Chloroplast DNA-based phylogeny of AsianPinus species (Pinaceae)

The genusPinus includes over 90 species with approximately 24 species native to Asia. We have analyzed the chloroplast (cp) DNA variation of 18Pinus species, including 15 Asian, two Eurasian, and one European species using seven restriction enzymes and ten non-overlapping probes and inferred their phylogenetic relationships. Results of phenetic and cladistic approaches to phylogeny reconstruction were largely in agreement, suggesting two major lineages within the genus and confirmed the ancient character of haploxylon and diploxylon subgenera. Species from sectionParrya appear to have diverged earliest from the hypothesized phylogenetic centre for the haploxylon pines, withP. bungeana andP. gerardiana forming two basal, monotypic lineages. The range of estimated pairwise nucleotide substitutions per site ( ) was higher among haploxylon pines than among diploxylon species. CpDNA divergence was found to be low within the sectionSylvestres, relative to the divergence among haploxylon species, suggesting that the radiation of this group of taxa from its common ancestor occurred after the diversification of other groups. The low cpDNA divergence in this subsection corroborated earlier evidence for its phylogenetic cohesiveness and existence as a monophyletic group.     

HYBRIDIZATION AND CHLOROPLAST DNA VARIATION IN A PINUS SPECIES COMPLEX FROM ASIA

Heterologous hybridization of chloroplast DNA (cpDNA) involving 30 endonucleaseprobe combinations was used to analyze cpDNA variation in multiple individuals and populations of Pinus tabulaeformis (Carr.), Pinus yunnanensis (Franchèt) and Pinus massoniana (Lamb.). Restriction fragment patterns detected by several combinations distinguished among the three species. The obtained cpDNA markers were subsequently used to examine cpDNA variation of Pinus densata (Masters), a putative tertiary hybrid between P. tabulaeformis and P. yunnanensis. The analysis demonstrated that P. densata populations harbor three different haplotypes. Two of these haplotypes are characteristic of P. tabulaeformis and P. yunnanensis. However, the third haplotype found in P. densata appears to be absent in other extant Asian Pinus species. It is suggested that the observed cpDNA composition of P. densata populations is a result of past hybridization involving P. tabulaeformis, P. yunnanensis, and a third unknown or extinct taxon. Chloroplast DNA polymorphism in P. densata was much greater than that for nuclear allozyme markers in this and the other Pinus species. Population differentiation was also substantial in P. densata and exceeded that for allozyme markers. In contrast, no cpDNA polymorphism was detected in populations of P. tabulaeformis, P. yunnanensis, and P. massoniana. The study suggests that interspecific gene exchange may lead to the creation of stable cpDNA polymorphism in conifer hybrids.     

Taxonomic differences among closely related pines Pinus sylvestris, P. mugo, P. uncinata, P. rotundata and P. uliginosa as revealed in needle sclerenchyma cells

The purpose of the present study was to test the taxonomic value of sclerenchyma in distinguishing Pinus sylvestris and P. mugo, P. uncinata, P. rotundata and P. uliginosa, all representing the subsection Sylvestres within the genus Pinus. Thirty-six samples were gathered in natural populations. Every sample was represented with 30 individuals, every individual with 10 brachyblasts. Three types of sclerenchymatic cells surrounding the resin canals and four between vascular bundles were distinguished. Relations among samples and taxa were verified using discriminant analysis and clustering based on Euclidean distances. The types of sclerenchymatic cells surrounding the resin canals and located between the vascular bundles differentiate the compared taxa when used as average frequencies but are extremely variable and do not allow the classification of every individual. The study demonstrated that the type of sclerenchymatic cells surrounding the resin canals and between the vascular bundles in needles could have an important taxonomic value in distinguishing the taxa of two-needle pines of the subsection Sylvestres in Europe at the population level. The distinguishing of individuals was difficult because of very high variation of sclerenchyma characters.     

