Taxon sampling

Fourteen individuals representing all eight species currently recognized in Calophaca were sampled for this study [14,17,25], shown in Table 1 and deposited in the herbaria. According to the previous phylogenetic studies [27–30], Calophaca and Halimodendron nest within Caragana. Thus the genera Halimodendron, Caragana, Hedysarum, and Astragalus were included as outgroups in this study (Table 1), with Astragalus serving to root the trees. To assess the monophyly of Calophaca, 21 species of the genus Caragana were also sampled, giving a total of 38 samples that were included in the study. All species materials vouchers in Table 1 are deposited in the public herbaria PE (Institute of Botany, Chinese Academy of Sciences, Beijing, China), XIJI (Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China), WUG (Northwest Institute of Botany, Yangling, Shaanxi, China), LE (Komarov Botanical Institute, Russian Academy of Sciences, St. Petersburg, Russia), MW (Moscow University, Moscow, Russia) and MAH (Main Botanical Garden, Russian Academy of Sciences, Moscow, Russia).

We state that all use of species materials were permitted by the authority of these herbaria. Our study did not concern Human Subject Research or Animal Research. We can declare that the leaf materials did not come from conservation parks, and none of the samples involved endangered or protected species.

DNA sequencing

Total genomic DNA was extracted using the CTAB method [31]. For primers of the ITS region, trnS-trnG spacer and rbcL, see Zhang et al. [27]. The polymerase chain reaction (PCR) was used for amplification of double stranded DNA. The 25 μl reaction system contained 0.25 μl of Ex Taq, 2.5 μl of 10× Ex Taq buffer (Mg²⁺ concentration of 25 mM), 2.0 μl of dNTP mix (2.5 mM concentration for each dNTP), 1 μl of the forward and reverse primers at 5 umol/μl, and 0.5 μl of template DNA. The protocol for amplification consisted of an initial hot start at 95°C for 2 min, followed by 30 cycles of denaturing at 94°C for 30 s, annealing at 52°C for 30 s, extension at 72°C for 90 s, and a final extension at 72°C for 10 min. PCR products were purified using the PEG precipitation procedure [32] and sequenced using an ABI Prism 3770 Genetic Analyzer (Shanghai Shenggong Biological Engineering Technology & Service, Shanghai, China).

Sequences were aligned with CLUSTAL X [33] and then adjusted manually. All gaps were treated as missing data cells. Finally, the combined 3-genic region data set comprised 3417 aligned nucleotide characters.

Phylogenetic analysis and divergence time estimate

The incongruence length difference (ILD) test [34] was carried out in PAUP* [35] to assess potential conflicts between data set partitions. This was implemented with 100 partition-homogeneity test replicates, a heuristic search option with simple addition of taxa, TBR branch swapping, and MaxTrees set to 1000. Phylogenetic analyses were performed using maximum likelihood (ML) and Bayesian inference. ML analysis was implemented with PAUP; clade support was estimated with 1,000 heuristic bootstrap replicates (100 random addition cycles per replicate, with tree bisection-reconnection and branch-swapping) [36,37]. For ML analysis, Modeltest 3.06 [38] was used to estimate the appropriate model of DNA substitution for sequence data. The models selected by the Akaike information criterion (AIC) were TIM+I+G. The related parameters of Modeltest were used for the ML analysis.

Bayesian phylogenetic analysis and divergence time estimates were implemented in BEAST 1.5.4 [39,40]. We used the uncorrelated lognormal relaxed clock model with a Yule process for the speciation model, and GTR+I+G for the substitution model (estimated for the data set). The age of tree prior (normal distribution Mean = 28, Stdev = 1) for Hedysareae and Astragaleae, i.e., the ancestral node of Astragalus and Caragana was defined as the root at 28 Ma following Lavin et al. [41], Wojciechowski [30] and Zhang and Fritsch [42]. A Markov chain Monte Carlo was run for 50 million generations and sampled every 1,000 generations. Two independent runs were performed to confirm convergence of the analysis. The stationarity of each run was examined using the effective sampling size of each parameter (>200). The last 40 million generations were used to construct the maximum clade credibility tree and the associated 95% highest posterior density distributions around the estimated node ages using program TreeAnnotator 1.5.4, and visualized using FigTree 1.3.1.

Biogeographical analysis

We designated five biogeographical areas based on the distributions of the Calophaca species, especially its disjunctions, see Fig 1. Most of the species occurring in these areas are endemic, for example, C. grandiflora and C. sericea are endemic to the Pamir mountains, C. wolgarica to the Caucasus, and C. sinica to East Asia. The areas chosen are natural regions, and often independent biodiversity hotspots [19], for example, the Pamir and Tianshan mountains and the Caucasus. These areas also have distinct vegetation and floras; especially different are those of the Pamir, western Tianshan, and Tarbagatai mountains, see Fig 1. The five designated areas are thus: A: the Pamirs, Tadjikistan; B: the western Tianshan Mountains, including portions of Kyrgistan and Kazakhstan; C: the Tarbagatai, including portions of northwestern China and Kazakhstan; D: East Asia, and montane portions of Shanxi Province, China; E: the Caucasus, and plains along the Volga and Don Rivers.

