Phylogeography and population genetics of Acanthophyllum squarrosum complex (Caryophyllaceae) in the Irano-Turanian region

Acanthophyllum squarrosum and two closely related species, A. heratense and A. laxiusculum (Caryophyllaceae), form a complex that covers parts of subalpine steppes of the Irano-Turanian (IT) region. In this study, we explored the genetic structure and phylogeography of this complex based on partial sequences of two chloroplasts (psbA–trnH and rpl32–trnL (UAG)) and two nuclear (EST24 and nrITS) DNA regions. We analysed 80 individuals from eight populations and detected 12 chloroplast haplotypes, 16 and eight nuclear alleles in EST24 and nrITS sequences, respectively. Phylogenetic trees and haplotype networks did not show distinct genetic groups in the complex and this could be explained by incomplete lineage sorting or introgression between species. Divergence time analysis revealed a Quaternary origin for A. squarrosum complex at approximately 1.8 million years ago (Mya) and the neutrality test results indicated that this complex experienced a recent population expansion. AMOVA analysis of the chloroplast regions showed a significant genetic differentiation among populations and low genetic differentiation within populations, but opposite results were found with nuclear markers, implying introgression between A. squarrosum complex populations.     

Phylogenetic relationships of the chloroplast genomes in the genus Glycine inferred from four intergenic spacer sequences

The nucleotide sequences of four intergenic spacer regions of chloroplast DNA, atpB-rbcL, trnS-trnG, rps11-rpl36, and rps3-rpl16, were analyzed in the genus Glycine. Phylogenetic analysis based on the sequence data using Neonotonia wightii as the outgroup generated trees supporting the classification of two subgenera, Soja and Glycine, and three plastome groups in the subgenus Glycine. The results were consistent with the presence of diversified chloroplast genomes within tetraploid plants of G. tabacina and G. tomentella, as well as with a close relationship between G. tomentella and G. dolichocarpa that had been suggested based on morphological analyses. Little sequence variation was found in the subgenus Soja, suggesting that G. soja rapidly expanded its distribution in East Asia. The analysis also showed that the differentiation into three plastome groups in the subgenus Glycine occurred in the early stages of its evolution, after the two subgenera diverged.     

Multiple autopolyploidizations and range expansion of Allium przewalskianum Regel. (Alliaceae) in the Qinghai‐Tibetan Plateau

We used the Allium przewalskianum diploid–tetraploid complex on the Qinghai‐Tibetan Plateau (QTP) as a model to examine how this complex responded to the Quaternary climatic oscillations, and whether multiple autopolyploidizations have occurred. We sequenced five chloroplast DNA (cpDNA) fragments (accD‐psaI, trnH‐psbA, trnL‐trnF, trnS‐trnG and rpl16‐intron) in 306 individuals (all of known ploidy level) from 48 populations across the distribution of this species complex. We identified a total of 32 haplotypes—11 in diploids only, 13 in tetraploids only, and 8 found in both cytotypes. This, plus network analyses, indicated that tetraploids have arisen independently from diploids at least eight times. Most populations in the eastern QTP contained multiple haplotypes, but only a single haplotype was found for 17 tetraploid populations on the western QTP, suggesting a recent colonization of the western QTP. We further found that this species complex underwent an earlier range expansion around 5–150 thousand years ago (kya), after the largest glacial period (800–170 kya) in the QTP. In addition, the high frequencies of tetraploids in the QTP suggested that the tetraploid A. przewalskianum cytotype has evolutionary advantages over diploids in colonizing and/or surviving the arid habitats of the QTP.     

Phylogeny of the Madagascan endemic family Didiereaceae

A molecular phylogeny of the Didiereaceae was produced through parsimony analysis of chloroplastrpl16 intron andtrnL-trnF andtrnT-trnL intergenic spacer sequences of all eleven species of the Didiereaceae and several outgroup taxa from the Portulacaceae. Results indicated that: 1) the Didiereaceae were embedded within the Portulacaceae, withCalyptrotheca as the sister group of the family; 2) present generic limits were supported; 3)Alluaudiopsis was the most basal lineage; 4) at least two separate episodes of polyploidization within the genusAlluaudia had occurred, and 5) unusually low amounts of variation were present in rapidly evolving noncoding plastid sequences.     

