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ABSTRACT: Comparisons of closely related species are needed to understand the fine-scale dynamics of retrotransposon evolution in flowering plants. Towards this goal we classified the LTR retrotransposons from six diploid and one tetraploid species of Orobanchaceae. The study species are the autotrophic, non-parasitic Lindenbergia philippensis (as an outgroup) and six closely related holoparasitic species of Orobanche (O. crenata, O. cumana, O. gracilis (tetraploid), O. pancicii) and Phelipanche (P. lavandulacea, P. ramosa). All major plant LTR retrotransposon clades could be identified and appear to be inherited from a common ancestor. Species of Orobanche, but not Phelipanche, are enriched in Ty3/Gypsy retrotransposons due to a diversification of elements, especially chromoviruses. This is particularly striking in O. gracilis where tetraploidization seems to have contributed to the Ty3/Gypsy enrichment and led to the emergence of seven large species-specific families of chromoviruses. The preferential insertion of chromoviruses in heterochromatin via their chromodomains might have favored their diversification and enrichment. Our phylogenetic analyses of LTR retrotransposons from Orobanchaceae revealed that the Bianca clade of Ty1/Copia and SMART-related elements are much more widely distributed among angiosperms than previously known. This article is protected by copyright. All rights reserved.
The Plant Journal 05/2013; · 6.16 Impact Factor
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ABSTRACT: Ribulose-1,5-Biphosphate-carboxylase-oxygenase (RuBisCO) has a crucial role in carbon fixation but a slow catalytic rate, a problem overcome in some plant lineages by physiological and anatomical traits that elevate carbon concentrations around the enzyme. Such carbon-concentrating mechanisms are hypothesized to have evolved during periods of low atmospheric CO(2). Hornworts, the sister to vascular plants, have a carbon-concentrating mechanism that relies on pyrenoids, proteinaceous bodies mostly consisting of RuBisCO. We generated a phylogeny based on mitochondrial and plastid sequences for 36% of the approximately 200 hornwort species to infer the history of gains and losses of pyrenoids in this clade; we also used fossils and multiple dating approaches to generate a chronogram for the hornworts. The results imply five to six origins and an equal number of subsequent losses of pyrenoids in hornworts, with the oldest pyrenoid gained ca. 100 Mya, and most others at <35 Mya. The nonsynchronous appearance of pyrenoid-containing clades, the successful diversification of pyrenoid-lacking clades during periods with low [CO(2)], and the maintenance of pyrenoids during episodes of high [CO(2)] all argue against the previously proposed relationship between pyrenoid origin and low [CO(2)]. The selective advantages, and costs, of hornwort pyrenoids thus must relate to additional factors besides atmospheric CO(2).
Proceedings of the National Academy of Sciences 10/2012; · 9.68 Impact Factor
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ABSTRACT: • Premise of the study: Understanding the flexibility of monocot genomes requires a phylogenetic framework, which so far is available for few of the ca. 2800 genera. Here we use a molecular tree for the South American genus Alstroemeria to place karyological information, including fluorescent in situ hybridization (FISH) signals, in an explicit evolutionary context. • Methods: From a phylogeny based on plastid, nuclear, and mitochondrial sequences for most species of Alstroemeria, we selected early-branching (Chilean) and derived (Brazilian) species for which we obtained 18S-25S and 5S rDNA FISH signals; we also analyzed chromosome numbers, 1C-values, and telomere FISH signals (in two species). • Key results: Chromosome counts for Alstroemeria cf. rupestris and A. pulchella confirm 2n = 16 as typical of the genus, which now has chromosomes counted for 29 of its 78 species. The rDNA sites are polymorphic both among and within species, and interstitial telomeric sites in Alstroemeria cf. rupestris suggest chromosome fusion. • Conclusions: In spite of a constant chromosome number, closely related species of Alstroemeria differ drastically in their rDNA, indicating rapid increase, decrease, or translocations of these genes. Previously proposed Brazilian and Chilean karyotype groups are not natural, and the n = 8 chromosomes in Alstroemeria compared to n = 9 in its sister genus Bomarea may result from a Robertsonian fusion.
