Phylogeny of Populus-Salix (Salicaceae) and their relative genera using molecular datasets

Although extensive studies have demonstrated that several genera formerly placed in the family Flacourtiaceae are the closest relatives of Populus-Salix. However, the closest relative or relatives remain uncertain due to the relatively low phylogenetic resolution and insufficient phylogenetic information. In addition, the question as to whether Populus and Salix are truly monophyletic remains open because of the absence of comprehensive studies with large-scale samples of both genera. In the present study, 54 species representing 11 genera of Salicaceae sensu lato (now including the genera of Flacourtiaceae) were studied using a combined rbcL and matK gene sequence dataset with a total length of 2134 bp, to explore the closest genera that are relatives of Populus-Salix and to determine the relationships between Populus and Salix. The resulting phylogenetic trees showed high resolution in each of the main clades. The results confirmed that (1) Idesia and Bennettiodendron are the closest relatives to Populus-Salix, followed by Poliothyrsis, and (2) Populus and Salix are a truly monophyletic lineage in which the most recent ancestor is shared by the two genera. This finding is significant for a wide variety of evolutionary studies and for understanding the classification and biosystematics of Salicaceae.     

Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows

Phylogenetic relationships and lineage diversification of the family Salicaceae sensu lato (s.l.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, Flacourtia was identified as the most basal and the successive clades comprised both Itoa and Poliothyrsis, Idesia, two genera of the Salicaceae sensu stricto (s.s.) (Populus and Salix). Five major subclades were recovered within the Populus clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the Salix clade. Molecular dating suggested that species diversification of the major subclades in the Populus and Salix clades occurred mainly within the recent Pliocene. In addition, we found that the rpl32 gene was lost and the rps7 gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae s.l. Compared with previous studies, our results provide a well‐resolved phylogeny from the perspective of the plastomes.     

More Malpighiales: Woods of Achariaceae and/or Salicaceae from the Deccan Intertrappean beds,India

The families Achariaceae and Salicaceae (Malpighiales) are characterized by wood anatomical ranges that partly overlap. Formerly these families were treated together in the polyphyletic Flacourtiaceae and a much more narrowly circumscribed Salicaceae. Here we attribute two recently collected fossil woods from the Deccan Intertrappean Beds to the clade that contain these two families, i.e., the Parietal Clade of the Malpighiales. The new genus Elioxylon shares features with several extant genera of Achariaceae and Salicaceae, but does not completely match with any of them. A new record of Hydnocarpoxylon indicum Bande & Khatri is a good match for extant Hydnocarpus Gaertn. (Achariaceae). Elioxylon and Hydnocarpoxylon share an absence of parenchyma, the presence of septate fibres and 1–3 seriate heterocellular rays with long uniseriate margins consistent with Achariaceae and Salicaceae. Elioxylon has mixed simple and scalariform perforations, whereas Hydnocarpxylon has exclusively scalariform perforations. Other Deccan fossils formerly attributed to “Flacourtiaceae” in the literature are critically discussed and mostly excluded from Achariaceae and Salicaceae. Elioxylon and Hydnocarpoxylon from the Maastrichtian ‐ Danian of India are the oldest fossil records of the Parietal Clade of the Malpighiales. With their occurrence on the Indian plate during its northward journey from Gondwana to Laurasia, these fossils provide further support for an ‘out‐of‐India’ hypothesis for Achariaceae and/or Salicaceae. “Baileyan trends” in vessel perforation plate and vessel grouping evolution are apparent in the phylogeny of the Parietal Clade.     

Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments

Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1) the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2) three advanced sections (Populus, Aigeiros and Tacamahaca) are of hybrid origin; (3) species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4) many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments.     