West to east dispersal and subsequent rapid diversification of the mega‐diverse genus Begonia (Begoniaceae) in the Malesian archipelago

Aim The complex palaeogeography of the Malesian archipelago, characterized by the evolution of an ever‐changing mosaic of terrestrial and marine areas throughout the Cenozoic, provides the geographic backdrop for the remarkable diversification of Malesian Begonia (> 450 species). This study aimed to investigate the origin of Malesian Begonia, the directionality of dispersal events within the Malesian archipelago and the impact of ancient water gaps on colonization patterns, and to identify drivers of diversification. Location Asia, Southeast Asia, Malesia. Methods Plastid DNA sequence data of representatives of all families of the Cucurbitales and Fagales (matK, rbcL, trnL intron, trnL–F spacer, 4076 aligned positions, 92 taxa) and a sample of all major Asian Begonia sections (ndhA intron, ndhF–rpl32 spacer, rpl32–trnL spacer, 4059 aligned positions, 112 taxa) were analysed under an uncorrelated‐rates relaxed molecular clock model to estimate the age of the Begonia crown group divergence and divergence ages within Asian Begonia. Ancestral areas were reconstructed using a likelihood approach implementing a dispersal–extinction–cladogenesis model, and with a Bayesian approach to dispersal–vicariance analysis. Results The results indicated an initial diversification of Asian Begonia in continental Asia in the Miocene, and subsequent colonization of Malesia by multiple lineages. There was support for at least six independent dispersal events from continental Asia and western Malesia to Wallacea dating from the late Miocene to the Pleistocene. Begonia section Petermannia (> 270 species) originated in Western Malesia, and subsequently dispersed to Wallacea, New Guinea and the Philippines. Lineages within this section diversified rapidly since the Pliocene, coinciding with rapid orogenesis on Sulawesi and New Guinea. Main conclusions The predominant trend of Begonia dispersals between continental Asia and Malesia, and also within Malesia, has been from west to east. The water bodies separating the Sunda Shelf region from Wallacea have been porous barriers to dispersal in Begonia following the emergence of substantial land in eastern Malesia from the late Miocene onwards. We hypothesize two major drivers of the diversification of Malesian Begonia: (1) the formation of topographical heterogeneity and the promotion of microallopatry by orogenesis in the Pliocene and Pleistocene; and (2) cyclic vicariance by frequent habitat fragmentations and amalgamations due to climate and sea‐level fluctuations during the Pleistocene.     

Phylogeography of two closely related species of Allium endemic to East Asia: Population evolution in response to climate oscillations

This study investigated the effects of climate oscillations on the evolution of two closely related Allium species, A. neriniflorum and A. tubiflorum. We sequenced three cp DNA (cpDNA) fragments (rps16, rpl32‐trnL, and trnD‐trnT, together approximately 2,500 bp in length) of two closely related Allium species, with samples from 367 individuals in 47 populations distributed across the total range of these species. The interspecific and intraspecific divergence times of the two species were in the Quaternary glaciation. The population divergence was high for the cpDNA variation, suggesting a significant phylogeographic structure (N_ST = 0.844, G_ST = 0.798, p < 0.05). Remarkable ecological differentiation was also revealed by Niche models and statistical analyses. Our results suggest the speciation event of the two species was triggered by violent climatic changes during the Quaternary glaciation.     

Autecological traits determined two evolutionary strategies in Mediterranean plants during the Quaternary: low differentiation and range expansion versus geographical speciation in Linaria

The evolutionary patterns of the Mediterranean flora during the Quaternary have been relatively well documented based on phylogenetic and biogeographic analyses, but few studies have addressed the evolutionary traits that determined diversification and range expansion success during this period. We analysed previously published and newly generated sequences of three plastid noncoding regions (rpl32‐trnL^UAG, trnS‐trnG and trnL‐trnF), the nuclear ribosomal internal transcribed spacer (ITS) and a low‐copy nuclear gene intron (AGT1) of Linaria sect. Supinae, a group of angiosperms that diversified in the Quaternary. The origin and recent colonization dynamics of closely related lineages were inferred by biogeographic reconstruction and phylogeographic analyses, while breeding system experiments coupled with ecological and morphological data were used to test association with range expansion and diversification. A combination of traits, including selfing, short lifespan and the ability to tolerate a wide variety of substrates, were key factors underlying range expansion after long‐distance dispersal throughout the Mediterranean basin. By contrast, self‐incompatibility may have promoted higher diversification rates in narrow ranges of the Iberian Peninsula. We argue that a few traits contributed to the adoption of two contrasting strategies that may have been predominant in the evolution of Mediterranean angiosperms.     

