Molecular and morphological evidence for a sister group relationship of the classes Armophorea and Litostomatea (Ciliophora, Intramacronucleata, Lamellicorticata infraphyl. nov.), with an account on basal litostomateans

Based solely on the localization of the cytostome, Cavalier-Smith (2004) divided the ciliate subphylum Intramacronucleata into three infraphyla: the Spirotrichia, including Armophorea and Spirotrichea; the Rhabdophora, containing exclusively Litostomatea; and the Ventrata, comprising the remaining six intramacronucleate classes. This scheme is supported largely by 18S rRNA phylogenetic analyses presented here, except for the placement of the Armophorea. We argue that this group does not belong to the Spirotrichia but forms a lineage together with the Litostomatea because the molecular sister relationship of the Armophorea and Litostomatea is supported by two morphological and morphogenetic synapomorphies: (i) plate-like arranged postciliary microtubule ribbons, forming a layer right of and between the ciliary rows and (ii) a telokinetal stomatogenesis. Thus, we unite them into a new infraphylum, Lamellicorticata, which replaces Cavalier-Smith's Rhabdophora. Further, our phylogenetic analyses consistently classify the most complex haptorian genus Dileptus basal to all other litostomateans, though morphological investigations suggest dileptids to be highly derived and possibly originating from a spathidiid ancestor. These discrepancies between molecular and morphological classifications have not as yet been investigated in detail. Thus, we propose an evolutionary scenario, explaining both the sister relationship of the Armophorea and Litostomatea, as well as the basal position of the morphologically complex dileptids.     

Multilocus phylogenetic analysis of the genus Aeromonas

A broad multilocus phylogenetic analysis (MLPA) of the representative diversity of a genus offers the opportunity to incorporate concatenated inter-species phylogenies into bacterial systematics. Recent analyses based on single housekeeping genes have provided coherent phylogenies of Aeromonas. However, to date, a multi-gene phylogenetic analysis has never been tackled. In the present study, the intra- and inter-species phylogenetic relationships of 115 strains representing all Aeromonas species described to date were investigated by MLPA. The study included the independent analysis of seven single gene fragments (gyrB, rpoD, recA, dnaJ, gyrA, dnaX, and atpD), and the tree resulting from the concatenated 4705 bp sequence. The phylogenies obtained were consistent with each other, and clustering agreed with the Aeromonas taxonomy recognized to date. The highest clustering robustness was found for the concatenated tree (i.e. all Aeromonas species split into 100% bootstrap clusters). Both possible chronometric distortions and poor resolution encountered when using single-gene analysis were buffered in the concatenated MLPA tree. However, reliable phylogenetic species delineation required an MLPA including several “bona fide” strains representing all described species.     

Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony,likelihood and species tree inference methods

Background and aims

Despite a recent new classification, a stable phylogeny for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study, five single-copy nuclear genes (SCNGs) are applied to the phylogeny of the order Cycadales. The specific aim is to evaluate several gene tree–species tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve the erstwhile problematic phylogenetic position of these three genera.

Methods

DNA sequences of five SCNGs were obtained for 20 cycad species representing all ten genera of Cycadales. These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene tree–species tree reconciliation, using Cycas as the outgroup. A calibrated date estimation was developed with Bayesian methods, and biogeographic analysis was also conducted.

Key Results

Concatenated parsimony, ML and three species tree inference methods resolve exactly the same tree topology with high support at most nodes. Dioon and Bowenia are the first and second branches of Cycadales after Cycas, respectively, followed by an encephalartoid clade (Macrozamia–Lepidozamia–Encephalartos), which is sister to a zamioid clade, of which Ceratozamia is the first branch, and in which Stangeria is sister to Microcycas and Zamia.

Conclusions

A single, well-supported phylogenetic hypothesis of the generic relationships of the Cycadales is presented. However, massive extinction events inferred from the fossil record that eliminated broader ancestral distributions within Zamiaceae compromise accurate optimization of ancestral biogeographical areas for that hypothesis. While major lineages of Cycadales are ancient, crown ages of all modern genera are no older than 12 million years, supporting a recent hypothesis of mostly Miocene radiations. This phylogeny can contribute to an accurate infrafamilial classification of Zamiaceae.     

