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ABSTRACT: Most extant genus-level radiations in gymnosperms are of Oligocene age or younger, reflecting widespread extinction during climate cooling at the Oligocene/Miocene boundary [∼23 million years ago (Ma)]. Recent biogeographic studies have revealed many instances of long-distance dispersal in gymnosperms as well as in angiosperms. Acting together, extinction and long-distance dispersal are likely to erase historical biogeographic signals. Notwithstanding this problem, we show that phylogenetic relationships in the gymnosperm family Cupressaceae (162 species, 32 genera) exhibit patterns expected from the Jurassic/Cretaceous breakup of Pangea. A phylogeny was generated for 122 representatives covering all genera, using up to 10,000 nucleotides of plastid, mitochondrial, and nuclear sequence per species. Relying on 16 fossil calibration points and three molecular dating methods, we show that Cupressaceae originated during the Triassic, when Pangea was intact. Vicariance between the two subfamilies, the Laurasian Cupressoideae and the Gondwanan Callitroideae, occurred around 153 Ma (124-183 Ma), when Gondwana and Laurasia were separating. Three further intercontinental disjunctions involving the Northern and Southern Hemisphere are coincidental with or immediately followed the breakup of Pangea.
Proceedings of the National Academy of Sciences 05/2012; 109(20):7793-8. · 9.68 Impact Factor
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ABSTRACT: • A central aim of biogeography is to understand when and how modern patterns of species diversity and distribution developed. Many plant groups have disjunct distributions within the Northern Hemisphere, but among these very few have been studied that prefer warm semi-arid habitats. • Here we examine the biogeography and diversification history of Juniperus, which occurs in semi-arid habitats through much of the Northern Hemisphere. A phylogeny was generated based on > 10,000 bp of cpDNA for 51 Juniperus species plus many outgroups. Phylogenies based on fewer species were also constructed based on nuclear internal transcribed spacer (nrITS) and combined nrITS/cpDNA data sets to check for congruence. Divergence time-scales and ancestral distributions were further inferred. • Both long dispersal and migration across land bridges probably contributed to the modern range of Juniperus, while long-term climatic changes and the uplift of the Qinghai-Tibetan plateau probably drove its diversification. Diversification apparently slowed down during climate-stable period of the Oligocene, and then speeded up from the Miocene onwards. • Juniperus probably originated in Eurasia, and was a part of the south Eurasian Tethyan vegetation of the Eocene to Oligocene. It reached America once at this time, once in the Miocene and once more recently.
New Phytologist 10/2010; 188(1):254-72. · 6.64 Impact Factor
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ABSTRACT: 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.
Molecular Ecology 03/2010; 19(8):1691-704. · 5.52 Impact Factor
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ABSTRACT: Species delimitation detected by molecular markers is complicated by introgression and incomplete lineage sorting between species. Recent modeling suggests that fixed genetic differences between species are highly related to rates of intraspecific gene flow. However, it remains unclear whether such differences are due to high levels of intraspecific gene flow overriding the spread of introgressed alleles or favoring rapid lineage sorting between species. In pines, chloroplast (cp) and mitochondrial (mt) DNAs are normally paternally and maternally inherited, respectively, and thus their relative rates of intraspecific gene flow are expected to be high and low, respectively. In this study, we used two pine species with overlapping geographical distributions in southeast China, P. massoniana and P. hwangshanensis, as a model system to examine the association between organelle gene flow and variation within and between species. We found that cpDNA variation across these two pine species is more species specific than mtDNA variation and almost delimits taxonomic boundaries. The shared mt/cp DNA genetic variation between species shows no bias in regard to parapatric versus allopatric species' distributions. Our results therefore support the hypothesis that high intraspecific gene flow has accelerated cpDNA lineage sorting between these two pine species.