Allium ursinum L. in Germany – surprisingly low genetic variability

Allium ursinum s.l. is a widely spread species of the herb layer in beech forests throughout Europe. Little is known about its phylogenetic origin and its biogeographic history. Molecular genetic analyses of eleven populations from Germany were used to clarify the relationship between populations of A. ursinum s.l. and its relationship to several other species of the genus Allium. The study focused mainly on the Teutoburg Forest in Lower Saxony and the Franconian mountain area in Bavaria. Sequences of the nuclear internal transcribed spacer ITS, and the external transcribed spacer ETS, as well as the plastidic trn L‐rpl 32 and the trn L‐trn F spacer regions were compared. No variation was detected within the species. Even sequences of populations from Belfast, Ireland did not differ from populations of Germany. The closest relative to Allium ursinum s.l. turned out to be Allium moly or Allium scorzonerifolium from the section Molium. Random amplified polymorphic DNA fingerprinting was performed and revealed 29% polymorphic bands. Genetic distances of the populations within the Teutoburg Forest coincided with geographical distances. Three populations (Osnabrück Westerberg, Osnabrück Honeburg and Leer, East Frisia) out of eleven analysed populations were identified as garden escapes. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Are linear‐leaved Potamogeton hybrids really so rare? Molecular evidence for multiple hybridizations between P. acutifolius and P. compressus in central Europe

Due to insufficient morphological differentiation, hybridization among linear‐leaved species of Potamogeton is rarely observed and recognized. Here, we applied molecular tools (sequencing of nrITS and rpl32‐trnL cpDNA intergenic spacer) to study several natural, central European populations of morphologically intermediate forms between two closely related species, P. acutifolius and P. compressus, to examine their taxonomical status and test whether they represented the variation range of the species or are results of interspecific hybridization. Both DNA regions provided distinguishing characters between putative parental species. The ITS sequences from all the morphologically intermediate specimens displayed an additive pattern combining the variation of both parental species, providing evidence for the hybrid origin of all these plants. This case study suggests that hybrids of linear‐leaved Potamogeton species are more common than usually believed, but have been difficult to identify without molecular tools.     

基于叶绿体DNA片段的槭属鸡爪槭组系统进化和生物地理学研究

东亚地区经历过复杂的地质事件及气候变化,针对东亚地区进行专科专属的植物区系及地理演化研究具有重要的意义。基于3个叶绿体片段（psbA-trnH、rpl16和trnL-trnF）,对主要分布于东亚地区的鸡爪槭组（section Palmata Pax）18个分类群的分化时间、祖先地理分布、物种扩散路径等进行了分析。叶绿体片段总长度为2,232bp,其中变异位点341个（15.2%）,有效信息位点231个（10.3%）;18个鸡爪槭组内物种（包含亚种）被高度支持为单系群（99/95/1.0）,且组内物种间的支持度相对较高;鸡爪槭组内出现物种分化的时间多集中于中新世时期,组内物种的多样性速率保持相对稳定;根据BioGeoBears分析得出,东亚大陆局部地区是该组物种的祖先分布区,且现今分布于岛屿的物种分布在不同分支。通过讨论与分析得出：我国西南地区可能是鸡爪槭组植物的起源地;东海陆桥隐没与抬升,直接影响着鸡爪槭组物种的迁移与扩散;分布于亚热带亚洲大陆的鸡爪槭组物种,存在多次往同纬度高海拔地区扩散的现象。该研究有助于对东亚地区植物生物地理历史的进一步了解。     

Hidden phylogeographic complexity in the Sierra Madre Oriental: the case of the Mexican tulip poppy Hunnemannia fumariifolia (Papaveraceae)