Multilocus sequence analysis reveals multiple symbiovars within Mesorhizobium species

The genus Mesorhizobium includes species nodulating several legumes, such as chickpea, which has a high agronomic importance. Chickpea rhizobia were originally described as either Mesorhizobium ciceri or M. mediterraneum. However, rhizobia able to nodulate chickpea have been shown to belong to several different species within the genus Mesorhizobium. The present study used a multilocus sequence analysis approach to infer a high resolution phylogeny of the genus Mesorhizobium and to confirm the existence of a new chickpea nodulating genospecies. The phylogenetic structure of the Mesorhizobium clade was evaluated by sequence analysis of the 16S rRNA gene, ITS region and the five core genes atpD, dnaJ, glnA, gyrB, and recA. Phylogenies obtained with the different genes are in overall good agreement and a well-supported, almost fully resolved, phylogenetic tree was obtained using the combined data. Our phylogenetic analyses of core genes sequences and their comparison with the symbiosis gene nodC, corroborate the existence of one new chickpea Mesorhizobium genospecies and one new symbiovar, M. opportunistum sv. ciceri. Furthermore, our results show that symbiovar ciceri spreads over six species of mesorhizobia. To our knowledge this study shows the most complete Mesorhizobium multilocus phylogeny to date and contributes to the understanding of how a symbiovar may be present in different species.     

Phylogenetic relationships within Chamaecrista sect. Xerocalyx (Leguminosae, Caesalpinioideae) inferred from the cpDNA trnE-trnT intergenic spacer and nrDNA ITS sequences

Chamaecrista belongs to subtribe Cassiinae (Caesalpinioideae), and it comprises over 330 species, divided into six sections. The section Xerocalyx has been subjected to a profound taxonomic shuffling over the years. Therefore, we conducted a phylogenetic analysis using a cpDNA trnE-trnT intergenic spacer and nrDNA ITS/5.8S sequences from Cassiinae taxa, in an attempt to elucidate the relationships within this section from Chamaecrista. The tree topology was congruent between the two data sets studied in which the monophyly of the genus Chamaecrista was strongly supported. Our analyses reinforce that new sectional boundaries must be defined in the Chamaecrista genus, especially the inclusion of sections Caliciopsis and Xerocalyx in sect. Chamaecrista, considered here paraphyletic. The section Xerocalyx was strongly supported as monophyletic; however, the current data did not show C. ramosa (microphyllous) and C. desvauxii (macrophyllous) and their respective varieties in distinct clades, suggesting that speciation events are still ongoing in these specimens.     

Phylogenetic Analysis of the Hoplolaiminae Inferred from Combined D2 and D3 Expansion Segments of 28S rDNA

DNA sequences of the D2-D3 expansion segments of the 28S gene of ribosomal DNA from 23 taxa of the subfamily Hoplolaiminae were obtained and aligned to infer phylogenetic relationships. The D2 and D3 expansion regions are G-C rich (59.2%), with up to 20.7% genetic divergence between Scutellonema brachyurum and Hoplolaimus concaudajuvencus. Molecular phylogenetic analysis using maximum likelihood and maximum parsimony was conducted using the D2-D3 sequence data. Of 558 characters, 254 characters (45.5%) were variable and 198 characters (35.4%) were parsimony informative. All phylogenetic methods produced a similar topology with two distinct clades: One clade consists of all Hoplolaimus species while the other clade consists of the rest of the studied Hoplolaiminae genera. This result suggests that Hoplolaimus is monophyletic. Another clade consisted of Aorolaimus, Helicotylenchus, Rotylenchus, and Scutellonema species. Phylogenetic analysis using the outgroup species Globodera rostocheinsis suggests that Hoplolaiminae is paraphyletic. In this study, the D2-D3 region had levels of DNA sequence divergence sufficient for phylogenetic analysis and delimiting species of Hoplolaiminae.     