Regrowth and tannin production in woody and succulent karoo shrubs in response to simulated browsing

Allocation of carbon to chemical defences has often been suggested to be a direct response to browsing or grazing by herbivores. This study quantitatively compares total polyphenol and tannin production in response to simulated browsing of three karoo shrubs in order to test this induced defence hypothesis. The three species studied responded to browsing either by rapid regrowth or by increasing polyphenol production in the remaining tissues. The patterns did not follow any phylogenetic relationships but were weakly associated with the palatability of each species. The highly palatable deciduous species Osteospermum sinuatum, which is capable of rapid regrowth, showed no or very low levels of constitutive and browsing-induced total polyphenols, condensed tannins and protein-precipitating tannins. The evergreen sclerophyllous species Pteronia pallens showed a limited regrowth capacity and had intermediate levels of polyphenols, while the evergreen succulent species Ruschia spinosa showed almost no regrowth over the study period. R. spinosa contained the highest constitutive and browsing-induced levels of polyphenols, condensed tannins and protein-precipitating tannins. In two of the species more than one anti-herbivore defence feature co-occur. P. pallens foliage contains both hepatotoxins and polyphenols while R. spinosa has both structural (spines) and chemical defences. Responses of karoo shrubs to simulated browsing are interpreted as the result of passive alterations in plant chemistry rather than as an active defence response to herbivores.     

PATTERNS OF ALLOZYME RELATIONSHIPS COMPARED WITH MORPHOLOGY,HYBRIDIZATION, AND GEOLOGIC HISTORY IN ALLOPATRIC ISLAND-DWELLING MOSQUITOES

Allozyme relationships were compared with morphology, interspecific hybridization, and geologic history in 14 closely-related species in the Aedes (Stegomyia) scutellaris subgroup. The phylogeny generated by the electrophoretic data was generally in agreement with morphological classifications except that one morphologically distinct species pair (A. alcasidi and A. malayensis) showed only populational differentiation and several nearly identical morphological pairs in Polynesia (e.g., A. pseudoscutellaris and A. polynesiensis) were very distant genetically. A molecular clock, based on the ratio between genetic distance and divergence time (one unit of Nei's distance = 11 million years) inferred from a dated geologic event, was used to compare zoogeography, morphology, and biochemical relationships. Genetic distances between species from the Solomon Islands and the Vanuatu-Polynesia area correspond to an early Pliocene separation of these areas. An invasion of Micronesia occurred approximately 5 million years ago. Most remaining speciation occurred during the mid-Pliocene as islands moved into their present-day positions. The close relationship between southeast Asian and Philippine species could have resulted from the recent onset of isolation in the Pleistocene. Interspecific hybridization potential was not significantly correlated with Nei's genetic distance. Many quite distantly related species readily hybridize, while some closely related pairs show only unidirectional compatibility. Slight interspecific morphological divergence and the independence of hybridization capabilities from phylogeny are not unexpected in a group in which species are allopatric and occupy similar habitats.     

Parental origin of the allotetraploid tobacco Nicotiana benthamiana

Nicotiana section Suaveolentes is an almost all‐Australian clade of allopolyploid tobacco species including the important plant model Nicotiana benthamiana. The homology relationships of this clade and its formation are not completely understood. To address this gap, we assessed phylogenies of all individual genes of N. benthamiana and the well studied N. tabacum (section Nicotiana) and their homologues in six diploid Nicotiana species. We generated sets of 44 424 and 65 457 phylogenetic trees of N. benthamiana and N. tabacum genes, respectively, each collectively called a phylome. Members of Nicotiana sections Noctiflorae and Sylvestres were represented as the species closest to N. benthamiana in most of the gene trees. Analyzing the gene trees of the phylome we: (i) dated the hybridization event giving rise to N. benthamiana to 4–5 MyA, and (ii) separated the subgenomes. We assigned 1.42 Gbp of the genome sequence to section Noctiflorae and 0.97 Gbp to section Sylvestres based on phylome analysis. In contrast, read mapping of the donor species did not succeed in separating the subgenomes of N. benthamiana. We show that the maternal progenitor of N. benthamiana was a member of section Noctiflorae, and confirm a member of section Sylvestres as paternal subgenome donor. We also demonstrate that the advanced stage of long‐term genome diploidization in N. benthamiana is reflected in its subgenome organization. Taken together, our results underscore the usefulness of phylome analysis for subgenome characterization in hybrid species.     