Divergence of 3′ ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae

Short interspersed nuclear elements (SINEs) are small, non‐autonomous and heterogeneous retrotransposons that are widespread in plants. To explore the amplification dynamics and evolutionary history of SINE populations in representative deciduous tree species, we analyzed the genomes of the six following Salicaceae species: Populus deltoides, Populus euphratica, Populus tremula, Populus tremuloides, Populus trichocarpa, and Salix purpurea. We identified 11 Salicaceae SINE families (SaliS‐I to SaliS‐XI), comprising 27 077 full‐length copies. Most of these families harbor segmental similarities, providing evidence for SINE emergence by reshuffling or heterodimerization. We observed two SINE groups, differing in phylogenetic distribution pattern, similarity and 3′ end structure. These groups probably emerged during the ‘salicoid duplication’ (~65 million years ago) in the Salix–Populus progenitor and during the separation of the genus Salix (45–65 million years ago), respectively. In contrast to conserved 5′ start motifs across species and SINE families, the 3′ ends are highly variable in sequence and length. This extraordinary 3′‐end variability results from mutations in the poly(A) tail, which were fixed by subsequent amplificational bursts. We show that the dissemination of newly evolved 3′ ends is accomplished by a displacement of older motifs, leading to various 3′‐end subpopulations within the SaliS families.     

Xylem-specific and tension stress-responsive coexpression of KORRIGAN endoglucanase and three secondary wall-associated cellulose synthase genes in aspen trees

In nature, angiosperm trees develop tension wood on the upper side of their leaning trunks and drooping branches. Development of tension wood is one of the straightening mechanisms by which trees counteract leaning or bending of stem and resume upward growth. Tension wood is characterized by the development of a highly crystalline cellulose-enriched gelatinous layer next to the lumen of the tension wood fibers. Thus experimental induction of tension wood provides a system to understand the process of cellulose biosynthesis in trees. Since KORRIGAN endoglucanases (KOR) appear to play an important role in cellulose biosynthesis in Arabidopsis, we cloned PtrKOR, a full-length KOR cDNA from aspen xylem. Using RT-PCR, in situ hybridization, and tissue-print assays, we show that PtrKOR gene expression is significantly elevated on the upper side of the bent aspen stem in response to tension stress while KOR expression is significantly suppressed on the opposite side experiencing compression stress. Moreover, three previously reported aspen cellulose synthase genes, namely, PtrCesA1, PtrCesA2, and PtrCesA3 that are closely associated with secondary cell wall development in the xylem cells exhibited similar tension stress-responsive behavior. Our results suggest that coexpression of these four proteins is important for the biosynthesis of highly crystalline cellulose typically present in tension wood fibers. Their simultaneous genetic manipulation may lead to industrially relevant improvement of cellulose in transgenic crops and trees.Suchita Bhandari and Takeshi Fujino contributed equally to this research.     

Reserve Lipids in Stem Root Primordia of Poplar

Lipids are reserve substances in stem root primordia of poplarand occur as droplets approximately uniformly in all cells ofroot primordia. In ultrathin sections they appear as sphericalelectron-dense particles (0.5–1.4 µm diameter),filling up virtually all the available space in the cytoplasm.The presence of lipids in stem root primordia was demonstratedin several species of the genus Populus from the section Aigeirosand Tacamahaca, as well as in another representative of thefamily Salicaceae, viz. in the genus Salix.     

Contributions to the Wood Anatomy of the Rubioideae (Rubiaceae)

Damnacanthus , Lasianthus, Saldinia, and Trichostachys are also included. Wood anatomical characters are compared with recent phylogenetic insights into the study group on the basis of molecular data. The observations demonstrate that the delimitation and separation of several taxa from the former Coussareeae/Morindeae/Prismatomerideae/Psychotrieae aggregate is supported by wood anatomical data. The Coussareeae can be distinguished from the other Rubioideae by their scanty parenchyma, septate libriform fibres, and the combination of uniseriate and very high multiseriate rays with sheath cells. Axial parenchyma bands and fibre-tracheids characterise Gynochtodes and some species of Morinda (Morindeae s.str.), but the latter genus is variable with respect to several features (e.g. vessel groupings and axial parenchyma distribution). Wood data support separation of Rennellia and Prismatomeris from Morindeae s.str.; vessels in both genera are exclusively solitary and axial parenchyma is always diffuse to diffuse-in-aggregates. Damnacanthus differs from the Morindeae alliance by the occurrence of septate fibres, absence of axial parenchyma, and the occasional presence of fibre wall thickenings. There are interesting similarities between members of the Lasianthus clade and the Pauridiantheae/Urophyleae group such as the sporadic occurrence of spiral thickenings in axial parenchyma cells. Received 26 January 2001/ Accepted in revised form 6 June 2001     

Phylogenetic position and revised classification of Acacia s.l. (Fabaceae: Mimosoideae) in Africa,including new combinations in Vachellia and Senegalia

Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need of reclassification. A proposal to conserve the name Acacia for the larger Australian contingent of the genus (formerly subgenus Phyllodineae) resulted in the retypification of the genus with the Australian A. penninervis. However, Acacia s.l. comprises at least four additional distinct clades or genera, some still requiring formal taxonomic transfer of species. These include Vachellia (formerly subgenus Acacia), Senegalia (formerly subgenus Aculeiferum), Acaciella (formerly subgenus Aculeiferum section Filicinae) and Mariosousa (formerly the A. coulteri group). In light of this fragmentation of Acacia s.l., there is a need to assess relationships of the non‐Australian taxa. A molecular phylogenetic study of Acacia s.l and close relatives occurring in Africa was conducted using sequence data from matK/trnK, trnL‐trnF and psbA‐trnH with the aim of determining the placement of the African species in the new generic system. The results reinforce the inevitability of recognizing segregate genera for Acacia s.l. and new combinations for the African species in Senegalia and Vachellia are formalized. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 500–523.     

Molecular phylogeny ofSalicaceae and closely relatedFlacourtiaceae: Evidence from 5.8 S, ITS 1 and ITS 2 of the rDNA

A ribosomal DNA region, including the entire 5.8S RNA gene and the internal transcribed spacers ITS 1 and ITS 2, was used for studying the phylogeny ofSalicaceae and the relationship betweenSalicaceae andFlacourtiaceae. The length of the ITS regions withinSalicaceae andFlacourtiaceae was similar to that found in other angiosperms. The GC content of both ITS regions was high, varying 62.7-72.2%. The most parsimonious tree clusters the wind-pollinatedChosenia bracteosa among theSalix species, suggesting that it should be included in the genusSalix. The grouping withinSalix leaves subg.Salix as paraphyletic, for which reason the subgeneric division is questionable.Populus was monophyletic and formed a sister group toSalix. The interspecific variation of the ITS sequences was very small inSalicaceae, which is in contradiction to the age of the group according to the evidence from fossil data.Idesia polycarpa fromFlacourtiaceae shows great sequence similarity withSalicaceae, but the analysis of 5.8S rDNA supports monophyly of the four species ofFlacourtiaceae sampled for this study.     

Changes in the Rooting and Growth of Willows and Poplars Induced by Cadmium

Growth parameters of six fast growing trees showed that the roots responded to Cd treatment more sensitively than the shoots. Cd-treatment suppressed rooting and root growth (length and biomass production) as well as its development in all tested species. Root systems of Salix cinerea, Salix alba, and Populus cv. Robusta were more tolerant to Cd stress than the root system of the other studied species. Shoot growth parameters of Salix species were significantly reduced unlike Populus species, which were not affected by Cd treatment.     

Phytoextraction of Risk Elements by Willow and Poplar Trees

To characterize the phytoextraction efficiency of two clones of willow trees (Salix x smithiana Willd., Salix rubens) and two clones of poplar trees (Populus nigra x maximowiczii, Populus nigra Wolterson) were planted in contaminated soil (0.4–2.0 mg Cd.kg^?1, 78–313 mg Zn.kg^?1, 21.3–118 mg Cu.kg^?1). Field experiment was carried out in Czech Republic. The study investigated their ability to accumulate heavy metals (Cd, Zn, and Cu) in harvestable plant parts. The poplars produced higher amount of biomass than willows. Both Salix clones accumulated higher amount of Cd, Zn and Cu in their biomass (maximum 6.8 mg Cd.kg^?1, 909 mg Zn.kg^?1, and 17.7 mg Cu.kg^?1) compared to Populus clones (maximum 2.06 mg Cd.kg^?1, 463 mg Zn.kg^?1, and 11.8 mg Cu.kg^?1). There were no significant differences between clones of individual species. BCs for Cd and Zn were greater than 1 (the highest in willow leaves). BCs values of Cu were very low. These results indicate that Salix is more suitable plant for phytoextraction of Cd and Zn than Populus. The Cu phytoextraction potential of Salix and Populus trees was not confirmed in this experiment due to low soil availability of this element.     