Genetic diversity of rhizobia nodulating lentil (Lens culinaris) in Bangladesh

In order to determine the bacterial diversity and the identity of rhizobia nodulating lentil in Bangladesh, we performed a phylogenetic analysis of housekeeping genes (16S rRNA, recA, atpD and glnII) and nodulation genes (nodC, nodD and nodA) of 36 bacterial isolates from 25 localities across the country. Maximum likelihood (ML) and Bayesian analyses based on 16S rRNA sequences showed that most of the isolates (30 out of 36) were related to Rhizobium etli and Rhizobium leguminosarum. Only these thirty isolates were able to re-nodulate lentil under laboratory conditions. The protein-coding housekeeping genes of the lentil nodulating isolates showed 89.1-94.8% genetic similarity to the corresponding genes of R. etli and R. leguminosarum. The same analyses showed that they split into three distinct phylogenetic clades. The distinctness of these clades from closely related species was also supported by high resolution ERIC-PCR fingerprinting and phenotypic characteristics such as temperature tolerance, growth on acid-alkaline media (pH 5.5-10.0) and antibiotic sensitivity. Our phylogenetic analyses based on three nodulation genes (nodA, nodC and nodD) and cross-inoculation assays confirmed that the nodulation genes are related to those of R. leguminosarum biovar viciae, but clustered in a distinct group supported by high bootstrap values. Thus, our multi-locus phylogenetic analysis, DNA fingerprinting and phenotypic characterizations suggest that at least three different clades are responsible for lentil nodulation in Bangladesh. These clades differ from the R. etli-R. leguminosarum group and may correspond to novel species in the genus Rhizobium.     

Phylogenetic analyses of a combined data set suggest that the Attheya lineage is the closest living relative of the pennate diatoms (Bacillariophyceae)

A Bayesian analysis of a seven gene data set was conducted to reconstruct phylogenetic relationships among a sample of centric and pennate diatoms and to test alternative hypotheses about the closest living relative of Bacillariophyceae. A lineage, composed of two Attheya species, was inferred to share the most recent common ancestor with Bacillariophyceae--a relationship that was also corroborated by the combined parsimony analysis. All competing hypotheses about the closest living relative of Bacillariophyceae were rejected because 100% of the trees in the post-burn-in sample in the Bayesian analysis supported the Attheya-Bacillariophyceae clade. According to a partitioned Bremer support analysis, the majority of the genes in the combined data matrix supported the Attheya--Bacillariophyceae relationship. The global topology of the phylogenetic tree indicated that a monophyletic group consisting of Thalassiosirales and Toxarium undulatum formed the deepest branch followed by a node uniting a clade composed of Bacillariophyceae/Attheya species and a lineage made up of Eucampia zoodiacus, Chaetocerotales, Lithodesmiales, Triceratiales, Biddulphiales and Cymatosirales. Except for the phylogenetic positions of Lithodesmiales, Thalassiosira sp and Skeletonema costatum, the optimal tree obtained from the combined parsimony analysis showed the same branching order of taxa as those seen in the consensus tree inferred from three independent Markov chain Monte Carlo analyses. Noteworthy findings are that Toxarium undulatum shares a strongly supported node with Thalassiosirales and that the genus Attheya is not a member of the Chaetocerotales lineage.     

Estimating trees from filtered data: Identifiability of models for morphological phylogenetics

As an alternative to parsimony analyses, stochastic models have been proposed ( [Lewis, 2001] and [Nylander et al., 2004]) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A key feature of these models is that they account for ascertainment bias, in that only varying, or parsimony-informative characters are observed. However, statistical consistency of such model-based inference requires that the model parameters be identifiable from the joint distribution they entail, and this issue has not been addressed.Here we prove that parameters for several such models, with finite state spaces of arbitrary size, are identifiable, provided the tree has at least eight leaves. If the tree topology is already known, then seven leaves suffice for identifiability of the numerical parameters. The method of proof involves first inferring a full distribution of both parsimony-informative and non-informative pattern joint probabilities from the parsimony-informative ones, using phylogenetic invariants. The failure of identifiability of the tree parameter for four-taxon trees is also investigated.     

