Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation

The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trnT-trnF and trnS-trnG sequence variation within Juniperus przewalskii, a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G(ST) = 0.772, N(ST) = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N(ST) > G(ST), P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.     

Potential refugium on the Qinghai–Tibet Plateau revealed by the chloroplast DNA phylogeography of the alpine species Metagentiana striata (Gentianaceae)

Metagentiana striata is an alpine annual herbaceous plant endemic to the east of the Qinghai–Tibet (Q–T) Plateau and adjacent areas. The phylogeography of M. striata was studied by sequencing the chloroplast DNA (cpDNA) trn S– trn G intergenic spacer. Ten haplotypes were identified from an investigation of 232 individuals of M. striata from 14 populations covering the entire geographical range of this species. The level of differentiation amongst populations was very high ( G _ST = 0.746; N _ST = 0.774) and a significant phylogeographical structure was observed ( P  < 0.05). An analysis of molecular variance found a high variation amongst populations (76%), with F _ST = 0.762 (highly significant, P  < 0.001), indicating that little gene flow occurred amongst the different regions; this was explained by the isolation of populations by high mountains along the Q–T Plateau and adjacent areas ( N _m = 0.156). Only one ancestral haplotype (A) was common and widespread throughout the distributional range of M. striata. The populations of the Hengduan Mountains region of the south-eastern Q–T Plateau showed high diversity and uniqueness of haplotypes. It is suggested that this region was the potential refugium of M. striata during the Quaternary glaciation, and that interglacial and postglacial range expansion occurred from this refugium. This scenario was in good agreement with the results of nested clade analysis, which inferred that the current spatial distribution of cpDNA haplotypes and populations resulted from range expansion, together with past allopatric fragmentation events.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 125–140.     

Biogeography and Divergence in Guaiacum sanctum (Zygophyllaceae) Revealed in Chloroplast DNA: Implications for Conservation in the Florida Keys

Guaiacum sanctum (lignumvitae, guayacán) comprises economically important and globally endangered trees endemic to the dry neotropics. These trees were historically over-harvested and now G. sanctum is among the species listed by IUCN and CITES. Guaiacum sanctum was once found throughout the Florida Keys, but anthropogenic habitat fragmentation and exploitation have left only one significant population, on Lignumvitae Key. The ecology of this population is additionally subject to hurricane-mediated effects and an endemic parasite. Genetic profiles were determined for the Lignumvitae and putative source populations of G. sanctum to assess variability and to test biogeographic hypotheses. These data were analyzed by phylogenetic and statistical parsimony analyses. The results were most readily interpreted as indicating historical fragmentation followed by long-term isolation. However, recent dispersal or gene flow could not be entirely excluded. Both types of analyses strongly support a significant genetic divergence between Caribbean and Mexican populations of G. sanctum and also suggest bidirectional dispersal of G. sanctum into Lignumvitae Key from both the Caribbean and Mexico. These results inform the process of restoring G. sanctum in the Keys.     

Long-distance colonization of the Western Mediterranean by Cistus ladanifer (Cistaceae) despite the absence of special dispersal mechanisms

Aim There are few biogeographical and evolutionary studies that address plant colonization and lineage origins in the Mediterranean. Cistus serves as an excellent model with which to study diaspore dispersal and distribution patterns of plants exhibiting no special long‐distance dispersal mechanisms. Here we analyse the pattern of genetic variation and divergence times to infer whether the African–European disjunction of C. ladanifer L. is the result of long‐distance dispersal or of vicariance events. Location Principally the Western Mediterranean region, with a focus on the Strait of Gibraltar. Methods We used DNA sequence phylogenetic approaches, based on plastid (rbcL/trnK‐matK) and nuclear (ITS) sequence data sets, and the penalized likelihood method, to date the diversification of the 21 species of Cistus. Phylogenetic relationships and phylogeographical patterns in 47 populations of C. ladanifer were also analysed using two plastid DNA regions (trnS‐trnG, trnK‐matK). These sequence data were analysed using maximum parsimony, Bayesian inference and statistical parsimony. Results Dating estimates indicated divergence dates of the C. ladanifer lineage in the Pleistocene. Eight nucleotide‐substitution haplotypes distributed on the European (four haplotypes) and African (five haplotypes) sides of the Strait of Gibraltar were revealed from C. ladanifer sequences. Both the haplotype network and the phylogenetic analyses depicted two main Cistus lineages distributed in both Europe and North Africa. An Iberian haplotype forms part of the North African lineage, and another haplotype distributed on both continents is related to the European lineage. Haplotype relationships with respect to outgroup sequences supported the hypothesis that the centre of genetic diversity is in northern Africa. Main conclusions Based on lineage divergence‐time estimates and disassociation between geographical and lineage haplotype distributions, we inferred at least two intercontinental colonization events of C. ladanifer post‐dating the opening of the Strait of Gibraltar (c. 5 Ma). This result supports a hypothesis of long‐distance dispersal rather than a hypothesis of vicariance. We argue that, despite limited dispersal abilities, preference for disturbed habitats was integral to historical colonization after the advent of the Mediterranean climate (c. 3.2 Ma), when Cistus species diverged and became established as a dominant element in the Mediterranean scrub.     

Re-evaluation of morphological and chloroplast DNA variation in Juniperus osteosperma Hook and Juniperus occidentalis Torr. Little (Cupressaceae) and their putative hybrids

Relationships between variation in cpDNA and morphology were examined to test the hypothesis of hybridization between Juniperus osteosperma and Juniperus occidentalis. Principal components analysis of 11 taxonomically-important characters distinguished individuals collected from eastern Nevada and Utah from those of southern Oregon. In contrast, many individuals collected from sympatric populations in western Nevada were morphologically intermediate to these two groups. Comparative sequencing of the trnS-trnG intergenic spacer and restriction site analysis of a trnL-trnF PCR product revealed nine haplotypes, and examination of haplotype-morphology associations allowed identification of species-specific genetic markers as well as those that transcend species limits. The confinement of morphological intermediacy and transcendent haplotypes to zones of sympatry, the discovery of haplotypes characteristic of one species in the morphological background of the other, and determination that the character intermediacy encountered is of the type expected under interspecific gene flow are marshaled in support of introgressive hybridization between J. osteosperma and J. occidentalis.     

Molecular markers in Viola L. subsect. Viola: Application and taxonomic implications for the identification of dubious herbarium specimens

Abstract

The authors report the use of nuclear [internal transcribed spacer (ITS) sequences 1 and 2] and chloroplast DNA (trnS-trnG intergenic spacer sequences) in Viola subsect. Viola for separate tracking of maternal lineages and detecting dubious herbarium specimens. A phylogenetic investigation carried out on ITS data after removal of all material with possible hybrid origin showed that V. hirta is a monophyletic unit, whereas V. odorata includes at least V. collina and V. jaubertiana, as well as three sequences of V. alba subsp. dehnhardtii from literature. In some, among the sampled individuals, the morphological attribution to one species is contradicted by nuclear DNA, which indicated a wide distance from other non-specific individuals from different locations and closer proximity to a different species. Chloroplast DNA data for the same individuals, on the contrary concurred with morphological evidence. These findings confirm document univocal correlation between our chosen chloroplast sequences and the studied taxa at species or subspecies level; these sequences have the appropriate variability range to be employed for detection of the maternal lineage of unknown Viola samples.