Mitochondrial DNA variation in pearl millet and related species

Summary Mitochondrial DNA (mtDNA) restriction endonuclease fragment patterns and patterns of mtDNA hybridized by mitochondrial gene probes were used to study phylogenetic relationships of seven Pennisetum species, including five P. americanum (pearl millet) ecotypes and a reference species from the distantly related genus, Panicum. The restriction patterns of the pearl millet ecotypes were uniform with the exception of the ecotype collected in Ethiopia. The probe hybridization method revealed more variability, with both the Rhodesian and Ethiopian ecotypes differing from the others and from each other. Considerable restriction pattern polymorphism was noted among different species of Pennisetum, and Panicum. Significant relationships were noted of Pennisetum polystachyon to P. pedicellatum and of P. purpureum to P. squamulatum using the restriction pattern method. In addition to those relationships, the hybridization method showed relationships of pearl millet to P. purpureum and to P. squamulatum. The relationships noted between species by the hybridization method agreed more closely to the cytological data than those indicated by the restriction pattern method. Therefore, the hybridization method appeared to be the preferred method for studying species relationships. The mitochondrial genome size of pearl millet was calculated to be 407 kb and the mitochondrial genome sizes of other Pennisetum species ranged from 341 to 486 kb.Florida Agricultural Experiment Station Journal Series No. 8485.     

NATURAL HYBRIDIZATION AMONG FOUR SPECIES OF BAPTISIA (LEGUMINOSAE)

Alston , R. E., and B. L. Turner . (U. Texas, Austin.) Natural hybridization among four species of Baptisia (Leguminosae). Amer. Jour. Bot. 50(2): 159–173. Illus. 1963.— Interspecific hybridization involving 4 species of Baptisia (B. leucophaea, B. sphaerocarpa, B. nuttalliana, and B. leucantha) has been studied by means of extensive field work and subsequent morphological and chromatographic analyses. As a result of these studies, numerous hybridizing populations involving any 2, 3 and, in 1 instance, 4 species have been located. Near Dayton, Texas, all 4 species and all 6 of the possible 2-way hybrid combinations have been found in a single field. Approximately 125 different chemical compounds have now been detected in the 4 species. Many of these compounds serve as species specific markers useful in the validation of specific hybrid types. Hybrids between B. leucophaea and B. sphaerocarpa and between B. leucophaea and B. nuttalliana are numerous, and in these large hybrid swarms a chromatographic and morphological analysis of population structure is possible. The former combination provides an excellent opportunity for the utilization of chemical markers as criteria for introgressive hybridization. The hybrid B. leucantha × B. sphaerocarpa is frequently encountered and contains a large number of compounds species-specific for one or the other parental species. The other 3 hybrid types have been found infrequently. Certain hybrid types are generally similar morphologically (e.g., B. leucantha × B. sphaerocarpa as opposed to B. leucantha × B. nuttalliana), and chromatographic techniques are of great value in the absolute identification of such plants, especially in complex populations where backcrossing further complicates the interpretation of the background of a plant from exomorphic features alone.     

Comparative plastid genomics of Pinus species: Insights into sequence variations and phylogenetic relationships

Pinus L. is the largest genus of conifers and provides a classical model for studying species divergence and phylogenetic evolution by gymnosperms. However, our poor understanding of sequence divergence in the whole plastid genomes of Pinus species severely hinders studies of their evolution and phylogeny. Thus, we analyzed the sequences of 97 Pinus plastid genomes, including four newly sequenced genomes and 93 previously published plastomes, to explore the evolution and phylogenetic relationships in the genus Pinus. The complete chloroplast genomes of Pinus species ranged in size from 109 640 bp (P. cembra L.) to 121 976 bp (P. glabra Walter), and these genomes comprised circular DNA molecules in a similar manner to those of most gymnosperms. We identified 9108 repeats where most of the repeats comprised the dispersed type with 3983 (44%), followed by tandem repeats with 2999 (33%), and then palindromic repeats with 2126 (23%). Sixteen divergence hotspot regions were identified in Pinus plastid genomes, which could be useful molecular markers for future population genetics studies. Phylogenetic analysis showed that Pinus species could be divided into two diverged clades comprising the subgenera Strobus (single needle section) and Pinus (double needles section). Molecular dating suggested that the genus Pinus originated approximately 130.38 Mya during the late Cretaceous. The two subgenera subsequently split 85.86 Mya, which was largely consistent with the other molecular results based on partial DNA markers. These findings provide important insights into the sequence variations and phylogenetic evolution of Pinus plastid genomes.     