American Journal of Botany 09/2012; 99(9):1501-12. · 2.66 Impact Factor
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ABSTRACT: • Premise of the study: In its current circumscription, Echinopsis with 100-150 species is one of the largest and morphologically most diverse genera of Cactaceae. This diversity and an absence of correlated characters have resulted in numerous attempts to subdivide Echinopsis into more homogeneous subgroups. To infer natural species groups in this alliance, we here provide a plastid phylogeny and use it to infer changes in growth form, pollination mode, and ploidy level. • Methods: We sequenced 3800 nucleotides of chloroplast DNA from 162 plants representing 144 species and subspecies. The sample includes the type species of all genera close to, or included in, Echinopsis as well as a dense sample of other genera of the Trichocereeae and further outgroups. New and published chromosome counts were compiled and traced on the phylogeny, as were pollination modes and growth habits. • Key results: A maximum likelihood phylogeny confirms that Echinopsis s.l. is not monophyletic nor are any of the previously recognized genera that have more than one species. Pollination mode and, to a lesser extent, growth habit are evolutionarily labile, and diploidy is the rule in Echinopsis s.l., with the few polyploids clustered in just a few clades. • Conclusions: The use of evolutionary labile floral traits and growth habit has led to nonnatural classifications. Taxonomic realignments are required, but further study of less evolutionary labile traits suitable for circumscribing genera are needed. Surprisingly, polyploidy seems infrequent in the Echinopsis alliance and hybridization may thus be of minor relevance in the evolution of this clade.
American Journal of Botany 08/2012; 99(8):1335-49. · 2.66 Impact Factor
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Journal of Biogeography 07/2012; 39(10):1806. · 4.54 Impact Factor
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ABSTRACT: The family Araceae (3790 species, 117 genera) has one of the oldest fossil records among angiosperms. Ecologically, members of this family range from free-floating aquatics (Pistia and Lemna) to tropical epiphytes. Here, we infer some of the macroevolutionary processes that have led to the worldwide range of this family and test how the inclusion of fossil (formerly occupied) geographical ranges affects biogeographical reconstructions. Using a complete genus-level phylogeny from plastid sequences and outgroups representing the 13 other Alismatales families, we estimate divergence times by applying different clock models and reconstruct range shifts under different models of past continental connectivity, with or without the incorporation of fossil locations. Araceae began to diversify in the Early Cretaceous (when the breakup of Pangea was in its final stages), and all eight subfamilies existed before the K/T boundary. Early lineages persist in Laurasia, with several relatively recent entries into Africa, South America, South-East Asia and Australia. Water-associated habitats appear to be ancestral in the family, and DNA substitution rates are especially high in free-floating Araceae. Past distributions inferred when fossils are included differ in nontrivial ways from those without fossils. Our complete genus-level time-scale for the Araceae may prove to be useful for ecological and physiological studies.
New Phytologist 07/2012; 195(4):938-50. · 6.64 Impact Factor
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ABSTRACT: BACKGROUND: The Cucurbitaceae genus Trichosanthes comprises 90-100 species that occur from India to Japan and southeast to Australia and Fiji. Most species have large white or pale yellow petals with conspicuously fringed margins, the fringes sometimes several cm long. Pollination is usually by hawkmoths. Previous molecular data for a small number of species suggested that a monophyletic Trichosanthes might include the Asian genera Gymnopetalum (four species, lacking long petal fringes) and Hodgsonia (two species with petals fringed). Here we test these groups' relationships using a species sampling of c. 60% and 4759 nucleotides of nuclear and plastid DNA. To infer the time and direction of the geographic expansion of the Trichosanthes clade we employ molecular clock dating and statistical biogeographic reconstruction, and we also address the gain or loss of petal fringes. RESULTS: Trichosanthes is monophyletic as long as it includes Gymnopetalum, which itself is polyphyletic. The closest relative of Trichosanthes appears to be the sponge gourds, Luffa, while Hodgsonia is more distantly related. Of six morphology-based sections in Trichosanthes with more than one species, three are supported by the molecular results; two new sections appear warranted. Molecular dating and biogeographic analyses suggest an Oligocene origin of Trichosanthes in Eurasia or East Asia, followed by diversification and spread throughout the Malesian biogeographic region and into the Australian continent. CONCLUSIONS: Long-fringed corollas evolved independently in Hodgsonia and Trichosanthes, followed by two losses in the latter coincident with shifts to other pollinators but not with long-distance dispersal events. Together with the Caribbean Linnaeosicyos, the Madagascan Ampelosicyos and the tropical African Telfairia, these cucurbit lineages represent an ideal system for more detailed studies of the evolution and function of petal fringes in plant-pollinator mutualisms.
BMC Evolutionary Biology 07/2012; 12(1):108. · 3.52 Impact Factor
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ABSTRACT: We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%-28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%-22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types.