Alignment of a <Emphasis Type="Italic">Salix</Emphasis> linkage map to the <Emphasis Type="Italic">Populus</Emphasis> genomic sequence reveals macrosynteny between willow and poplar genomes

Poplars (genus Populus) and willows (genus Salix) are members of the Salicaceae, a family of catkin-bearing trees, shrubs and sub-shrubs. Poplar is considered the model system for biological studies in trees and considerable genetic and genomic resources have become available in recent years. The transfer of information to research studies in willow, for which fewer resources are currently available, would be highly beneficial. However, the extent of conservation between poplar and willow genomes has not yet been extensively studied. To address this, we have constructed a linkage map of willow based on a large mapping population derived from a cross between two Salix viminalis × (S. viminalis × S. schwerinii) hybrid sibs, and aligned this to the publicly available poplar genome sequence. A set of genome-wide, expressed poplar sequences was selected and used to design primer sets that efficiently amplified homeologous regions in willow. Direct sequencing of the willow products confirmed homology with the poplar target in the majority of instances and allowed identification of single nucleotide polymorphisms (SNPs) that were used to map these loci. In total, 202 amplified fragment length polymorphisms (AFLPs), 75 microsatellites and 79 SNPs were used to construct a willow consensus map that spanned 1,856.7 cM with an average interval between markers of 6.3 cM. Poplar sequences homologous to those of the mapped willow microsatellite loci were identified and used in addition to the SNP markers to putatively align all but two minor linkage groups to the poplar genome sequence. A high degree of macrosynteny was revealed.     

Development and characterization of microsatellite markers for the poplar rust fungi Melampsora medusae and Melampsora larici‐populina

Melampsora species and their hybrids are obligate parasites of Populus and Salix species worldwide. The increasing interest in Populus and Salix for biomass and fibre production necessitates genetic markers for population studies of Melampsora spp. Libraries enriched for simple sequence repeats were used to develop five microsatellite markers for Melampsora medusae and Melampsora larici‐populina. The variation detected by these markers will be valuable for phylogenetic and population genetic studies, substantiate putative hybrids, and deployment of resistant poplar clones.     

Diversity in specific gravity and water content of wood among Bornean tropical rainforest trees

Wood properties were measured for trees in lowland dipterocarp forests in West Kalimantan. In 1993 and 1994, 353 samples of 286 species were collected from trunk base of trees of approximately 5 cm in diameter, and the specific gravities (SG: oven dry weight/fresh volume) and water contents of wood including bark were measured. The SG of each species ranged from 0.21 to 0.84, and the mean ± SD was 0.53 ± 0.13. The wide range of SG suggests that the forest had a high diversity in wood properties. The most dominant and diversified genus in this area was Shorea, and the SG of 15 species varied from 0.21 to 0.71. The range covered SG of pioneer (six Macaranga, 0.29–0.43) and small trees in primary forests (nine Eugenia and 10 Xanthophyllum, 0.55–0.77). The SG average for tree species of secondary forests of 2–6 years old was 0.31. It was significantly smaller than that of primary forests (0.58). In a primary dipterocarp forest plot, light-wood species grew faster in diameter than heavy-wood species. Water content ranged from 0.26 to 0.76. Heavy wood had low water content. Among light-wood species, some (Shorea, Artocarpus) had low water contents and others (Ficus) had high water contents. Some riverine trees also had high water contents. These wood properties appear strongly related to the life history of trees and successional stage.     

G‐fibres in storage roots of Trifolium pratense (Fabaceae): tensile stress generators for contraction

Root contraction has been described for many species within the plant kingdom for over a century, and many suggestions have been made for mechanisms behind these contractions. To move the foliage buds deeper into the soil, the proximal part of the storage root of Trifolium pratense contracts by up to 30%. Anatomical studies have shown undeformed fibres next to strongly deformed tissues. Raman imaging revealed that these fibres are chemically and structurally very similar to poplar (Populus) tension wood fibres, which are known to generate high tensile stresses and bend leaning stems or branches upright. Analogously, an almost pure cellulosic layer is laid down in the lumen of certain root fibres, on a thin lignified secondary cell wall layer. To reveal its stress generation capacities, the thick cellulosic layer, reminiscent of a gelatinous layer (G‐layer) in tension wood, was selectively removed by enzymatic treatment. A substantial change in the dimensions of the isolated wood fibre bundles was observed. This high stress relaxation indicates the presence of high tensile stress for root contraction. These findings indicate a mechanism of root contraction in T. pratense (red clover) actuated via tension wood fibres, which follows the same principle known for poplar tension wood.     