Evolution 03/2010; 64(8):2342-52. · 5.15 Impact Factor
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ABSTRACT: Although allopatric speciation is viewed as the most common way in which species originate, allopatric divergence among a group of closely related species has rarely been examined at the population level through phylogeographic analysis. Here we report such a case study on eight putative cypress (Cupressus) species, which each have a mainly allopatric distribution in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. The analysis involved sequencing three plastid DNA fragments (trnD-trnT, trnS-trnG and trnL-trnF) in 371 individuals sampled from populations at 66 localities.
Both phylogenetic and network analyses showed that most DNA haplotypes recovered or haplotype-clustered lineages resolved were largely species-specific. Across all species, significant phylogeographic structure (N(ST) > G(ST), P < 0.05) implied a high correlation between haplotypes/lineages and geographic distribution. Two species, C. duclouxiana and C. chengiana, which are distributed in the eastern QTP region, contained more haplotypes and higher diversity than five species with restricted distributions in the western highlands of the QTP. The remaining species, C. funebris, is widely cultivated and contained very little cpDNA diversity.
It is concluded that the formation of high mountain barriers separating deep valleys in the QTP and adjacent regions caused by various uplifts of the plateau since the early Miocene most likely promoted allopatric divergence in Cupressus by restricting gene flow and fixing local, species-specific haplotypes in geographically isolated populations. The low levels of intraspecific diversity present in most species might stem from population bottlenecks brought about by recurrent periods of unfavorable climate and more recently by the negative impacts of human activities on species' distributions. Our findings shed new light on the importance of geographical isolation caused by the uplift of the QTP on the development of high plant species diversity in the QTP biodiversity hotspot.
BMC Evolutionary Biology 01/2010; 10:194. · 3.52 Impact Factor
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ABSTRACT: How coniferous trees in northern China changed their distribution ranges in response to Quaternary climatic oscillations remains largely unknown. Here we report a study of the phylogeography of Pinus tabulaeformis, an endemic and dominant species of coniferous forest in northern China. We examined sequence variation of maternally inherited, seed-dispersed mitochondrial DNA (mtDNA) (nad5 intron 1 and nad4/3-4) and paternally inherited, pollen- and seed-dispersed chloroplast DNA (cpDNA) (rpl16 and trnS-trnG) within and among 30 natural populations across the entire range of the species. Six mitotypes and five chlorotypes were recovered among 291 trees surveyed. Population divergence was high for mtDNA variation (G(ST) = 0.738, N(ST) = 0.771) indicating low levels of seed-based gene flow and significant phylogeographical structure (N(ST) > G(ST), P < 0.05). The spatial distribution of mitotypes suggests that five distinct population groups exist in the species: one in the west comprising seven populations, a second with a north-central distribution comprising 15 populations, a third with a southern and easterly distribution comprising five populations, a fourth comprising one central and one western population, and a fifth comprising a single population located in the north-central part of the species' range. Each group apart from the fourth group is characterized by a distinct mitotype, with other mitotypes, if present, occurring at low frequency. It is suggested, therefore, that most members of each group apart from Group 4 are derived from ancestors that occupied different isolated refugia in a previous period of range fragmentation of the species, possibly at the time of the Last Glacial Maximum. Possible locations for these refugia are suggested. A comparison of mitotype diversity between northern and southern subgroups within the north-central group of populations (Group 2) showed much greater uniformity in the northern part of the range both within and between populations. This could indicate a northward migration of the species from a southern refugium in this region during the postglacial period, although alternative explanations cannot be ruled out. Two chlorotypes were distributed across the geographical range of the species, resulting in lower levels of among-population chlorotype variation. The geographical pattern of variation for all five chlorotypes provided some indication of the species surviving past glaciations in more than one refugium, although differentiation was much less marked, presumably due to the greater dispersal of cpDNA via pollen.
