Phylogeny and evolutionary history of Pinaceae updated by transcriptomic analysis.

Pinaceae comprises 11 genera, and represents the largest family of conifers with an extensive wild distribution in the Northern Hemisphere. Intergeneric relationships of Pinaceae have been investigated using many morphological characters and molecular markers, but phylogenetic positions of four genera, including Cathaya, Cedrus, Nothotsuga and Pseudolarix, remain controversial or have not been completely resolved. To completely resolve the intergeneric relationships of Pinaceae, we conducted a comparative transcriptomic study of 14 species representing all Pinaceae genera. Multiple data sets, containing up to 6,369,681 sites across 4676 loci, were analyzed using concatenation and coalescent methods. Our study generated a robust topology, which divides Pinaceae into two clades, one (pinoid) including Cathaya, Larix, Picea, Pinus, and Pseudotsuga, and the other (abietoid) including Abies, Cedrus, Keteleeria, Nothotsuga, Pseudolarix, and Tsuga. Cathaya and Pinus form a clade sister to Picea; Cedrus is sister to the remaining abietoid genera, and the two genera Nothotsuga and Tsuga form a clade sister to Pseudolarix. The discordant positions of Cathaya, Cedrus and Pseudolarix in different gene trees could be explained by ancient radiation and/or molecular homoplastic evolution. The hybrid origin hypothesis of Nothotsuga is not supported. Based on molecular dating, extant Pinaceae genera diverged since about 206 Mya, earlier than the break-up of Pangea, and the divergence among the pinoid genera occurred earlier than the split among the abietoid genera. Moreover, our study indicates that two radiation events occurred in the evolution of Pinaceae genera, and some important morphological characters evolved multiple times based on ancestral state reconstruction.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.

Late Miocene Pseudolarix amabilis bract-scale complex from Zhejiang, East China.

Previously, the identification of fossil Pseudolarix at the species level has been based on the morphology of the bract-scale complex of the seed cone. The morphological consistence of fossils through most of the Cenozoic with extant P. amabilis has led them to be considered conspecific, suggesting that P. amabilis is an extraordinary example of morphological stasis. However, the lack of cuticular evidence, especially for the leaf-homologous bract, reduces the accuracy of fossil identification based on morphology, thus weakening the evidence for morphological stasis in P. amabilis. For the first time, we provide cuticular evidence of the bract-scale of fossil P. amabilis based on the bract-scale complex from the late Miocene Shengxian Formation, Zhejiang, East China, which improves the identification accuracy and reinforces the concept of morphological stasis in this species. Second, we preliminarily reveal the niche stability of P. amabilis, which corresponds to its morphological stasis. Finally, we infer that the late Miocene forest containing P. amabilis in Zhejiang was an evergreen sclerophyllous broad-leaved or mixed mesophytic forest, which combined with the evergreen broad-leaved forest suggested by previous megafossil studies, indicates the occurrence of vertical vegetation zonation.

The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae.

Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild.

The complete chloroplast genome of the Taiwan red pine Pinus taiwanensis (Pinaceae).

The complete nucleotide sequence of the Taiwan red pine Pinus taiwanensis Hayata chloroplast genome (cpDNA) is determined in this study. The genome is composed of 119,741 bp in length, containing a pair of very short inverted repeat (IRa and IRb) regions of 495 bp, which was divided by a large single-copy (LSC) region of 65,670 bp and a small single-copy (SSC) region of 53,080 bp in length. The cpDNA contained 115 genes, including 74 protein-coding genes (73 PCG species), 4 ribosomal RNA genes (four rRNA species) and 37 tRNA genes (22 tRNA species). Out of these genes, 12 harbored a single intron, and one (rps12) contained a couple of introns. The overall AT content of the Taiwan red pine cpDNA is 61.5%, while the corresponding values of the LSC, SSC and IR regions are 62.2%, 60.6% and 63.6%, respectively. A maximum parsimony phylogenetic analysis suggested that the genus Pinus, Picea, Abies and Larix were strongly supported as monophyletic, and the cpDNA of P. taiwanensis is closely related to that of P. thunbergii.