Molecular Biology and Evolution 06/2012; 29(11):3601-11. · 5.55 Impact Factor
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ABSTRACT: Papaya (Carica papaya) is a crop of great economic importance, and the species was among the first plants to have its genome sequenced. However, there has never been a complete species-level phylogeny for the Caricaceae, and the crop's closest relatives are therefore unknown. We investigated the evolution of the Caricaceae based on sequences from all species and genera, the monospecific Carica, African Cylicomorpha with two species, South American Jacaratia and Vasconcellea with together c. 28 species, and Mexican/Guatemalan Jarilla and Horovitzia with four species. Most Caricaceae are trees or shrubs; the species of Jarilla, however, are herbaceous. We generated a matrix of 4711 nuclear and plastid DNA characters and used maximum likelihood (ML) and Bayesian analysis to infer species relationships, rooting trees on the Moringaceae. Divergence times were estimated under relaxed and strict molecular clocks, using different subsets of the data. Ancestral area reconstruction relied on a ML approach. The deepest split in the Caricaceae occurred during the Late Eocene, when the ancestor of the Neotropical clade arrived from Africa. In South America, major diversification events coincide with the Miocene northern Andean uplift and the initial phase of the tectonic collision between South America and Panama resulting in the Panamanian land bridge. Carica papaya is sister to Jarilla/Horovitzia, and all three diverged from South American Caricaceae in the Oligocene, 27 (22-33) Ma ago, coincident with the early stages of the formation of the Panamanian Isthmus. The discovery that C. papaya is closest to a clade of herbaceous or thin-stemmed species has implications for plant breeders who have so far tried to cross papaya only with woody highland papayas (Vasconcellea).
Molecular Phylogenetics and Evolution 05/2012; 65(1):46-53. · 3.61 Impact Factor
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ABSTRACT: We describe and illustrate Coccinia pwaniensis Holstein from eastern Tanzania and southeast Kenya, and C. samburuensis Holstein from the Samburu area in Kenya. The new species were already recognised by Charles Jeffrey in 1967 and are now known
from eight and four collections, respectively. Ongoing monographic work also revealed three new synonyms and the need for
a new combination, Coccinia heterophylla (Hook. f.) Holstein.
Key wordsCoastal forests-
Coccinia pwaniensis
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Coccinia samburuensis
-Kenya-Tanzania
Kew Bulletin 05/2012; 65(3):435-441.
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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: The European rewardless, bee-pollinated orchidDactylorhiza sambucina commonly produces yellow-flowered and purple-flowered individuals in frequencies that range from balanced (per population)
to very unbalanced, with parts of the species’ range entirely monochromatic. We studied male and female reproductive success
of the two morphs in 22 populations in the Czech Republic, relating it to morph frequency, population size and density, and
presence and abundance of yellow and purple co-flowering nectar-providing species visited by the same bee species. Cumulative
abundances of yellow nectar-producing co-flowering species (of which, on average,Primula veris made up 56%) had a negative effect on male reproductive success of the yellow morph, and spectral analyses showed that to
bumblebees the colours ofP. veris and yellowD. sambucina are different, permitting ready visual discrimination. The cumulative abundance of purple co-flowering species had no significant
effect on morph reproductive success. Morph frequencies were unrelated to reproductive success and population size, and there
was no evidence of frequency-dependent selection except in one highly unbalanced population. Density of flowering conspecifics
was negatively correlated with male reproductive success of the purple morph. Seed mass, viability, and germination success
depended on whether seeds resulted from outcrossed or selfed matings and on morph colour. Selfed seeds and seeds produced
by the yellow morph from yellow × yellow and yellow × purple crosses had zero germination (after three months), providing
the first hint that differential vegetative fitness, rather than differential reproductive fitness via pollinator selection,
may explain morph frequencies inD. sambucina.
Folia Geobotanica 04/2012; 41(1):61-76. · 1.50 Impact Factor
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ABSTRACT: Hallucinogenic or toxic species of Brunfelsia (Solanaceae: Petunieae) are important in native cultures throughout South America, and the genus also contains several horticulturally important species. An earlier morphological revision of the c. 50 species recognized three main groups, one consisting of the 23 Antillean species, another of southern South American and Andean species, and a third of species from the Amazon Basin and Guiana Shield. Based on plastid and nuclear DNA sequences from up to 65 accessions representing 80% of the species, we generated a phylogeny and a calibrated chronogram for Brunfelsia to infer clade expansion and shifts in pollinators and fruit types. Brunfelsia flowers offer nectar, and attract lepidoptera, hummingbirds, or bees; the fruits are dry or fleshy. Our results imply that Brunfelsia is 16-21 Myr old and entered the Antilles from South America early during its history, with subsequent expansion along the island arc. The ancestor of the Antillean clade was hawk-moth-pollinated and had fleshy capsules, perhaps facilitating dispersal by birds. The only shift to hummingbird pollination occurred on Cuba, which also harbors the largest single radiation, with 11 species (10 included in our study) that apparently arose over the past 4 Myr. Jamaica, Hispaniola, and Puerto Rico each sustained smaller radiations. The data also reveal at least one new species.
