Z. sinica) have at least partly overlapping distributions. The phylogenetic and phylogeographic status of these East Asian species is still not well understood, mainly since all previous studies used almost exclusively plant material collected in botanical gardens and were based on very small numbers of individuals. Our study is the first based on 33 natural populations covering all important areas with Zelkova species in the Sino-Japanese Floristic Region. Chloroplast and microsatellite markers were used, and Bayesian analyses were run for both types of markers. East Asian Zelkova species cluster into two groups that partially overlap when comparing the two types of markers. For chloroplast markers, the two groups coincide with all Japanese, some Korean and northern Chinese Z. serrata in one group and all other individuals in the other group, regardless of whether they are attributed to Z. serrata, Z. sinica or Z. schneideriana from Korea, mainland China and Taiwan. At the nuclear level, however, the clustering clearly groups all the Z. serrata individuals together, regardless of whether they are from Japan, Korea or China, and the two other species in a second group. This complex genetic pattern in East Asian Zelkova species is most likely due to a combination of ancient diversification and speciation events and more recent hybridization during the last glacial/interglacial retractions and recolonizations. One of the surprising results of our study concerns the populations from Taiwan, which are genetically similar to Z. schneideriana. Thus, their assignation to a separate taxon (Z. tarokoensis) or to a variety of Z. serrata (Z. serrata var. tarokoensis), as currently reported in all local and national floras, might be in need of revision. Furthermore, our results indicate that the East Asian species are more closely related to Z. carpinifolia than to any other Western European species. Haplotypes of Z. sicula and Z. abelicea (Mediterranean region) as well as those of Z. sinica and Z. schneideriana (East Asia) seem to have diversified more recently. The most ancient haplotypes are found among the western Eurasian Z. carpinifolia and the East Asian Z. serrata. This result is in agreement with the carpinifolia and serrata-like morphotypes commonly found in the fossil record.

Long-term survival and successful conservation? Low genetic diversity but no evidence for reduced reproductive success at the north-westernmost range edge of Poa badensis (Poaceae) in Central Europe

Many steppe species reach their (north)westernmost distribution limit in western Central Europe. This also applies to Poa badensis, a rare steppe plant of calcareous rock/sand vegetation. To explore potential differences in reproductive success and genetic composition of peripheral populations, we analysed the absolute (north)westernmost occurrences in Western Germany and populations at the western margin (Eastern Austria) and the centre (Central Hungary) of the Pannonicum, representing a part of the continuous range. Specifically, we discuss the genetic and reproductive constitution of the (north)westernmost exclave and draw conclusions on the species' biogeographical and conservation history in this region. Therefore, we used two independent molecular marker systems (AFLPs, cpDNA sequences) and a set of performance parameters. Overall, lowest regional genetic diversity was found in Western Germany, which is mainly a result of the specific history of two populations. However, this low genetic diversity was not accompanied by reduced reproductive success. The Eastern Austrian populations showed reduced genetic diversity and predominantly reduced performance, interpreted as a consequence of small population sizes. Central Hungarian populations showed the overall highest genetic diversity and comparatively high performance values. We observed high admixture and haplotype sharing between Austrian and Hungarian populations, indicating gene flow among these regions. In contrast, we interpreted the increased population differentiation within, and the clear distinctiveness of the German exclave as a long-term isolation of these (north)westernmost occurrences. Our results, overall, prove the good constitution of these populations and, together with their particular biogeographical history, highlight their conservation value.

Intercontinental migration pattern and genetic differentiation of arctic-alpine Rhodiola rosea L.: A chloroplast DNA survey

Our study describes genetic lineages and historical biogeography of Rhodiola rosea a widely distributed arctic-alpine perennial species of the Northern Hemisphere based on sequence analysis of six chloroplast regions. Specimens of 44 localities from the Northern Hemisphere have been sequenced and compared with those available in the GenBank. Our results support the migration of the species into Europe via the Central Asian highland corridor, reaching the European Alpine System (EAS) and also the western European edge, the British Isles. The EAS proved to be an important center of genetic diversity, especially the region of the Eastern Alps and the Dolomites where signs of glacial refugia was observed. Apart from those of the EAS, a common lineage was detected along the Atlantic coast from the British Isles toward Scandinavia as well as Iceland and the eastern parts of North America. Accordingly, the British Isles represent a main link between the northern Atlantic and southern EAS lineages.