To infer vicariance and dispersal events, a Bayesian parsimony-based method (S-DIVA) and BBM (Bayesian Binary Method) were employed [43,44]. DIVA is an event-based method that optimizes ancestral distributions by assuming a vicariance explanation, while incorporating the potential contributions of dispersal and extinction [45]. Nylander et al. [46] proposed a modified approach to DIVA named Bayes-DIVA that integrates biogeographical reconstructions of DIVA over the posterior distribution of a Bayesian MCMC sample of tree topologies. Bayes-DIVA is also referred to as S-DIVA [43]. BBM infers ancestral areas using a full hierarchical Bayesian approach; it hypothesizes a special “null distribution” which means that an ancestral range contains none of the unit areas [44]. S-DIVA and BBM can be performed in RASP (Reconstruct Ancestral State in Phylogenies) 2.0 beta. http://mnh.scu.edu.cn/soft/blog/RASP.

The BEAST molecular dating tree (Fig 2) was treated as a fully resolved phylogram for use as the basis for S-DIVA and BBM, with 1000 post-burnin trees derived from the BEAST analysis used for ancestral area reconstruction in the program RASP. Multiple samples of the same taxon in a clade are combined into one branch, or many identical terminal areas in a clade are regarded as one; consequently, the tree is reduced to maximum simplicity. RASP was performed with various constraints of maximum areas 2 at each node, to infer possible ancestral areas and potential vicariance and dispersal events [47–49].

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Fig 2. Chronogram of Calophaca and outgroups Caragana, Halimodendron, Hedysarum, and Astragalus, with maximum clade credibility performed by BEAST.

Dates of divergence are shown to the right of nodes, and posterior probability values are shown to the left of nodes.

https://doi.org/10.1371/journal.pone.0123228.g002

The outgroups used in the phylogeny were also used in the biogeographical analyses throughout data processing, but are not shown in the resulting Fig 3.

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Fig 3. Ancestral area optimizations performed with S-DIVA and BBM.

Pie chartsat nodes are conducted from S-DIVA (on the branch above) and BBM (on the branch below). The three thicked arrowheaded lines at branches show four dispersals.

Area labels, as stated in the text: A: Pamir Mountains, Tadjikistan; B: western Tianshan Mountains, plus parts of Kyrgistan and Kazakhstan; C: Tarbagatai Mountains, including adjacent regions of China and Kazakhstan; D: East Asia, mountains of Shanxi Province, China; E: Caucasus, and plains along the Volga River and Don River.

https://doi.org/10.1371/journal.pone.0123228.g003

Phylogenetic analysis and divergence time estimate

The data partitions of the three genes were not significantly incongruent on the basis of the ILD tests (P = 0.133). ML analysis yielded three optimal trees. Topologies of the three were on the whole equivalent to the Bayesian BEAST tree. Since the BEAST tree also has a dating result, it is used to illustrate phylogenetic relationships and the dating results (see Fig 2).

Our phylogenetic analyses show that Calophaca is monophyletic, with high bootstrap (bt) support and posterior probability (pp) (bt = 96%, pp = 1.00) (node I), and is nested within Caragana (Fig 2). The phylogenetic analysis yielded a topology largely in accordance with the current infrageneric classification of Calophaca. The two species of C. sect. Glabriflorae formed a clade (bt = 100%, pp = 1.00), which is sister to the other taxa, and the two samples of C. sinica also formed a clade (bt = 98%, pp = 1.00). Samples of C. soongorica, C. hovenii, C. pskemica, C. wolgarica, and C. tianshanica comprised a clade (bt = 97%, pp = 1.00) (node III), equivalent to section Calophaca. These three clades within Calophaca had high bootstrap and posterior probability values (Fig 2).

The estimated divergence (stem) age of Calophaca was ca. 8.0 (95% HPD: 3.44–11.09) Ma, the crown age between the Pamirian sect. Glabriflorae and the other two sections was ca. 7.0 (95% HPD: 1.66–7.29, crown age) Ma (node I), and the age between the East Asian sect. Trichomeae and the Tianshan Mountains sect. Calophaca was ca. 6.0 Ma (Fig 2, node II, crown age). The diversification time range within sect. Calophaca was from Pliocene to Pleistocene, i.e., 2.6–0.2 Ma (Fig 2, node III). The diversification time of the two species of sect. Glabriflorae was ca. 0.4 Ma. Calophaca wolgarica, distributed from the Caucasus to Russian Europe, was formed more recently at ca. 0.2 Ma.