Aim A phylogeographic study of the endemic Mexican tulip poppy Hunnemannia fumariifolia (Papaveraceae) was conducted to determine: (1) the historical processes that influenced its geographical pattern of genetic variation; (2) whether isolation by distance was one of the main factors that caused genetic divergence in populations of this species; and (3) whether genetic flow still exists between populations from northern arid zones (Chihuahuan Desert and Sierra Madre Oriental) and those from southern arid zones (Tehuacán‐Cuicatlán Valley) – populations that are separated by the Transvolcanic Belt. Location Xerophytic vegetation in Mexico. Methods Chloroplast DNA (cpDNA) sequences of three regions, trnH‐psbA, rpl32‐trnL(UAG) and ndhF‐rpl32, were obtained for 85 individuals from 17 populations sampled in the field, covering the entire range of H. fumariifolia. The evolutionary history of these populations was investigated using a nested clade phylogeographic analysis and also by conducting various population genetic analyses. Results In total, 17 haplotypes were detected, 14 of which were found in the Sierra Madre Oriental. Differentiation among populations based on cpDNA variation (G_ST = 0.787, SE 0.0614) indicated population structure in H. fumariifolia, corroborated by a fixation index (F_ST) of 0.907. Results from analysis of molecular variance found that most of the total variation (90.71%, P < 0.001) was explained by differences among populations. Three regions were determined based on geological correspondence – the Chihuahuan Desert, Sierra Madre Oriental and Tehuacán‐Cuicatlán Valley – and the variation between them was significant (43.39%, P < 0.001). Results of a Mantel test showed a significant correlation between genetic and geographic distances (r = 0.511; P = 0.0001), suggesting a pattern of isolation by distance, which was corroborated by nested clade phylogeographic analysis. Mismatch distribution analysis indicated a sudden demographic expansion. Main conclusions Our study found that isolation by distance influenced genetic divergence in populations of H. fumariifolia. The finding that allopatric fragmentation influenced genetic divergence in populations in the Sierra Madre Oriental may be a reflection of the complex geology of the area. Our results suggest that the areas located in the north of the Sierra Madre Oriental acted as post‐glacial refugia for some populations.     

Phylogeny and biogeography of Sassafras (Lauraceae) disjunct between eastern Asia and eastern North America

Sassafras (Lauraceae) consists of three species disjunct between eastern Asia (S. tzumu and S. randaiense) and eastern North America (S. albidum). Phylogenetic analysis based on sequences of nuclear ribosomal ITS and three chloroplast non-coding regions (rpl16, trnL-F, and psbA-trnH) showed that Sassafras is monophyletic and that the eastern North American S. albidum is sister to the clade of its two eastern Asian counterparts. Their intercontinental divergence was estimated to be 13.80 ± 2.29−16.69 ± 2.52 million years ago (mya) using the penalized likelihood method with the ITS and three chloroplast markers. Biogeographic analyses combined with fossil evidence suggest that Sassafras has a relict distribution in the Northern Hemisphere without a Gondwanan link. The divergence time of the two eastern Asian species (the continental Chinese Sassafras tzumu and S. randaiense endemic to Taiwan) is estimated to be 0.61 ± 0.75−2.23 ± 0.76 mya. Sassafras randaiense from Taiwan was most likely derived from an ancestor from continental China.     

Phylogenetic relationships of Ruteae (Rutaceae): new evidence from the chloroplast genome and comparisons with non-molecular data

Phylogenetic analyses of three cpDNA markers (matK, rpl16, and trnL–trnF) were performed to evaluate previous treatments of Ruteae based on morphology and phytochemistry that contradicted each other, especially regarding the taxonomic status of Haplophyllum and Dictamnus. Trees derived from morphological, phytochemical, and molecular datasets of Ruteae were then compared to look for possible patterns of agreement among them. Furthermore, non-molecular characters were mapped on the molecular phylogeny to identify uniquely derived states and patterns of homoplasy in the morphological and phytochemical datasets. The phylogenetic analyses determined that Haplophyllum and Ruta form reciprocally exclusive monophyletic groups and that Dictamnus is not closely related to the other genera of Ruteae. The different types of datasets were partly incongruent with each other. The discordant phylogenetic patterns between the phytochemical and molecular trees might be best explained in terms of convergence in secondary chemical compounds. Finally, only a few non-molecular synapomorphies provided support for the clades of the molecular tree, while most of the morphological characters traditionally used for taxonomic purposes were found to be homoplasious. Within the context of the phylogenetic relationships supported by molecular data, Ruta, the type genus for the family, can only be diagnosed by using a combination of plesiomorphic, homoplasious, and autapomorphic morphological character states.     