Molecular Phylogenetics and Evolution 03/2012; 64(1):1-11. · 3.61 Impact Factor
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ABSTRACT: Among the World's most challenging environments for plant life is the Atacama Desert, an arid zone extending over 1300 km and from sea level to 2000/3000 m altitude along the southwestern Andean foothills. Plants there and in the adjacent Mediterranean zone exhibit striking adaptations, and we here address the question whether in a species-rich clade such adaptations arose in parallel, at different times, or simultaneously. Answering this type of question has been a major concern of evolutionary biology over the past few years, with a growing consensus that lineages tend to be conservative in their vegetative traits and niche requirements. Combined nuclear and chloroplast DNA sequences for 112 species of Oxalidales (4900 aligned nucleotides) were used for a fossil-calibrated phylogeny that includes 43 of the 54 species of Chilean Oxalis, and species distribution models (SDMs) incorporating precipitation, temperature, and fog, and the phylogeny were used to reconstruct ancestral habitat preferences, relying on likelihood and Bayesian techniques. Since uneven collecting can reduce the power of SDMs, we compared 3 strategies to correct for collecting effort. Unexpectedly, the Oxalis flora of Chile consists of 7 distant lineages that originated at different times prior to the last Andean uplift pulse; some had features preadapting them to seasonally arid or xeric conditions. Models that incorporated fog and a "collecting activity surface" performed best and identified the Mediterranean zone as a hotspot of Oxalis species as well as lineage diversity because it harbors a mix of ancient and young groups, including insufficiently arid-adapted species. There is no evidence of rapid adaptive radiation.
Systematic Biology 02/2012; 61(5):823-34. · 10.23 Impact Factor
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ABSTRACT: Chronograms from molecular dating are increasingly being used to infer rates of diversification and their change over time. A major limitation in such analyses is incomplete species sampling that moreover is usually nonrandom. While the widely used γ statistic with the Monte Carlo constant-rates test or the birth-death likelihood analysis with the δ AICrc test statistic are appropriate for comparing the fit of different diversification models in phylogenies with random species sampling, no objective automated method has been developed for fitting diversification models to nonrandomly sampled phylogenies. Here, we introduce a novel approach, CorSiM, which involves simulating missing splits under a constant rate birth-death model and allows the user to specify whether species sampling in the phylogeny being analyzed is random or nonrandom. The completed trees can be used in subsequent model-fitting analyses. This is fundamentally different from previous diversification rate estimation methods, which were based on null distributions derived from the incomplete trees. CorSiM is automated in an R package and can easily be applied to large data sets. We illustrate the approach in two Araceae clades, one with a random species sampling of 52% and one with a nonrandom sampling of 55%. In the latter clade, the CorSiM approach detects and quantifies an increase in diversification rate, whereas classic approaches prefer a constant rate model; in the former clade, results do not differ among methods (as indeed expected since the classic approaches are valid only for randomly sampled phylogenies). The CorSiM method greatly reduces the type I error in diversification analysis, but type II error remains a methodological problem.
Systematic Biology 02/2012; 61(5):785-92. · 10.23 Impact Factor
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ABSTRACT: Patterns of species richness and relative abundance at some scales cannot be distinguished from predictions of null models, including zero-sum neutral models of population change and random speciation-extinction models of evolutionary diversification. Both models predict that species richness or population abundance produced by independent iterations of the same processes in different regions should be uncorrelated. We find instead that the number of species and individuals in families of trees in forest plots are strongly correlated across Southeast Asia, Africa, and tropical America. These correlations imply that deterministic processes influenced by evolutionarily conservative family-level traits constrain the number of confamilial tree species and individuals that can be supported in regional species pools and local assemblages in humid tropical forests.
Science 01/2012; 335(6067):464-7. · 31.20 Impact Factor
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ABSTRACT: Brunfelsia plowmaniana N.Filipowicz & M.Nee sp. nov., a species from humid and cloud forests of the Bolivian and Argentinean Andes, is described and provided with a molecular diagnosis, using provisions available in the recently approved International Code of Nomenclature for algae, fungi and plants. Specimens belonging to the new species were previously placed in the polymorphic Brunfelsia uniflora (Pohl) D.Don, which a molecular phylogeny revealed as polyphyletic. Revision of numerous collections revealed clear morphological differences between the new species and Brunfelsia uniflora, the type locality of which is in the state of São Paulo, Brazil.