基于叶绿体psaA和psbA基因的中国熊野藻属植物系统发育分析

以中国产熊野藻属Kumanoa的两个种, 绞扭熊野藻K. intorta (=绞扭串珠藻Batrachospermum intortum), 弯形熊野藻K. curvata (=弯形串珠藻B. curvatum)和其他6种淡水红藻为实验材料, 对其psaA和psbA基因进行扩增和测序, 并与GenBank中相近序列进行比对分析, 以贝叶斯法、最大似然法和邻接法分别构建了单基因和联合基因系统发育树. 结果表明, 3种方法构建的系统树具有相似的拓扑结构, 反映的系统发育关系基本一致, 熊野藻属中的两个种聚为一支, 与串珠藻属相分离, 支持该属的建立; 中国产的熊野藻属分子学研究结果与来自南美洲及澳洲的该属植物结果一致, 说明该属的建立具有广泛的地理适用性. 系统发育树聚类结果也明确反映了熊野藻属与串珠藻属较近的亲缘关系, 根据果胞枝形态特点, 推测熊野藻属进化地位晚于串珠藻属植物, 而早于顶丝藻目和红索藻目. 此外, 胶串珠藻与其他串珠藻组植物分离, 支持将其单独分组, 红索藻目植物与串珠藻目植物分离, 支持红索藻目的建立. 同时也表明psaA和psbA基因用于淡水红藻分析, 能够较好地反映其系统发育关系.       

Leaf trait co-ordination in relation to construction cost, carbon gain and resource-use efficiency in exotic invasive and native woody vine species

Background and Aims

Success of invasive plant species is thought to be linked with their higher leaf carbon fixation strategy, enabling them to capture and utilize resources better than native species, and thus pre-empt and maintain space. However, these traits are not well-defined for invasive woody vines.

Methods

In a glass house setting, experiments were conducted to examine how leaf carbon gain strategies differ between non-indigenous invasive and native woody vines of south-eastern Australia, by investigating their biomass gain, leaf structural, nutrient and physiological traits under changing light and moisture regimes.

Key Results

Leaf construction cost (CC), calorific value and carbon : nitrogen (C : N) ratio were lower in the invasive group, while ash content, N, maximum photosynthesis, light-use efficiency, photosynthetic energy-use efficiency (PEUE) and specific leaf area (SLA) were higher in this group relative to the native group. Trait plasticity, relative growth rate (RGR), photosynthetic nitrogen-use efficiency and water-use efficiency did not differ significantly between the groups. However, across light resource, regression analyses indicated that at a common (same) leaf CC and PEUE, a higher biomass RGR resulted for the invasive group; also at a common SLA, a lower CC but higher N resulted for the invasive group. Overall, trait co-ordination (using pair-wise correlation analyses) was better in the invasive group. Ordination using 16 leaf traits indicated that the major axis of invasive-native dichotomy is primarily driven by SLA and CC (including its components and/or derivative of PEUE) and was significantly linked with RGR.

Conclusions

These results demonstrated that while not all measures of leaf resource traits may differ between the two groups, the higher level of trait correlation and higher revenue returned (RGR) per unit of major resource need (CC) and use (PEUE) in the invasive group is in line with their rapid spread where introduced.     

Phylogenetic Relationships Among Selected Heteroderoidea Based on 18S and ITS Ribosomal DNA

In a study of relationships among selected cyst-forming and noncyst-forming species of Heteroderoidea, combined sequences comprised of DNA from part of the conserved 18S ribosomal RNA gene (rDNA) plus the complete ITS rDNA segment were more similar to analyses based on the ITS data alone than to analyses based on the 18S data alone. One of the two noncyst-forming species, Ekphymatodera thomasoni, grouped with cyst-forming species of Heteroderoidea. Bilobodera flexa, also a noncyst-forming species, was separated from all the other taxa by a long branch. Afenestrata koreana, with a weakly sclerotized cyst, grouped closely with H. bifenestra. These observations suggest that phylogenetic analyses using molecular data may aid in our understanding of the evolution of cyst formation in nematodes, including the possibility of secondary loss. The usefulness of molecular phylogenetic analyses in nematodes may depend more on the particular selection of taxa than on mere addition of data from additional genes.     

Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae

Background and Aims

Molecular phylogenetic studies of palms (Arecaceae) have not yet provided a fully resolved phylogeny of the family. There is a need to increase the current set of markers to resolve difficult groups such as the Neotropical subtribe Bactridinae (Arecoideae: Cocoseae). We propose the use of two single-copy nuclear genes as valuable tools for palm phylogenetics.

Methods

New primers were developed for the amplification of the AGAMOUS 1 (AG1) and PHYTOCHROME B (PHYB) genes. For the AGAMOUS gene, the paralogue 1 of Elaeis guineensis (EgAG1) was targeted. The region amplified contained coding sequences between the MIKC K and C MADS-box domains. For the PHYB gene, exon 1 (partial sequence) was first amplified in palm species using published degenerate primers for Poaceae, and then specific palm primers were designed. The two gene portions were sequenced in 22 species of palms representing all genera of Bactridinae, with emphasis on Astrocaryum and Hexopetion, the status of the latter genus still being debated.

Key Results

The new primers designed allow consistent amplification and high-quality sequencing within the palm family. The two loci studied produced more variability than chloroplast loci and equally or less variability than PRK, RPBII and ITS nuclear markers. The phylogenetic structure obtained with AG1 and PHYB genes provides new insights into intergeneric relationships within the Bactridinae and the intrageneric structure of Astrocaryum. The Hexopetion clade was recovered as monophyletic with both markers and was weakly supported as sister to Astrocaryum sensu stricto in the combined analysis. The rare Astrocaryum minus formed a species complex with Astrocaryum gynacanthum. Moreover, both AG1 and PHYB contain a microsatellite that could have further uses in species delimitation and population genetics.

Conclusions

AG1 and PHYB provide additional phylogenetic information within the palm family, and should prove useful in combination with other genes to improve the resolution of palm phylogenies.     

New insights into Trimezieae (Iridaceae) phylogeny: what do molecular data tell us?

Background and Aims

The Neotropical tribe Trimezieae are taxonomically difficult. They are generally characterized by the absence of the features used to delimit their sister group Tigridieae. Delimiting the four genera that make up Trimezieae is also problematic. Previous family-level phylogenetic analyses have not examined the monophyly of the tribe or relationships within it. Reconstructing the phylogeny of Trimezieae will allow us to evaluate the status of the tribe and genera and to examine the suitability of characters traditionally used in their taxonomy.

Methods

Maximum parsimony and Bayesian phylogenetic analyses are presented for 37 species representing all four genera of Trimezieae. Analyses were based on nrITS sequences and a combined plastid dataset. Ancestral character state reconstructions were used to investigate the evolution of ten morphological characters previously considered taxonomically useful.

Key Results

Analyses of nrITS and plastid datasets strongly support the monophyly of Trimezieae and recover four principal clades with varying levels of support; these clades do not correspond to the currently recognized genera. Relationships within the four clades are not consistently resolved, although the conflicting resolutions are not strongly supported in individual analyses. Ancestral character state reconstructions suggest considerable homoplasy, especially in the floral characters used to delimit Pseudotrimezia.

Conclusions

The results strongly support recognition of Trimezieae as a tribe but suggest that both generic- and species-level taxonomy need revision. Further molecular analyses, with increased sampling of taxa and markers, are needed to support any revision. Such analyses will help determine the causes of discordance between the plastid and nuclear data and provide a framework for identifying potential morphological synapomorphies for infra-tribal groups. The results also suggest Trimezieae provide a promising model for evolutionary research.     

Thaptomys Thomas 1915 (Rodentia, Sigmodontinae, Akodontini) with karyotypes 2n = 50, FN = 48, and 2n = 52, FN = 52: Two monophyletic lineages recovered by molecular phylogeny