Natural Hybridization and Introgression between Ligularia cymbulifera and L. tongolensis (Asteraceae,Senecioneae) in Four Different Locations

Natural hybridization has been considered to represent an important factor influencing the high diversity of the genus Ligularia Cass. in the Hengduan Mountains, China. Natural hybridization has been confirmed to occur frequently in Ligularia. To date, however, it has been demonstrated only within a single population. In this paper, we present evidence of natural hybridization in Ligularia from four different locations. The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and three chloroplast intergenic spacers (trnK-rps16, trnL-rpl32 and trnQ-5''rps16) of 149 accessions of putative hybrids and their putative parents (L. cymbulifera and L. tongolensis) were analyzed for evidence of hybridization. The ITS data clearly distinguished two putative parental species and sympatric L. vellerea and supported the hypothesis that those morphological intermediates were products of natural hybridization between L. cymbulifera and L. tongolensis. Moreover, several identified morphological parents were actual introgressed products. Because of hybridization and introgression, chloroplast DNA sequences generated a poorly resolved network. The present results indicate that varying degrees of hybridization and introgression occur differently depending on the habitat context. We conclude that gene flow caused by natural hybridization in Ligularia indeed plays an important role in the species diversity.     

A molecular phylogenetic study of Hemsleya (Cucurbitaceae) based on ITS, rpl16, trnH-psbA, and trnL DNA sequences

This paper presents the first molecular phylogeny of the genus Hemsleya using nuclear ITS and plastid trnH-psbA, rpl16, and trnL DNA sequences to examine the relationships among Hemsleya species. Phylogenetic relationships were elucidated using a combined analysis of all four datasets, however, the number of parsimony-informative characters was still insufficient to resolve all relationships. Parsimony and Bayesian trees were highly congruent. Twenty-three species of Hemsleya split into two major clades corresponding to two subgenera, i.e., subg. Graciliflorae and subg. Hemsleya. These results are partly in agreement with Li’s sectional classification. However, the molecular data are inconsistent with Li’s classification at the subsectional level. The molecular phylogeny revealed a striking overall correlation between the phylogenetic relationships of the species and their geographical distribution. The Kangdian ancient landmass could be the center of origin of the genus.     

Phylogenetic relationships between disjunctly occurring groups of Tristicha trifaria (Podostemaceae)

Aim To reveal the phylogeographic relationship of disjunct specimens of Tristicha trifaria (Bory ex Willd.) Spreng., a member of the Podostemaceae river‐weed family, which is distributed exceptionally widely, but disjunctly, in Africa and the Americas. Location Brazil, Mexico, Ghana, Tanzania and Madagascar. Methods The chloroplast matK and rbcL genes, a trnK intron, the trnS‐trnG intergenic spacer (IGS), the two IGSs of trnT‐trnL‐trnF, a trnL intron, and nuclear ribosomal ITS regions were sequenced and analysed. Phylogenetic analyses were conducted using maximum likelihood and maximum parsimony methods. Results The T. trifaria samples analysed were separated into two groups in a rooted tree based on a combined matK/rbcL/ITS dataset; one contained the West African and all of the American samples, and the other contained the East African and Madagascan samples. An unrooted tree obtained from a combined analysis of all the chloroplast DNA and nuclear ITS data showed that a sample from West Africa was sister to an American T. trifaria group. Main conclusions The American and West African T. trifaria are closely related, despite the great distance between their locations. This observation, along with a tree of the whole Tristichoideae subfamily and estimated divergence times, suggests that an ancestor of T. trifaria migrated from Asia to Africa during the early Tertiary, and that this was followed by further westward migration to the Americas at the end of the Miocene or in the early Pliocene.     

Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis saxicola

The increasingly wide application of chloroplast (cp) genome super‐barcode in taxonomy and the recent breakthrough in cp genetic engineering make the development of new cp gene resources urgent and significant. Corydalis is recognized as the most genotypes complicated and taxonomically challenging plant taxa in Papaveraceae. However, there currently are few reports about cp genomes of the genus Corydalis. In this study, we sequenced four complete cp genomes of two endangered lithophytes Corydalis saxicola and Corydalis tomentella in Corydalis, conducted a comparison of these cp genomes among each other as well as with others of Papaveraceae. The cp genomes have a large genome size of 189,029–190,247 bp, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955–42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola, and Papaveraceae species, five NADH dehydrogenase‐like genes (ndhF, ndhD, ndhL, ndhG, and ndhE) with psaC, rpl32, ccsA, and trnL‐UAG normally located in the SSC region have migrated to IRs, resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI‐CAU, and trnL‐CAA) was found within IR regions. The accD gene was found to be absent and the ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis based on the sequences of common CDS showed that the genus Corydalis is quite distantly related to the other genera of Papaveraceae, it provided a new clue for recent advocacy to establish a separate Fumariaceae family. Our results revealed one special cp genome structure in Papaveraceae, provided a useful resources for classification of the genus Corydalis, and will be valuable for understanding Papaveraceae evolutionary relationships.     