Contrasting patterns of genetic diversity in two tropical pines: Pinus kesiya (Royle ex Gordon) and P. merkusii (Jungh et De Vriese)

We studied allozyme and chloroplast (cp) DNA variation in natural populations of Pinus kesiya and P. merkusii from Thailand and Vietnam. The results showed striking differences between the two species in the amount and distribution of allozyme variation. P. kesiya harboured considerable allozyme variation and showed weak interpopulational differentiation. In contrast, P. merkmii had very low intrapopulational variability but a high level of interpopulational differentiation. The average Nei's genetic distance separating the two species was exceptionally high (0.701) taking into account their close taxonomic placement in the same subsection Sylvestres. The constructed phylogenetic trees revealed very early divergence of P. kesiya and P. merkusii. The present analysis of cpDNA variation also confirmed the dissimilar character of these two species and was compatible with other evidence indicating the outstanding position of P. merkusii as compared to other Asian members of the subsection Sylvestres. Analysis of cpDNA variation in sympatric populations of P. kesiya and P. merkusii revealed that they are pure representatives of the species in question. This result indicates that despite an overlapping distribution P. kesiya and P. merkusii do not hybridise in nature. We suggest that the distinctive character of P. merkusii is a result of an early separation from other Eurasian pines. Despite spatial proximity, P. kesiya and P. merkusii are kept apart by strong reproductive barriers. The low genetic variability of P. merkusii may be explained by previous bottlenecks, reduced gene flow among populations, and an inbreeding due to small population size and asynchronous flowering.     

Phylogenetic analysis of pines using ribosomal DNA restriction fragment length polymorphisms

Phylogenetic relationships among 30 species of the genusPinus were studied using restriction site polymorphism in the large subunit of nuclear rDNA. Of the 58 restriction sites scored, 48 were phylogenetically informative, and the 30 species reduced to ten taxa when species with identical restriction site patterns were combined. These ten taxa corresponded to the currently recognized subsections of the genus, with the sole exception ofP. leiophylla, which was identical in its pattern of restriction sites to all three species included from subsect.Oocarpae despite its being in a different section of subg.Pinus (Pinea instead ofPinus). A measure of the proportion of phylogenetic information contained within the data set (Homoplasy Excess Ratio, or HER) revealed that the character states were significantly non-randomly distributed among the ten taxa (HER = 0.71, p < 0.01). Branchand-bound searches using either Wagner or Dollo parsimony as the optimization criterion were carried out using PAUP in order to estimate phylogenetic relationships among the ten taxa. Three taxa (Picea pungens, Tsuga canadensis, andLarix decidua) were used independently as outgroups for purposes of rooting the trees. Despite the extreme differences in the assumptions underlying the Wagner and Dollo parsimony, the two gave surprisingly similar estimates of phylogeny, with both analyses supporting the monophyly of the two major subgeneraPinus andStrobus and differing in topology only in the placement of subsect.Ponderosae within subg.Pinus. The likelihood for the Wagner tree was only slightly higher than that computed for the Dollo tree.     

Numerical taxonomic studies of the genus Pyrus using both chemical and botanical characters*

Of three computer-generated classifications of Pyrus species, produced respectively from 29 chemical characters, 22 botanical characters and all 51 characters taken together, the classification based upon both chemical and botanical characters agrees best with the known geographical distributions of the species. Where either chemical or botanical characters are separately employed, the classifications contain seriously misplaced species. The numerical classification based upon all 51 characters lends some support to the division of the genus into four principal groups of species: the East Asian pea pears, the larger-fruited East Asian pears, the North African pears and the European and West Asian pears. P. longipes, P. betulifolia and P. cordata are considered as being connecting links between the East Asian pea pears, the larger-fruited East Asian pears and the European and West Asian pears. Some speculations are made on the phylogenetic relationships among Pyrus species.     