Ancestral area reconstructions

Within Calophaca sect. Calophaca, the ancestral area (node III, Fig 3) estimated from S-DIVA (B and BC at equal probability) and BBM (B), thus we chose it as B (western Tianshan Mountains). The remaining area C (Tarbagatai Mountains) within this section (Fig 3), is shown as a dispersal many times. The most incongruent and uncertain node of the ancestral distribution estimates is at the root of Calophaca (node I). Considering S-DIVA, showing the likely ancestral area as AD (union of Pamir Mountains and East Asia) and AB (union of the Pamir and western Tianshan mountains), A is the intersection, occurring in both ancestral areas. Concerning the value of AD at node I, and the reason for the selection of A (ignoring D), was that we mainly thought A, with C. sericea and C. grandiflora at the phylogenetic tree base (stem age ca. 6.98 Ma, see Fig 2), to be more “old” than D of C. sinica (stem age ca. 5.98 Ma). This indicates that A (Pamir) should be the ancestral area instead of D (East Asia). In addition, ignoring AD as an ancestral area would mean ignoring an impossibly large ancestral area union, covering two separate portions, the Pamir and East Asia (North China, Shanxi Province), and consequently the first speciation of Calophaca would have had to be speculated as a vicariance between Pamir and East Asia, in contrast with the unique place of origin of the Pamirs. Therefore, we felt we should choose the single area A as ancestral. In addition, BBM, with a most likely estimated area of A, confirmed and justified the S-DIVA result. Therefore, it appeares preferable to choose A as the ancestral area of Calophaca.

After deciding the ancestral areas at the nodes (Fig 3), several dispersals can be recognized, see Figs 3 and 1. First, two dispersals are inferred from area A (Pamir) (node I) to B (western Tianshan) and D (East Asia). A dispersal is shown from node III to node V, and finally to the Caucasus. Another dispersal is from B (node IV) to C (Tarbagatai).

Classification of Calophaca

The monophyly of Calophaca was verified with high bootstrap (bt) support and posterior probability (pp) (bt = 96%, pp = 1.00, node I, Fig 2). The present phylogenetic tree (Fig 2) indicates three clades with high support within Calophaca, one consisting of C. grandiflora and C. sericea, a second containing C. sinica, and a third containing C. soongorica, C. tianschanica, C. hovenii, C. wolgorica, and C. pskemica. This is well consistent with previous morphological classification except for C. sinica. According to Gorbunova’s [15] classification system for the genus, C. grandiflora and C. sericea are included in sect. Glabriflora, while C. soongorica and C. wolgorica, etc. belong to sect. Calophaca. Calophaca sinica has a combination of distinctive characters, with dense glandular trichomes on the standard, peduncle, calyx, ovary, style, and a legume different from other species within the genus, and has an endemic distribution in East Asia. Therefore, we can use it to establish a new section Trichomeae, to contrast with the two sections of Gorbanova [15], see S1 File. This effectively completes the classification for the genus, with a total of three sections.

The five accessions of Calophaca soongorica formed a clade with the inclusion of C. hovenii. Calophaca hovenii Schrenk, C. tianshanica (B. Fedtsch.) Borissova, and C. soongorica (C. soongorica 1 and 2 = C. chinensis Borissova, see Table 1) were included within C. soongorica as varieties [14,15,18]. Clearly, C. hovenii and the others should be placed within C. soongorica.

In the traditional taxonomy, Calophaca, Halimodendron, and Caragana are regarded as related and distinctive genera [20,21]. Previously the three were included in subtribe Astragaleae of tribe Galegeae [20], and later changed to tribe Hedysareae [21]. Diagnostic characters of Calophaca and Caragana are that while both are shrubs with pinnate leaflets, Calophaca is imparipinnate but Caragana is paripinnate. Contrasting with the flat pods of Calophaca and Caragana, Halimodendron has an inflated pod. Calophaca, particularly, has a distribution of montane grassland, shrubland, and dry forest.

Since Calophaca and Halimodendron are nested within Caragana (Fig 2), it results in Caragana being paraphyletic. In terms of the taxonomic identities of Calophaca, Halimodendron, and Caragana, Caragana should be subdivided into segregate taxa. Currently it has been recognized as six phylogenetic clades (Fig 2), which include the three sections labeled, as well as clades representative by Car. jubata, Car. acanthophylla, and Car. spinosa. However, in view of the limitation of sampled taxa in our study, further research should be conducted examining sufficient taxa and more genes. Essentially, the present paper focuses on Calophaca.