Phylogeny and evolution of Dyckia (Bromeliaceae) inferred from chloroplast and nuclear sequences

The genus Dyckia (Bromeliaceae) comprises more than 150 terrestrial or epilithic species with a strongly xeromorphic habit. Most of its members belong to the azonal rock vegetation of Neotropical savannas and forests of Brazil and adjacent countries. Dyckia is relatively species-rich compared with its closest relatives Encholirium (27 species) and Deuterocohnia (17 species). Here, we present the first molecular phylogenetic analysis of Dyckia using DNA sequence data from six plastid loci (matK gene, rps16 intron, petD intron, rpl32-trnL, rps16-trnK and trnD-trnT) and a portion of the nuclear gene phyC. A total of 124 accessions were included, corresponding to 79 taxa from six genera. Phylogenetic trees were generated using parsimony, likelihood and Bayesian methods. DNA sequence variation among Dyckia species turned out to be extremely low, and phylogenies were poorly resolved. The monophyly of Dyckia is supported, whereas evidence is provided that Encholirium is paraphyletic. Based on a dated plastid DNA tree, Dyckia experienced a recent radiation starting around 2.9 million years ago. Four major clades could be identified that roughly correspond to the geographic origin of the samples. A parsimony network based on plastid DNA haplotypes shows a star-like pattern, indicating recent range expansions. Our data are compatible with a scenario where Dyckia and Encholirium diverged in northeastern Brazil, whereas one lineage of Dyckia dispersed to southern Brazil from where a rapid colonization of suitable habitats was initiated. We discuss our results in relation to species delimitation in Dyckia.     

The complete plastid genome of Cotinus coggygria and phylogenetic analysis of the Anacardiaceae

Cotinus coggygria Scop. (Anacardiaceae) is an important ornamental tree with beautiful characteristics that is grown in China. In this study, the complete plastid genome of C. coggygria was sequenced and assembled. This genome was 158,843 bp in size and presented a typical tetrad structure, consisting of a large single-copy region (87,121 bp), a pair of inverted repeat regions (26,829 bp), and a small single-copy region (18,064 bp). A total of 134 genes were annotated, including 88 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We observed a deletion that caused the loss of the rpl32 gene, and a small expansion of IR regions resulted in the trnH gene accessing IR regions; two copies were obtained. Phylogenetic analysis showed that C. coggygria was most closely related to Pistacia, with 100% bootstrap support within Anacardiaceae. In this study, we report the plastid genome of Cotinus species for the first time, which provides insight into the evolution of the plastid genome in Anacardiaceae and promotes the understanding of Cotinus plants.     

Colour polymorphism in common primrose (Primula vulgaris Huds.): many colours–many species?

Primula vulgaris exhibits flower colour polymorphism in the eastern part of its range, especially pronounced on the NE coast of the Black Sea. This polymorphism in the Caucasian populations has been taxonomically described and some segregated species are listed as rare and endangered. We used sequence variation in two chloroplast noncoding regions (trnL–trnF and rpll32–trnL) and the complete nuclear internal transcribed spacer (ITS) of ribosomal DNA region to investigate correspondence between flower colour and geographical distribution of both nuclear and chloroplast haplotypes. It appears that variability in these DNA regions does not correlate with flower colour, being, however, clearly structured geographically. We used nested clade analysis to explore this geographical structure. It seems that the territory of the Colchis refugium on the E coast of the Black Sea contains both the highest flower colour and haplotype diversities. The results suggest that common primroses colonized the NE coast of the Black Sea from this refugium, spreading along the coast westward. At the same time, the analysis of ITS haplotypes indicates that P. vulgaris colonized the Crimea from NW Anatolia. This makes it clear that no segregated species can be recognized within flower colour polymorphic P. vulgaris in the Caucasus region. However, its phylogeography needs further detailed study on a broader scale.