Taxonomic Revision of Pinus fujiii (Yasui) Miki (Pinaceae) and Its Implications for the Phytogeography of the Section Trifoliae in East Asia.

Pinus trifolia Miki 1939 (Pinaceae) was originally proposed based on seed cones from the upper Miocene of Aichi and Gifu Prefectures, central Japan. However, before the publication of P. trifolia, a different name (Pinus fujiii (Yasui) Miki) was given to a female cone with the same morphology. On the other hand, P. fujiii auct. non (Yasui) Miki has been used for seed cones with different morphologies from Yasui's holotype, i.e., apophyses arranged in 5:8 parastichies and a perexcentromucronate slightly-pointed umbo. As a result of re-examination on the Miki and Yasui specimens, we concluded that P. trifolia was a synonym for P. fujiii and proposed here Pinus mikii sp. nov. for cones assigned to P. fujiii auct. non (Yasui) Miki. We also emended the diagnosis of P. fujiii based on these specimens. Pinus fujiii is characterized by a large female cone in which the apophyses with a centromucronate prickle-like umbo are arranged in 8:13 parastichies, and deciduous seed wings. These characters suggest that P. fujiii belongs to the section Trifoliae of the subgenus Pinus, which is now restricted to North and Central America and the Caribbean islands. Fossil data suggest that the P. fujiii lineage firstly appeared in Japan around the Eocene/Oligocene boundary. We speculate that the P. fujiii lineage might have moved southward to Japan from a refugium located elsewhere in high-latitude areas in response to the late Eocene cooling event, as occurred with other Trifoliae species in North America.

A Multiscale Vibrational Spectroscopic Approach for Identification and Biochemical Characterization of Pollen.

BACKGROUND: Analysis of pollen grains reveals valuable information on biology, ecology, forensics, climate change, insect migration, food sources and aeroallergens. Vibrational (infrared and Raman) spectroscopies offer chemical characterization of pollen via identifiable spectral features without any sample pretreatment. We have compared the level of chemical information that can be obtained by different multiscale vibrational spectroscopic techniques. METHODOLOGY: Pollen from 15 different species of Pinales (conifers) were measured by seven infrared and Raman methodologies. In order to obtain infrared spectra, both reflectance and transmission measurements were performed on ground and intact pollen grains (bulk measurements), in addition, infrared spectra were obtained by microspectroscopy of multigrain and single pollen grain measurements. For Raman microspectroscopy measurements, spectra were obtained from the same pollen grains by focusing two different substructures of pollen grain. The spectral data from the seven methodologies were integrated into one data model by the Consensus Principal Component Analysis, in order to obtain the relations between the molecular signatures traced by different techniques. RESULTS: The vibrational spectroscopy enabled biochemical characterization of pollen and detection of phylogenetic variation. The spectral differences were clearly connected to specific chemical constituents, such as lipids, carbohydrates, carotenoids and sporopollenins. The extensive differences between pollen of Cedrus and the rest of Pinaceae family were unambiguously connected with molecular composition of sporopollenins in pollen grain wall, while pollen of Picea has apparently higher concentration of carotenoids than the rest of the family. It is shown that vibrational methodologies have great potential for systematic collection of data on ecosystems and that the obtained phylogenetic variation can be well explained by the biochemical composition of pollen. Out of the seven tested methodologies, the best taxonomical differentiation of pollen was obtained by infrared measurements on bulk samples, as well as by Raman microspectroscopy measurements of the corpus region of the pollen grain. Raman microspectroscopy measurements indicate that measurement area, as well as the depth of focus, can have crucial influence on the obtained data.

Conifer species adapt to low-rainfall climates by following one of two divergent pathways.