Out of Refugia: Population Genetic Structure and Evolutionary History of the Alpine Medicinal Plant Gentiana lawrencei var. farreri (Gentianaceae)

Understanding the genetic structure and evolutionary history of plants contributes to their conservation and utilization and helps to predict their response to environmental changes. The wildflower and traditional Chinese and Tibetan medicinal plant Gentiana lawrencei var. farreri is endemic to the Qinghai-Tibetan Plateau (QTP). To explore its genetic structure and evolutionary history, the genetic diversity, divergence, and demographics were analyzed in individuals from 31 locations across the QTP using 1 chloroplast marker and 10 nuclear microsatellite loci. High genetic diversity was detected in G. lawrencei var. farreri, and most of the genetic variance was found within populations. Values of F ST in G. lawrencei var. farreri from nuclear microsatellite and chloroplast data were 0.1757 and 0.739, respectively. The data indicated the presence of isolation by distance. The southeast edge of the QTP was the main refugium for G. lawrencei var. farreri, and one microrefugium was also detected in the plateau platform of the QTP. Both nuclear microsatellite and chloroplast data indicated that the populations were divided into two geographically structured groups, a southeast group and a northwest group. The current genetic pattern was mainly formed through recolonization from the two independent refugia. Significant melt was detected at the adjacent area of the two geographically structured groups. Approximate Bayesian computation showed that the northwest group had diverged from the southeast group, which then underwent population expansion. Our results suggest that the two-refugia pattern had a significant impact on the genetic structure and evolutionary history of G. lawrencei var. farreri.

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

Camellia flavida is an endangered species of yellow camellia growing in limestone mountains in southwest China. The current classification of C. flavida into two varieties, var. flavida and var. patens, is controversial. We conducted a genetic analysis of C. flavida to determine its taxonomic structure. A total of 188 individual plants from 20 populations across the entire distribution range in southwest China were analyzed using two DNA fragments: a chloroplast DNA fragment from the small single copy region and a single-copy nuclear gene called phenylalanine ammonia-lyase (PAL). Sequences from both chloroplast and nuclear DNA were highly diverse; with high levels of genetic differentiation and restricted gene flow. This result can be attributed to the high habitat heterogeneity in limestone karst, which isolates C. flavida populations from each other. Our nuclear DNA results demonstrate that there are three differentiated groups within C. flavida: var. flavida 1, var. flavida 2, and var. patens. These genetic groupings are consistent with the morphological characteristics of the plants. We suggest that the samples included in this study constitute three taxa and the var. flavida 2 group is the genuine C. flavida. The three groups should be recognized as three management units for conservation concerns.

Simultaneous speciation in the European high mountain flowering plant genus Facchinia (Minuartia s.l., Caryophyllaceae) revealed by genotyping-by-sequencing

Understanding the relative importance of different mechanisms of speciation in a given lineage requires fully resolved interspecific relationships. Using Facchinia, a genus of seven species centred in the European Alps, we explore whether the polytomy found by Sanger sequencing analyses of standard nuclear (ITS) and plastid markers (trnQ-rps16) is a hard or soft polytomy by substantially increasing the amount of DNA sequence data, generated by genotyping-by-sequencing. In comparison to 142 phylogenetically informative sites in the Sanger sequences the GBS sequences yielded 3363 phylogenetically informative sites after exclusion of apparently oversaturated SNPs. Maximum parsimony, maximum likelihood, NeighborNet, SVDquartets and Astral-II analyses all resulted in phylogenetic trees (and networks) in which interspecific relationships were largely unresolved. After excluding incomplete lineage sorting, hybridisation and oversaturation of characters as possible causes for lack of phylogenetic resolution, we conclude that the polytomy obtained most likely represents a hard polytomy. We hypothesize that diversification of Facchinia is best interpreted as the result of multiple simultaneous vicariance in response to climatic changes during the Early Quaternary.

Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species

Background

Four plastid regions, rpoB, rpoC1, matK, and trnH-psbA, have been recommended as DNA barcodes for plants. Their success in delimiting species boundaries depends on the existence of a clear-cut difference between inter- and intraspecific variability. We tested the ability of these regions to discriminate among closely related species in seven genera of flowering plants with different generation times (trees, perennials, and annuals). To ensure a maximum coverage of intraspecific diversity, and therefore to better evaluate the resolution power of each barcode, we applied a population genetics approach by sampling three to 45 individuals per species over a wide geographical range.

Results

All possible combinations between loci were analysed, which showed that using more than one locus does not always improve the resolution power. The trnH-psbA locus was most effective at discriminating among closely related species (Acer, Lonicera, Geranium, and Veronica), singly or in combination. For Salix, Adenostyles, and Gentiana, the best results were obtained with the combination of matK, rpoB, and trnH-psbA. No barcoding gap was found within six genera analysed, excepting Lonicera. This is due to shared polymorphisms among species, combined with very divergent sequences within species. These genetic patterns reflect incomplete lineage sorting and hybridization events followed by chloroplast capture.

Conclusions

Our results strongly suggest that adding trnH-psbA to the two obligate DNA barcodes proposed by the CBOL plant-working group (matK and rbcL) should be mandatory for closely related species. In our sampling, generation time had no influence on DNA barcoding success, as the best and worst identification successes were found for the two tree genera (Acer, 64 % success and Salix, 86 % failure). Evolutionary histories are the main factor influencing DNA barcoding success in the studied genera.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0678-0) contains supplementary material, which is available to authorized users.