Origin and diversification

Our results yielded a divergence time (stem age, or origin age) of ca. 8.0 Ma for Calophaca (Fig 2), and a place of origin in the Pamir Mountains (Fig 3), which implies that a global cooling and drying process at 8–7 Ma in the late Miocene [10,13], most likely drove generic origin. It is also possible more local events played a part in the origin, especially major tectonism in the Tianshan range at about 6.5 Ma [50,51]; the Pamir mass had experienced severe deformation and uplift from the India-Asia impact at a previous time [52]. Progressive aridification in connection with global cooling appears to have played an important role in the later Miocene [13]. The Pamir-western Tianshan mountains experienced progressively more arid climates. This climate transition possibly led to range restriction and isolation of organisms, and Calophaca may be one of the many lineages that then evolved and diversified in the Pamirs.

Compared with the diversification time of Caragana [42], the crown age (diversification age) of Calophaca at ca. 6.98 Ma coincided with the diversification times of the three sections within Caragana, whereas diversification times of the three Calophaca sections are younger at 2.6, 0.4 and 0.24 Ma (Fig 2). Most Central Asian Calophaca species, such as C. grandiflora, C. sericea, C. soongorica, and C. wolgarica, have young crown ages i.e., Pliocene to Pleistocene 0.84–0.2 Ma (Fig 2). These show that the genus is a relatively young taxon among lineages of temperate legume shrubs and the Central Asian flora.

In general, the Central Asian flora is speculated to have formed from Tertiary Tethys relicts [12]. Hippophae rhamnoides (Elaeagnaceae) distributed in Eurasia, was similarly shown to have originated from the QTP and migrated to Central Asia and Asia Minor ⁄ Europe [6]. Artemisia has been shown to have originated from the arid-semiarid middle latitudes of Asia in the late Eocene, and then spread westward and eastward in the Oligocene as the result of early QTP uplift and accompanying aridification [9]. Calophaca presents another pattern of Asian origin and dispersal that is somewhat different from that of Hippophae rhamnoides and Artemisia.

Parts of the QTP may have experienced rapid uplift contributing to global cooling during past 8–7 Ma [13,53–60]. Responding to this QTP uplift event and global cooling and drying, many biological cases mainly occurring in situ in the QTP have been contributed, for example, the Ligularia Cremanthodium—Parasenecio complex (Asteraceae) [61], Rheum (Polygonaceae) [62], Androsace (Primulaceae) [3] and Saussurea (Asteraceae) [63], and the glyptosternoid catfishes [64]. Even though absent in the QTP, Calophaca has a diversification crown age of ca. 6.98 Ma and a distribution located to the north of the QTP, and it can be supposed that the origin and evolution of Calophaca were driven by the same paleogeographic and paleoclimatic conditions.

Dispersal and disjunction

According to the biogeographical analysis (Fig 3), we can hypothesize that dispersal may be a dominant speciation mode in Calophaca. There are four remarkable dispersals from the late Miocene to Pleistocene in this genus, i.e., from the Pamir to the western Tianshan mountains, and to East Asia at ca. 7.0 Ma, northward to the Tarbagatai Mountains at ca. 2.2 Ma, and from the western Tianshan Mountains westward to the Caucasus—Russian Europe at 2.6 Ma (Fig 1). The great arid and semiarid belt, comprising the Tarim Basin, Junggar Basin, Hexi Corridor, and Loess Plateau in arid northwestern China forms a barrier between the Pamir-western Tianshan mountains and East Asia. Similarly, the Turan lowland and desert separates the Pamir—western Tianshan mountains and the Caucasus. The presence of these arid belts most likely resulted from the intensified Asian Interior aridification which is associated with global cooling and drying since the Middle Miocene optimum 8–7 Ma [13], and consequently to have fragmented the ranges of the Calophaca species and also eliminated the traces of their dispersals.

Montane distribution and refugia

Extant Calophaca species of the Pamir and western Tianshan mountains, such as C. grandiflora, C. sericea, C. tianshanica, C. pskemica, and C. soongorica, often occur in middle or low montane belts at altitudes of 800–2800 m, sometimes in meadows or steppe, with most individuals occurring in juniper forests or shrublands [14,17]. Calophaca sinica, in the northern China mountains, likewise grows in forest or shrubland [65]. Calophaca wolgarica, a shrub endemic to the Caucasus and eastern Europe, occurs on steppe, plains, and limestone hills [14,17]. In conclusion, the predominant habitat of the genus is the lower montane, in the Pamir—western Tianshan mountains, the Caucasus, and the northern China mountains.

These montane distribution centers of Calophaca, occupy several global biodiversity hotspots [19], especially the Pamir—western Tianshan mountains and the Caucasus. These areas are also regarded as plant refugia of the Quaternary, since the mountains have maintained a somewhat moist habitat, and thus have an advantage in protection of species from destruction caused by enhanced cooling and drying in the Quaternary [66–73]. The high level of genetic and taxonomic diversity of this area is indicative of its ecological stability [67,69]. Therefore, Calophaca is in fact a representative of the global biodiversity hotspots and refugia.