Water stress is one of the primary selective forces in plant evolution. There are characters often cited as adaptations to water stress, but links between the function of these traits and adaptation to drying climates are tenuous. Here we combine distributional, climatic, and physiological evidence from 42 species of conifers to show that the evolution of drought resistance follows two distinct pathways, both involving the coordinated evolution of tissues regulating water supply (xylem) and water loss (stomatal pores) in leaves. Only species with very efficient stomatal closure, and hence low minimum rates of water loss, inhabit dry habitats, but species diverged in their apparent mechanism for maintaining closed stomata during drought. An ancestral mechanism found in Pinaceae and Araucariaceae species relies on high levels of the hormone abscisic acid (ABA) to close stomata during water stress. A second mechanism, found in the majority of Cupressaceae species, uses leaf desiccation rather than high ABA levels to close stomata during sustained water stress. Species in the latter group were characterized by xylem tissues with extreme resistance to embolism but low levels of foliar ABA after 30 d without water. The combination of low levels of ABA under stress with cavitation-resistant xylem enables these species to prolong stomatal opening during drought, potentially extending their photosynthetic activity between rainfall events. Our data demonstrate a surprising simplicity in the way conifers evolved to cope with water shortage, indicating a critical interaction between xylem and stomatal tissues during the process of evolution to dry climates.

[Physical factors influencing the floristic relationships of pinyon pine (Pinaceae) from San Luis Potosi, Mexico]. / Factores físicos que influyen en las relaciones florísticas de los piñonares (Pinaceae) de San Luis Potosí, México.

In plant communities, the species distribution patterns and their relationships with environmental factors are of central importance in ecology. In San Luis Potosí of Mexico, woodlands of Pinus cembroides and P. johannis are sympatric, but P. cembroides tends to be located in South and Southwest slopes, in more disturbed sites; unlike, P. johannis, is mostly distributed in mesic areas, in North and Northeast slopes. The aim of this study was to analyze the influence of some physical factors on the floristic similarity of pinyon pine P. cembroides and P. johannis. The study area was located in the Sierra San Miguelito, San Luis Potosí, Mexico. We selected 40 sampling units spread over an area of 50km2. In each unit, we laid out two 20m long lines perpendicular to each other, in which we recorded cover data of the plant species intercepted. We developed two data matrices, the first one including cover values of 91 species, and the second one, considering seven topographical, climatic, and solar radiation variables. We applied cluster analysis and ordination to explore the influence of environmental variables on the floristic differentiation of pinyon pine woodlands. Clustering showed six groups, the first three characterized by P. cembroides. The ordination showed that variance represented by the first three axes was 65.9%. Axis 1 was positively correlated with altitude and negatively with mean annual temperature; axes two and three, showed low correlation with the variables tested. P. cembroides woodlands and accompanying flora tend to be located in lower altitude, higher mean annual temperature, and mainly in South-Southwestern slopes. In contrast, stands of P. johannis, mixed stands of P. johannis-P. cembroides, and Quercus potosina, were usually founded in greater altitudes, mean annual temperature slightly lower, and North-Northeastern exposure. The sites of these monospecific and mixed woodlands with associated species, indicators of environmental variables, generates the pre-diagnosis of the situation of the communities and their condition, so that future actions can be planned in agreement with the natural balance of the ecosystem.

Factores físicos que influyen en las relaciones florísticas de los piñonares (Pinaceae) de San Luis Potosí, México / Physical factors influencing the floristic relationships of pinyon pine (Pinaceae) from San Luis Potosi, Mexico