Molecular Ecology 10/2008; 17(19):4276-88. · 5.52 Impact Factor
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ABSTRACT: Hybrids between the acid-loving species Rhododendron ferrugineum and the basic soil species Rhododendron hirsutum occur on soils of intermediate pH in the European Alps. Material from two hybrid zones approximately 500 m apart, and also nearby populations of each parent species, was surveyed for presence/absence of 31 random amplified polymorphic DNA markers that distinguish parents. Based on morphological assessment, the material comprised 51 putative hybrids, 18 putative R. ferrugineum individuals and 26 putative R. hirsutum plants. RAPD data were analysed using a Bayesian approach implemented by the program newhybrids, and also by principal coordinates analysis. The identity of all R. ferrugineum plants examined was confirmed; however, of the putative R. hirsutum individuals examined, two were certainly and 11 possibly hybrid derivatives. Among all hybrid derivatives examined, about half were designated as F1s or a similar class, otherwise backcrosses to R. hirsutum appeared to be common whereas other hybrid classes were rare and backcrosses to R. ferrugineum possibly absent. Despite this, artificially generated seed of F2 class and backcrosses in each direction showed greater viability than one parent (R. hirsutum). Introgression from R. ferrugineum was also detected in a population that from morphology appeared to contain only R. hirsutum. Hence, the direction of backcrossing might be highly asymmetric within hybrid zones, causing unidirectional gene flow from R. ferrugineum into R. hirsutum. Conversely, the rarity of backcrosses to R. ferrugineum, F2s and later hybrid generations, which might be due to phenology effects and habitat-mediated selection, could play a part in restricting gene flow towards R. ferrugineum.
Molecular Ecology 03/2008; 17(4):1108-21. · 5.52 Impact Factor
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ABSTRACT: Many regional floras contain a high proportion of recently introduced plant species. Occasionally, hybridization between an introduced species and another species (introduced or native) can result in interspecific gene flow. This may occur even in instances where the F(1) hybrid shows very high sterility, but occasionally produces a few viable gametes. We provide examples of gene flow occurring between some rhododendrons recently introduced to the British flora, and between an introduced and native Senecio species. Neutral molecular markers have normally been employed to obtain evidence of interspecific gene flow, but the challenge now is to isolate and characterize functional introgressed genes and to determine how they affect the fitness of introgressants and whether they improve adaptation to novel habitats allowing introgressants to expand the range of a species. We outline a candidate gene approach for isolating and characterizing an allele of the RAY gene in Senecio vulgaris, which is believed to have introgressed from S. squalidus, and which causes the production of ray florets in flower heads. We discuss the effects of this introgressed allele on individual fitness, including those that originate directly from the production of ray florets plus those that may arise from pleiotropy and/or linkage.
Philosophical Transactions of The Royal Society B Biological Sciences 07/2003; 358(1434):1123-32. · 6.40 Impact Factor
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ABSTRACT: Information concerning the area of origin, genetic diversity and possible acquisition of germplasm through hybridization is fundamental to understanding the evolution, ecology and possible control measures for an introduced invasive plant species. Rhododendron ponticum is extensively naturalized in the British Isles, but it is not known whether native material in Turkey, Spain or Portugal gave rise to the naturalized material, or to what extent introgression has affected this material. Chloroplast (cp) and nuclear ribosomal DNA (rDNA) restriction fragment length polymorphisms (RFLPs) were sought which could distinguish between native material of R. ponticum, and between 15 other Rhododendron species including R. ponticum's closest relatives. Thereafter, a total of 260 naturalized accessions of R. ponticum from throughout the British Isles was examined with respect to informative polymorphisms. It was found that 89% of these accessions possessed a cpDNA haplotype that occurred in native material of R. ponticum derived almost entirely from Spain, while 10% of accessions had a haplotype unique to Portuguese material. These results therefore indicated an Iberian origin for British material. rDNA or cpDNA evidence of introgression from R. catawbiense was found in 27 British accessions of R. ponticum, and such accessions were significantly more abundant in Britain's coldest region, eastern Scotland, than elsewhere. This could indicate that introgression from R. catawbiense confers improved cold tolerance. Introgression from R. maximum and an unidentified species was also detected.
Molecular Ecology 04/2000; 9(5):541 - 556. · 5.52 Impact Factor