A novel karyotype with 2n = 50, FN = 48, was described for specimens of Thaptomys collected at Una, State of Bahia, Brazil, which are morphologically indistinguishable from Thaptomys nigrita, 2n = 52, FN = 52, found in other localities. It was hence proposed that the 2n = 50 karyotype could belong to a distinct species, cryptic of Thaptomys nigrita, once chromosomal rearrangements observed, along with the geographic distance, might represent a reproductive barrier between both forms. Phylogenetic analyses using maximum parsimony and maximum likelihood based on partial cytochrome b sequences with 1077 bp were performed, attempting to establish the relationships among the individuals with distinct karyotypes along the geographic distribution of the genus; the sample comprised 18 karyotyped specimens of Thaptomys, encompassing 15 haplotypes, from eight different localities of the Atlantic Rainforest. The intra-generic relationships corroborated the distinct diploid numbers, once both phylogenetic reconstructions recovered two monophyletic lineages, a northeastern clade grouping the 2n = 50 and a southeastern clade with three subclades, grouping the 2n = 52 karyotype. The sequence divergence observed between their individuals ranged from 1.9% to 3.5%.     

A world-wide perspective on crucifer speciation and evolution: phylogenetics,biogeography and trait evolution in tribe Arabideae

Background and Aims

Tribe Arabideae are the most species-rich monophyletic lineage in Brassicaceae. More than 500 species are distributed in the majority of mountain and alpine regions worldwide. This study provides the first comprehensive phylogenetic analysis for the species assemblage and tests for association of trait and characters, providing the first explanations for the enormous species radiation since the mid Miocene.

Methods

Phylogenetic analyses of DNA sequence variation of nuclear encoded loci and plastid DNA are used to unravel a reliable phylogenetic tree. Trait and ancestral area reconstructions were performed and lineage-specific diversification rates were calculated to explain various radiations in the last 15 Myr in space and time.

Key Results

A well-resolved phylogenetic tree demonstrates the paraphyly of the genus Arabis and a new systematic concept is established. Initially, multiple radiations involved a split between lowland annuals and mountain/alpine perennial sister species. Subsequently, increased speciation rates occur in the perennial lineages. The centre of origin of tribe Arabideae is most likely the Irano-Turanian region from which the various clades colonized the temperate mountain and alpine regions of the world.

Conclusions

Mid Miocene early diversification started with increased speciation rates due to the emergence of various annual lineages. Subsequent radiations were mostly driven by diversification within perennial species during the Pliocene, but increased speciation rates also occurred during that epoch. Taxonomic concepts in Arabis are still in need of a major taxonomic revision to define monophyletic groups.     

How the timberline formed: altitudinal changes in stand structure and dynamics around the timberline in central Japan

Background and Aims

Altitudinal timberlines are thought to move upward by global warming, a crucial topic in ecology. Tall tree species (the conifer Abies mariesii and the deciduous broad-leaved Betula ermanii) dominate the sub-alpine zone between 1600 and 2500 m a.s.l., the timberline, on Mount Norikura in central Japan. Dwarf pine Pinus pumila dominates above the timberline to near the summit (3026 m a.s.l.). This study evaluated how the timberline formed on Mount Norikura by examining altitudinal changes in stand structure and dynamics around the timberline.

Methods

One hundred and twenty-five plots of 10 m × 10 m were established around the timberline (2350–2600 m a.s.l.). Trunk diameter growth rate during 6 years was examined for A. mariesii, B. ermanii and P. pumila. Mortality during this period and mechanical damage scars on the trunks and branches due to strong wind and snow were examined for A. mariesii only.

Key Results

The density, maximum trunk height and diameter of A. mariesii in plots decreased with altitude. The maximum trunk height of B. ermanii decreased with altitude, but density and maximum trunk diameter did not decrease. In contrast, the density of P. pumila abruptly increased from around the timberline. A strong negative correlation was found between the densities of P. pumila and tall tree species, indicating their interspecific competition. Trunk diameter growth rates of A. mariesii and B. ermanii did not decrease with altitude, suggesting that these two tall tree species can grow at the timberline. The ratio of trees with mechanical damage scars increased with altitude for A. mariesii, a tendency more conspicuous for larger trees. The mortality of larger A. mariesii was also greater at higher altitude. Tall tree species may not increase their trunk height and survive around the timberline because of mechanical damage.

Conclusions

This study suggests that the altitudinal location of the timberline is mainly affected by mechanical damage due to strong wind and snow rather than by growth limitation due to low temperature. Therefore, the timberline would not move upward even under global warming if these growth and mortality characteristics do not change for a long time.