In plant communities, the species distribution patterns and their relationships with environmental factors are of central importance in ecology. In San Luis Potosi of Mexico, woodlands of Pinus cembroides and P. johannis are sympatric, but P. cembroides tends to be located in South and Southwest slopes, in more disturbed sites; unlike, P. johannis, is mostly distributed in mesic areas, in North and Northeast slopes. The aim of this study was to analyze the influence of some physical factors on the floristic similarity of pinyon pine P. cembroides and P. johannis. The study area was located in the Sierra San Miguelito, San Luis Potosi, Mexico. We selected 40 sampling units spread over an area of 50km². In each unit, we laid out two 20m long lines perpendicular to each other, in which we recorded cover data of the plant species intercepted. We developed two data matrices, the first one including cover values of 91 species, and the second one, considering seven topographical, climatic, and solar radiation variables. We applied cluster analysis and ordination to explore the influence of environmental variables on the floristic differentiation of pinyon pine woodlands. Clustering showed six groups, the first three characterized by P. cembroides. The ordination showed that variance represented by the first three axes was 65.9%. Axis 1 was positively correlated with altitude and negatively with mean annual temperature; axes two and three, showed low correlation with the variables tested. P. cembroides woodlands and accompanying flora tend to be located in lower altitude, higher mean annual temperature, and mainly in South-Southwestern slopes. In contrast, stands of P. johannis, mixed stands of P. johannis-P. cembroides, and Quercus potosina, were usually founded in greater altitudes, mean annual temperature slightly lower, and North-Northeastern exposure. The sites of these monospecific and mixed woodlands with associated species, indicators of environmental variables, generates the pre-diagnosis of the situation of the communities and their condition, so that future actions can be planned in agreement with the natural balance of the ecosystem.

El conocimiento de los patrones de distribución de especies en las comunidades vegetales y su relación con factores del medio es un objetivo fundamental en ecología. Las comunidades de Pinus cembroides y P. johannis coexisten en diversas regiones de México, pero P. cembroides tiende a distribuirse en laderas de exposiciones sur y suroeste en sitios deteriorados, a diferencia de P. johannis localizados en áreas mésicas en laderas con exposición norte y noreste. El objetivo de este trabajo fue analizar la influencia de algunos factores físicos en la semejanza florística de los piñonares de P. cembroides y P. johannis. El área de estudio se ubica en la Sierra San Miguelito, San Luis Potosí, México. Se seleccionaron 40 unidades de muestreo, distribuidas en una superficie de 50km²; en cada una se trazaron dos líneas de 20m perpendiculares entre sí, donde se registró la cobertura de los individuos interceptados. Se elaboraron dos tipos de matrices de datos: la primera con los valores de cobertura de 91 especies y la segunda, con siete variables topográficas, climáticas y de incidencia solar. Se aplicaron análisis de agrupamiento y de ordenación para explorar la influencia de variables ambientales en la diferenciación florística de los piñonares. El agrupamiento diferenció seis grupos; los tres primeros caracterizados por bosques de P. cembroides. La ordenación mostró que la varianza representada por los tres primeros ejes fue de 65.9%. El eje uno se correlacionó positivamente con la altitud y negativamente con la temperatura media anual y la orientación; los ejes dos y tres mostraron bajos valores de correlación con las variables probadas. Se observó que los piñonares de P. cembroides y flora acompañante, tienden a localizarse en sitios de menor altitud, con mayor temperatura media anual y en laderas con orientación al sur y suroeste. En contraste, los sitios de P. johannis, los de P. johannis-P. cembroides y de éstos con Quercus potosina, por lo regular están ubicados en condiciones de mayor altitud, temperatura media anual baja y con orientación al norte-noreste. La localización de estos bosques monoespecíficos y mixtos junto con las especies asociadas, indicadoras de variables ambientales, genera el pre-diagnóstico de la situación de las comunidades y su condición, para que en el futuro se planifiquen acciones acordes con el balance natural ecosistémico.

Development and characterization of 16 polymorphic microsatellite markers from Taiwan cow-tail fir, Keteleeria davidiana var. formosana (Pinaceae) and cross-species amplification in other Keteleeria taxa.