HYBRIDIZATION BETWEEN ANNUAL SPECIES OF PHLOX: POPULATION STRUCTURE

Phlox cuspidata (n = 7) and P. drummondii subsp. drummondii (n = 7) are closely related annuals which are indigenous to eastern and central Texas. The species typically occupy different ecological niches but may form contiguous or confluent populations in disturbed habitats and hybridize therein. On the basis of correlative interpretations of exomorphic, chromatographic and fertility information, hybridizing populations can be segregated into three distinct classes: (1) highly fertile plants with the morphological and phenolic attributes of P. drummondii; (2) highly fertile plants with the morphological and chemical attributes of P. cuspidata; (3) sterile plants with manifestly intermediate morphology and complementary chromatographic patterns. These data strongly suggest that hybridizing populations of P. drummondii and P. cuspidata are tritypic, being composed of “pure” or essentially “pure” parental species and a group of plants which has all of the attributes characteristic of an F₁ hybrid.     

Pinus MUTOI (Pinaceae), a new species of permineralized seed cone from the upper Cretaceous of Hokkaido,Japan

Pinus mutoi is described as a new species on the basis of a permineralized seed cone from the Upper Cretaceous of Hokkaido, Japan. The cone is at least 20 cm long and up to 6 cm in diameter, consisting of a cone axis and numerous cone-scale complexes that are arranged helically around the axis. Two winged seeds are borne on the adaxial surface of each ovuliferous scale. Each complex receives a single trace from the vascular cylinder of the cone axis. In the scale base, all the resin canals occur abaxially to the vascular strand. The spatulate bract of the fossil is unique to the specimen among the cones of both living and fossil Pinus. The central umbo, broad sclerotic cortex of cone axis, and absence of serotinous features of the fossil cone suggest affinity with the subsection Sylvestres of the section Pinus, subgenus Pinus. This is the first record of permineralized preserved Pinus cone from the Cretaceous of Eastern Eurasia.     

PINUS WOLFEI,A NEW PETRIFIED CONE FROM THE EOCENE OF WASHINGTON

A silicified cone from the Late Eocene of Washington is described as a new fossil species of Pinus. The cone was probably 9–10 cm long and 3–5 cm at its widest diam in the living condition and is peculiar in having abundant resin canals in the secondary xylem of the axis arranged in three concentric rings near the cone base. The bract of the fossil is also unusual in having resin canals of distinctly unequal sizes and a vascular strand that is adaxially concave. In the absence of external features of the scale tips, these anatomical conditions along with the construction of the outer cortex of the axis of thick-walled cells suggest closest affinity of the new species with the subsections Contortae, Oocarpae, and Sylvestres of the section Pinus, subgenus Pinus.     

Multi‐locus phylogenetics,lineage sorting,and reticulation in Pinus subsection Australes

Premise of the Study

Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long‐lived, wind‐pollinated plants with large population sizes and weak reproductive barriers.

Methods

We used solution hybridization for targeted enrichment and massive parallel sequencing to characterize low‐copy‐number nuclear genes and high‐copy‐number plastomes (Hyb‐Seq) in 74 individuals of Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance. We inferred relationships using methods that account for both incomplete lineage sorting and reticulation.

Key Results

Concatenation‐ and coalescent‐based trees inferred from nuclear genes mainly agreed with one another, but they contradicted the plastid DNA tree in recovering the Attenuatae (the California closed‐cone pines) and Oocarpae (the egg‐cone pines of Mexico and Central America) as monophyletic and the Australes sensu stricto (the southern yellow pines) as paraphyletic to the Oocarpae. The plastid tree featured some relationships that were discordant with morphological and geographic evidence and species limits. Incorporating gene flow into the coalescent analyses better fit the data, but evidence supporting the hypothesis that hybridization explains the non‐monophyly of the Attenuatae in the plastid tree was equivocal.

Conclusions

Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.     