Gut microbiomes of sympatric Amazonian wood‐eating catfishes (Loricariidae) reflect host identity and little role in wood digestion

Neotropical wood‐eating catfishes (family Loricariidae) can occur in diverse assemblages with multiple genera and species feeding on the same woody detritus. As such, they present an intriguing system in which to examine the influence of host species identity on the vertebrate gut microbiome as well as to determine the potential role of gut bacteria in wood digestion. We characterized the gut microbiome of two co‐occurring catfish genera and four species: Panaqolus albomaculatus, Panaqolus gnomus, Panaqolus nocturnus, and Panaque bathyphilus, as well as that of submerged wood on which they feed. The gut bacterial community did not significantly vary across three gut regions (proximal, mid, distal) for any catfish species, although interspecific variation in the gut microbiome was significant, with magnitude of interspecific difference generally reflecting host phylogenetic proximity. Further, the gut microbiome of each species was significantly different to that present on the submerged wood. Inferring the genomic potential of the gut microbiome revealed that the majority of wood digesting pathways were at best equivalent to and more often depleted or nonexistent within the catfish gut compared to the submerged wood, suggesting a minimal role for the gut microbiome in wood digestion. Rather, these fishes are more likely reliant on fiber degradation performed by microbes in the environment, with their gut microbiome determined more by host identity and phylogenetic history.     

Position of the genera <Emphasis Type="Italic">Lycenchelys</Emphasis> Gill and <Emphasis Type="Italic">Lycodapus</Emphasis> Gilbert in the family zoarcidae (Perciformes: Zoarcoidei) inferred from molecular genetic analysis

Sequence variation of the mitochondrial COI, cytochrome b, and 16S RNA genes, as well as nuclear RNF213 gene was examined in the genera Lycenchelys and Lycodapus with the purpose of determination of their positions in the system of the family Zoarcidae. It was demonstrated that the genus Lycodapus was considerably closer to the generic group of Lycogramminae (Lycogrammoides, Bothrocara, Allolepis, Bothrocarhichthys) than the genus Lycenchelys. However, on the phylogenetic trees both of these genera were located in the clade of the subfamily Lycodinae. Genetic heterogeneity of the genus Lycenchelys, represented by two species groups differing in distribution patterns (northeastern Pacific and Antarctic) and showing more profound differences than the genera of subfamily Lycodinae, was demonstrated.     

Phylogenetics and classification of the pantropical fern family Lindsaeaceae

The classification and generic definition in the tropical–subtropical fern family Lindsaeaceae have been uncertain and have so far been based on morphological characters only. We have now studied the evolutionary history of the Lindsaeaceae by simultaneously optimizing 55 morphological characters, two plastid genes (rpoC1 and rps4) and three non‐coding plastid intergenic spacers (trnL‐F, rps4‐trnS and trnH‐psbA). Our data set included all genera associated with Lindsaeaceae, except Xyropteris, and c. 73% of the currently accepted species. The phylogenetic relationships of the lindsaeoid ferns with two enigmatic genera that have recently been included in the Lindsaeaceae, Cystodium and Lonchitis, remain ambiguous. Within the monophyletic lindsaeoids, we found six well‐supported and diagnostic clades that can be recognized as genera: Sphenomeris, Odontosoria, Osmolindsaea, Nesolindsaea, Tapeinidium and Lindsaea. Sphenomeris was shown to be monotypic; most taxa formerly placed in that genus belong to the Odontosoria clade. Ormoloma is embedded within Lindsaea and therefore does not merit recognition as a genus. Tapeinidium is sister to a clade with some species formerly placed in Lindsaea that are morphologically distinct from that genus and are transferred to Osmolindsaea and Nesolindsaea, proposed here as two new genera. We do not maintain the current subgeneric classification of Lindsaea itself, because neither of the two generally accepted subgenera (Lindsaea and Odontoloma) is monophyletic, and most of the sections also appear unnatural. Nesolindsaea shows an ancient biogeographical link between Sri Lanka and the Seychelles and many of the main clades within Lindsaea have geographically disjunct distributions. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 305–359.