BACKGROUND: Keteleeria davidiana var. formosana (Pinaceae), Taiwan cow-tail fir, is an endangered species listed on the IUCN Red List of Threatened Species and only two populations remain, both on the Taiwan Island. Sixteen polymorphic microsatellite loci were developed in an endangered and endemic gymnosperm species, Keteleeria davidiana var. formosana, and were tested in an additional 6 taxa, K. davidiana var. calcarea, K. davidiana var. chienpeii, K. evelyniana, K. fortunei, K. fortunei var. cyclolepis, and K. pubescens, to evaluate the genetic variation available for conservation management and to reconstruct the phylogeographic patterns of this ancient lineage. FINDINGS: Polymorphic primer sets were developed from K. davidiana var. formosana using the modified AFLP and magnetic bead enrichment method. The number of alleles ranged from 3 to 16, with the observed heterozygosity ranging from 0.28 to 1.00. All of the loci were found to be interspecifically amplifiable. CONCLUSIONS: These polymorphic and transferable loci will be potentially useful for future studies that will focus on identifying distinct evolutionary units within species and establishing the phylogeographic patterns and the process of speciation among closely related species.

Vector affinity and diversity of Geosmithia fungi living on subcortical insects inhabiting Pinaceae species in central and northeastern Europe.

Fungi from the genus Geosmithia (Ascomycota: Hypocreales) are associated with bark beetles (Coleoptera: Scolytinae), though little is known about ecology, diversity, and distribution of these fungi across beetle and its host tree species. This study surveyed the diversity, distribution and vector affinity of Geosmithia isolated from subcortical insects that colonized trees from the family Pinaceae in Central and Northeastern Europe. Twelve Geosmithia species were isolated from 85 plant samples associated with 23 subcortical insect species (including 14 bark beetle species). Geosmithia community composition was similar across different localities and vector species; although the fungal communities associated with insects that colonized Pinus differed from that colonizing other tree species (Abies, Larix, and Picea). Ten Geosmithia species from four independent phylogenetic lineages were not reported previously from vectors feeding on other plant families and seem to be restricted to the vectors from Pinaceae only. We conclude that presence of such substrate specificity suggests a long and stable association between Geosmithia and bark beetles.

Evolution of an ancient microsatellite hotspot in the conifer mitochondrial genome and comparison with other plants.

In plants, mitochondrial sequence tandem repeats (STRs) have been associated with intragenomic recombination, a process held responsible for evolutionary outcomes such as gene regulation or cytoplasmic male-sterility. However, no link has been established between the recurrent accumulation of STRs and increased mutation rates in specific regions of the plant mtDNA genome. Herein, we surveyed this possibility by comparing, in a phylogenetic context, the variation of a STR-rich mitochondrial intron (nad5-4) with eleven mtDNA genes devoid of STRs within Abies (Pinaceae) and its related genera. This intron has been accumulating repeated stretches, generated by at least three-independent insertions, before the split of the two Pinaceae subfamilies, Abietoideae and Pinoideae. The last of these insertions occurred before the divergence of Abies and produced, exclusively within this genus, a tenfold increase of both the indel and substitution rates in the STR hotspot of the intron. The regions flanking the STRs harbored mutation rates as low as those estimated in mitochondrial genes devoid of repeated stretches. Further searches in complete plant mtDNA genomes, and previous studies reporting polymorphic mtSTRs, revealed that repeated stretches are common in all sorts of plants, but their accumulation in STR hotspots appears to be taxa specific. Our study suggests a new mutagenic role for repeated sequences in the plant mtDNA.

Karyotype evolution in the Pinaceae: implication with molecular phylogeny.

The family Pinaceae is made up mostly of diploid species (2n = 24). Systematization of karyotype analysis was developed to make comparison of intra- and interspecific karyotypes among the Pinaceae more accurate and reliable. Considering all parameters, the genera Pseudotsuga and Pseudolarix have the "most derived" (or advanced) and asymmetric karyotypes in the Pinaceae, followed by Larix, Picea, Abies, and Cedrus. The genus Pinus was the "least derived" (or ancestral) of all the genera of the Pinaceae analyzed. Differences in karyotype formulae and asymmetry indices were found among species within the same genera, suggesting that structural changes may have contributed to the diversification of the genus. This review is a detailed analysis of comparative karyotyping based on similar parameters, including numeric data and cytogenetic information. Telomeric sequence repeats and rDNA distribution in the Pinaceae were surveyed. The role of transposition in rDNA chromosome distribution is analyzed. Cytogenetic implications of hybridization between related species are reported. Likewise, the relationships between molecular phylogenetic and karyotype evolution is discussed in light of several reports. Within many genera, chromosomal organization was conserved despite independent molecular divergence and adaptation through the evolutionary history of the species of the Pinaceae.