Two new spontaneous hybrids of American hard pines from Pinus sect. Trifoliae (Pinaceae) found in the unique Russian Sochi Arboretum

In the 1990s, an extraordinarily abundant live collection of the genus Pinus, including 49 species, 4 subspecies, and 7 interspecific hybrids, found in the Sochi Arboretum in Russia on the northeast coast of the Black Sea, was taxonomically revised. Among these taxa, two previously unknown interspecific hybrids of American hard pine species from P. sect. Trifoliae had arisen spontaneously in culture. These are described here as the new hybrid species Pinus × transamericana (P. muricata × P. rigida) and Pinus × critchfieldii (P. patula × P. taeda). All known natural or artificial interspecific hybrids within P. sect. Trifoliae are listed, and hybridization between American hard pine species is discussed. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The value of leaf cuticle characteristics in the identification and classification of Iberian Mediterranean members of the genus Pinus

This study reports the value of leaf cuticle characteristics in the identification and classification of Iberian Mediterranean species of the genus Pinus (P. nigra subsp. salzmannii, P. pinaster, P. pinea and P. halepensis), with the aim of using these characters to identify isolated cuticles and stomata in palynology slides. Preparations were made of the cuticles of pine needles belonging to one natural Iberian population of each of the above species. A number of epidermal morphological characteristics were then recorded with the aim of distinguishing these species from one another. The structure of the stomatal complex (the shape and arrangement of the subsidiary cells) was different in each species. The aperture of the epistomatal chamber was significantly smaller in P. pinea than in the other species examined, and the variables recorded for the thickening of the guard cells provided relationships that clearly distinguished all four taxa. The width and length of the stomata and the upper woody lamellae, the central distance between the external limits of the medial lamellae borders and the length of the stem were the most useful variables in this respect. The present results contribute to the ongoing discussion regarding the taxonomic classification of the members of Pinus, and provide valuable clues for the identification of Iberian Mediterranean pine species from small pine needle fragments or isolated stomata. After validation of the present results for multiple populations, these results could also be used to help identify fossil leaf macroremains and the scattered/isolated stomata commonly observed in palaeopalynological samples. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161 , 436–448.     

Competitive outcomes between two exotic invaders are modified by direct and indirect effects of a native conifer

When organisms interact in multi‐species groups, the direct effects of facilitation and competition can be modified by indirect interactions. We explored multispecies interactions among the native Pinus ponderosa, the invasive annual grass Bromus tectorum, and the invasive forb Centaurea stoebe in intermountain prairie of the northern Rocky Mountains. Centaurea is much less abundant under Pinus than in surrounding open grassland and Bromus is more abundant under Pinus. We found that the more fertile soil associated with Pinus facilitated both invasive species and did not alter competitive outcomes. Pinus litter and litter leachate inhibited both species, but litter also shifted competitive outcomes in favor of Bromus and against Centaurea. The effects of Pinus litter leachate were also strong and leachate eliminated the competitive effect of Centaurea on Bromus while not changing the competitive effect of Bromus on Centaurea. There are many other ways that Pinus may affect understory composition, but by altering the competitive playing field through leaf litter Pinus appears to indirectly facilitate Bromus by more strongly inhibiting Centaurea chemically, an unusual case of a native inhibiting an invader through allelopathy. Our results also provide an unexpected and novel perspective on indirect interactions among competitors, but not through intransitive competitive relationships. Instead, one species (Pinus) strongly ‘modified’ interactions between two other species in addition to disproportionately affecting one species more than another.     

MITOCHONDRIAL DNA VARIATION WITHIN AND BETWEEN SPECIES OF THE PAPILIO MACHAON GROUP OF SWALLOWTAIL BUTTERFLIES

Species limits and phylogenetic relationships in the Papilio machaon species group are potentially confounded by a complex pattern of Pleistocene range fragmentation, hybridization, and ecological race formation. Mitochondrial DNA (mtDNA) restriction-site analysis has been used to define genetic affinities and genetic population structure within this species group. The distribution of mtDNA haplotypes generally confirms prior phylogenetic hypotheses and species delineations, but there is poor correspondence between ecological races and mtDNA haplotypes. The amount and distribution of mtDNA sequence variation within species vary among species, reflecting differences in current patterns of gene flow and/or historical population structure. In spite of wing pattern characters that ally them with P. polyxenes, both P. joanae and P. brevicauda have mtDNA that is closely related to that of P. machaon. We suggest that P. joanae and P. brevicauda are of hybrid origin.