PhytoKeys. 01/2012;
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ABSTRACT: For 84 years, botanists have relied on calculating the highest common factor for series of haploid chromosome numbers to arrive at a so-called basic number, x. This was done without consistent (reproducible) reference to species relationships and frequencies of different numbers in a clade. Likelihood models that treat polyploidy, chromosome fusion and fission as events with particular probabilities now allow reconstruction of ancestral chromosome numbers in an explicit framework. We have used a modelling approach to reconstruct chromosome number change in the large monocot family Araceae and to test earlier hypotheses about basic numbers in the family.
Using a maximum likelihood approach and chromosome counts for 26 % of the 3300 species of Araceae and representative numbers for each of the other 13 families of Alismatales, polyploidization events and single chromosome changes were inferred on a genus-level phylogenetic tree for 113 of the 117 genera of Araceae.
The previously inferred basic numbers x = 14 and x = 7 are rejected. Instead, maximum likelihood optimization revealed an ancestral haploid chromosome number of n = 16, Bayesian inference of n = 18. Chromosome fusion (loss) is the predominant inferred event, whereas polyploidization events occurred less frequently and mainly towards the tips of the tree.
The bias towards low basic numbers (x) introduced by the algebraic approach to inferring chromosome number changes, prevalent among botanists, may have contributed to an unrealistic picture of ancestral chromosome numbers in many plant clades. The availability of robust quantitative methods for reconstructing ancestral chromosome numbers on molecular phylogenetic trees (with or without branch length information), with confidence statistics, makes the calculation of x an obsolete approach, at least when applied to large clades.
Annals of Botany 12/2011; 109(4):681-92. · 4.03 Impact Factor
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ABSTRACT: Alocasia comprises over 113 species of rainforest understorey plants in Southeast Asia, the Malesian region, and Australia. Several species, including giant taro, Alocasia macrorrhizos, and Chinese taro, Alocasia cucullata, are important food plants or ornamentals. We investigated the biogeography of this genus using plastid and nuclear DNA sequences (5200 nucleotides) from 78 accessions representing 71 species, plus 25 species representing 16 genera of the Pistia clade to which Alocasia belongs. Divergence times were inferred under strict and relaxed clock models, and ancestral areas with Bayesian and maximum likelihood approaches. Alocasia is monophyletic and sister to Colocasiagigantea from the SE Asian mainland, whereas the type species of Colocasia groups with Steudnera and Remusatia, requiring taxonomic realignments. Nuclear and plastid trees show topological conflict, with the nuclear tree reflecting morphological similarities, the plastid tree species' geographic proximity, suggesting chloroplast capture. The ancestor of Alocasia diverged from its mainland sister group c. 24 million years ago, and Borneo then played a central role in the expansion of Alocasia: 11-13 of 18-19 inferred dispersal events originated on Borneo. The Philippines were reached from Borneo 4-5 times in the Late Miocene and Early Pliocene, and the Asian mainland 6-7 times in the Pliocene. Domesticated giant taro originated on the Philippines, Chinese taro on the Asian mainland.
Molecular Phylogenetics and Evolution 12/2011; 63(1):43-51. · 3.61 Impact Factor
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ABSTRACT: The tribe Delphinieae (Ranunculaceae) comprises two species-rich genera, Aconitum and Delphinium, the latter including Consolida and Aconitella. The 650-700 species are distributed in Eurasia and North America; three species occur on tropical African mountains. Maximum likelihood analyses of 2088 aligned nucleotides of plastid and nuclear sequences obtained from up to 185 species of Delphinieae from throughout the geographic range (plus relevant outgroups) show that three short-lived (facultative annual or biennial) Mediterranean species belonging to Delphinium subgenus Staphisagria are the sister clade to all other Delphinieae, implying that Staphisagria needs to be raised to genus status if Delphinium and Aconitum are to become mutually monophyletic. Molecular clock dating suggests an origin of the sampled Delphinieae in the Early Oligocene (c. 32.3 Ma) and expansion to North America of Aconitum and Delphinium around 3.3 and 2.9 Ma ago, respectively; the East African Mts. were reached by long-distance dispersal some 2.4 Ma ago, coincident with the major uplift of the East African Rift system. The ancestral growth form of the Delphinieae could not be reconstructed, but Late Miocene bursts in diversification rates in the Himalayan and southwestern Chinese clades of Aconitum and Delphinium appear to be associated with transitions from short-lived to long-lived life histories.
Molecular Phylogenetics and Evolution 12/2011; 62(3):928-42. · 3.61 Impact Factor