The seed cone Eathiestrobus gen. nov.: fossil evidence for a Jurassic origin of Pinaceae.

PREMISE OF THE STUDY: Pinaceae and nonpinoid species are sister groups within the conifer clade as inferred from molecular systematic comparisons of living species and therefore should have comparable geological ages. However, the fossil record for the nonpinoid lineage of extant conifer families is Triassic, nearly 100 million years older than the oldest widely accepted Lower Cretaceous record for Pinaceae. An anatomically preserved fossil conifer seed cone described here extends the stratigraphic range of Pinaceae nearly 30 million years, thus reducing the apparent discrepancy between evidence from the fossil record and inferences from systematic studies of living species. METHODS: Material was prepared as serial thin sections by the cellulose acetate peel technique, mounted on microscope slides, and viewed and photographed using transmitted light. KEY RESULTS: A large cylindrical cone consisting of bract-scale complexes that diverge from the cone axis in a helical phyllotaxis has bracts and scales that separate from each other in the midregion and are of equal length and of nearly equal width. The cone has two inverted and winged seeds that are attached to the adaxial surface of each cone scale and, thus, represents an early member of the Pinaceae. CONCLUSIONS: Eathiestrobus mackenziei gen. et sp. nov. extends the fossil record for well-documented members of the family Pinaceae from the Lower Cretaceous to the Kimmeridgian Stage of the Upper Jurassic. This species also clarifies the set of characters that are diagnostic for seed cones of Pinaceae and reveals possible plesiomorphic characters for seed cones of the family.

Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies.

As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies-Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix-Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix-Pseudotsuga-Piceae-Cathaya-Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, and Piceae-Cathaya-Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, Picea, and Cathaya-Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.

Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms.

According to PCR assays and sequencing, we now report the shared presence of two rps3 introns, namely the rps3i74 and the rps3i249, in the mitochondria of all the classes representing the surviving lineages of gymnosperms, and unveil several lineages experiencing intron loss. Interestingly, the rps3 intron gains and losses within the four groups of gymnosperms let us sort out the Pinaceae and the non-Pinaceae into intron (+)- and intron (-)-lineages, respectively. Worthy of mention is also the finding that only Gnetum within the Gnetales harbours both the rps3 introns. This intron distribution pattern is consistent with the hypothesis that the two rps3 introns were likely present in the common ancestor of the seed plants and, then, independently lost in the non-Pinaceae during gymnosperm evolution. The derived secondary structural model of the novel group IIA intron improves our understanding of the significance and origin of the extraordinary length polymorphisms observed among rps3i249 orthologs. Despite the remarkable structural plasticity to adopt and reject introns, the rps3 mRNAs undergo accurate processing by splicing and extensive editing in gymnosperm mitochondria. This study provides additional insights into the evolutionarily high dynamics of mitochondrial introns which may come and go in closely related plant species. The turnover of the mitochondrial rps3 group II introns seen among lineages of seed plants further suggests that these introns might be an additional signature to discriminate between particularly cryptical taxonomic groups for which there is a need of a further evaluation of their evolutionary affiliation.

Clear genetic structure of Pinus kwangtungensis (Pinaceae) revealed by a plastid DNA fragment with a novel minisatellite.

BACKGROUND AND AIMS: Pinus kwangtungensis is a five-needled pine, inhabiting isolated mountain tops, cliffs or slopes in the montane areas of southern China and northern Vietnam. Global warming and long-term deforestation in southern China threaten its existence and genetic integrity, and this species is listed as vulnerable in the China Species Red List. However, the level and distribution of genetic diversity in this vulnerable species are completely unknown. In this paper, the genetic diversity and structure are examined using paternally inherited plastid markers to shed light on its evolutionary history and to provide a genetic perspective for its conservation. METHODS: By means of direct sequencing, a new polymorphic fragment containing a minisatellite site was identified within the plastid genome of P. kwangtungensis. Using the minisatellite site along with five SNPs (one indel and four substitutions) within the same fragment, the population genetic structure and pollen flow were analysed in 17 populations of P. kwangtungensis in southern China. KEY RESULTS: Analysis of 227 individuals from 17 populations revealed ten haplotypes at the minisatellite site. The haplotype diversity at species level was relatively high (0.629). Genetic diversity of each population ranged from 0 to 0.779, and the western populations harboured more genetic variation than the eastern and Hainan populations, although the former appeared to have experienced a bottleneck in recent history. Population subdivision based on this site was high (F(ST) = 0.540 under IAM; R(ST) = 0.677 under SMM). Three major clusters (eastern, western and Hainan) were identified based on a neighbor-joining dendrogram generated from genetic distances among the populations. The genetic structures inferred from all the polymorphic sites and the SNPs were in concordance with that from the minisatellite site. CONCLUSIONS: The results suggest that there are at least three refugia for P. kwangtungensis and that populations in these refugia should be treated as separate evolutionarily significant units or conservation units. The high diversities in the western populations suggest that these were much larger in the past (e.g. glacial stages) and that the shrinking population size might have been caused by recent events (e.g. deforestation, global warming, etc.). The western populations should be given priority for conservation due to their higher genetic diversity and limited population sizes. It is concluded that the newly found minisatellite may serve as a novel and applicable molecular marker for unravelling evolutionary processes in P. kwangtungensis.

Cytogenetic and molecular characterization of the Abies alba genome and its relationship with other members of the Pinaceae.

Genome size, karyotype structure, heterochromatin distribution, position and number of ribosomal genes, as well as the ITS2 sequence of the internal transcribed spacer (ITS) were analysed in silver fir (Abies alba Mill.). The analysis also included characterization of the Arabidopsis-type of telomeric repeats in silver fir and in related species. The results were compared with results from other species of the Pinaceae, to evaluate phylogeny and chromosomal and molecular evolution in the Pinaceae. Integrated chromosomal data provided insights into chromosome and karyotype evolution in the Pinaceae. The evolutionary trend for GC-rich heterochromatic blocks seems to involve loss of blocks that are not associated with rDNA. Similarly, numerous large blocks of interstitial plant telomeric repeats that are typical for all analysed species of the genus Pinus were not observed in the evolutionarily younger genera, such as Abies, Picea and Larix. On the contrary, the majority of telomeric sequences in these three genera appeared confined to the chromosome ends. We confirmed the current position of Abies and Tsuga in subfamily Abietoideae and the position of Pinus in the subfamily Pinoideae based on ITS2 sequences. Pseudotsuga is placed together with Larix into the subfamily Laricoideae. We conclude that the current position of the genus Picea in the subfamily Abietoideae should be reconsidered and, possibly, the genus Picea should be reclassified as a separate subfamily, Piceoideae, as recently proposed.

Distinctions among conifer exudates by proton magnetic resonance spectroscopy.

Proton nuclear magnetic resonance spectra have been recorded of exudates harvested from 12 species from the family Araucariaceae, 40 from the Cupressaceae, and one from the Podocarpaceae. These spectra were compared with the spectra previously recorded of 82 species from the Pinaceae. These four families together represent all major groups of extant, resin-bearing conifers. A common set of 10 COSY two-dimensional cross-peaks generally define samples from the Pinaceae, a different set of six peaks define the Araucariaceae, and yet a third set of 10 peaks define the Cupressaceae, with a few exceptions. It is important that proton spectra can distinguish the Araucariaceae and the Cupressaceae, since carbon-13 spectra do not. The one-dimensional peaks not only confirm these familial distinctions but also often characterize genus and species uniquely.