Clades In Trees Research Articles

Nitrogen addition increases mass loss of gymnosperm but not of angiosperm deadwood without changing microbial communities

Enhanced nitrogen (N) deposition due to combustion of fossil fuels and agricultural fertilization is a global phenomenon which has severely altered carbon (C) and N cycling in temperate forest ecosystems in the northern hemisphere. Although deadwood holds a substantial amount of C in forest ecosystems and thus plays a crucial role in nutrient cycling, the effect of increased N deposition on microbial processes and communities, wood chemical traits and deadwood mass loss remains unclear. Here, we simulated high N deposition rates by adding reactive N in form of ammonium-nitrate (40 kg N ha−1 yr−1) to deadwood of 13 temperate tree species over nine years in a field experiment in Germany. Non-treated deadwood from the same logs served as control with background N deposition. Our results show that chronically elevated N levels alters deadwood mass loss alongside respiration, enzymatic activities and wood chemistry depending on tree clade and species. In gymnosperm deadwood, elevated N increased mass loss by +38 %, respiration by +37 % and increased laccase activity 12-fold alongside increases of white-rot fungal abundance +89 % (p = 0.03). Furthermore, we observed marginally significant (p = 0.06) shifts of bacterial communities in gymnosperm deadwood. In angiosperm deadwood, we did not detect consistent effects on mass loss, physico-chemical properties, extracellular enzymatic activity or changes in microbial communities except for changes in abundance of 10 fungal OTUs in seven tree species and 28 bacterial OTUs in 10 tree species. We conclude that N deposition alters decomposition processes exclusively in N limited gymnosperm deadwood in the long term by enhancing fungal activity as expressed by increases in respiration rate and extracellular enzyme activity with minor shifts in decomposing microbial communities. By contrast, deadwood of angiosperm tree species had higher N concentrations and mass loss as well as community composition did not respond to N addition.

Taxonomic relationship among four European Physokermes species (Hemiptera: Coccomorpha) based on nuclear and mitochondrial DNA

IntroductionScale insects (Hemiptera: Coccomorpha) feed on a wide variety of agricultural crops and forest and ornamental trees worldwide. These pest insects damage plants not only by causing sap loss but also by reducing the plant's photosynthetic activity. This is because the honeydew they produce acts as a substrate for mold, which covers leaf surfaces. In the last decades, several outbreaks of Physokermes spp. (soft-scale insects) have occurred throughout Europe and have partly been attributed to unusual weather conditions or climate change, as some species seem to be expanding their distribution range. However, the small size of these insects and their large intraspecific morphological variation have hindered the identification of the species responsible for outbreaks.MethodsIn this study, mitochondrial DNA (cytochrome c oxidase subunit I, COI), ribosomal RNA (28S), and nuclear (elongation factor 1α, EF1α) DNA markers were used to reconstruct the phylogenetic relationships of four Physokermes species sampled throughout Europe in 2013–2015.Results and discussionThe results allowed us to clearly distinguish P. hellenicus and P. inopinatus from each other, as these appeared in well-supported clades in the phylogenetic trees and from P. piceae and P. hemicryphys. However, P. hemicryphus appeared in a single clade in trees based on 28S and EF1α but among P. piceae in the COI tree. Further investigations are therefore required to determine the taxonomic status of P. piceae and P. hemicryphys, which seem to comprise a species complex.

Genetic and morphological characterization of United States tea (Camellia sinensis): insights into crop history, breeding strategies, and regional adaptability.

Multiple introductions of tea (Camellia sinensis) to the United States since the 1850s have resulted in US tea germplasm that are currently poorly characterized. To resolve questions concerning the relatedness and regional adaptability of US tea germplasm, 32 domestic individuals were evaluated using 10 InDel markers, and compared with a background population of 30 named and registered Chinese varieties of tea. The marker data were analyzed via a neighbor-joining cladistic tree derived from Nei's genetic distance, STRUCTURE, and Discriminant Analysis of Principal Components, which revealed four genetic groups. Nineteen individuals selected from the four groups were assessed for seven leaf traits, two floral descriptors, and leaf yield, to identify plants best adapted to Florida field conditions. Our analyses compared with available historical records led us to estimate the most likely provenance of some of the US individuals, to precisely identify tea plant material and to choose most diverse accessions for breeding tea improved for adaptability, yield and quality.

A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem.

A large variety of pairwise measures of similarity or dissimilarity have been developed for comparing phylogenetic trees, for example, species trees or gene trees. Due to its intuitive definition in terms of tree clades and bipartitions and its computational efficiency, the Robinson–Foulds (RF) distance is the most widely used for trees with unweighted edges and labels restricted to leaves (representing the genetic elements being compared). However, in the case of gene trees, an important information revealing the nature of the homologous relation between gene pairs (orthologs, paralogs, and xenologs) is the type of event associated to each internal node of the tree, typically speciations or duplications, but other types of events may also be considered, such as horizontal gene transfers. This labeling of internal nodes is usually inferred from a gene tree/species tree reconciliation method. Here, we address the problem of comparing such event-labeled trees. The problem differs from the classical problem of comparing uniformly labeled trees (all labels belonging to the same alphabet) that may be done using the Tree Edit Distance (TED) mainly due to the fact that, in our case, two different alphabets are considered for the leaves and internal nodes of the tree, and leaves are not affected by edit operations. We propose an extension of the RF distance to event-labeled trees, based on edit operations comparable to those considered for TED: node insertion, node deletion, and label substitution. We show that this new Labeled Robinson–Foulds (LRF) distance can be computed in linear time, in addition of maintaining other desirable properties: being a metric, reducing to RF for trees with no labels on internal nodes and maintaining an intuitive interpretation. The algorithm for computing the LRF distance enables novel analyses on event-label trees such as reconciled gene trees. Here, we use it to study the impact of taxon sampling on labeled gene tree inference and conclude that denser taxon sampling yields trees with better topology but worse labeling. [Algorithms; combinatorics; gene trees; phylogenetics; Robinson–Foulds; tree distance.]

The phylogeny of Salix revealed by whole genome re-sequencing suggests different sex-determination systems in major groups of the genus.

The largest genus of Salicaceae sensu lato, Salix, has been shown to consist of two main clades: clade Salix, in which species have XY sex-determination systems (SDSs) on chromosome 7, and clade Vetrix including species with ZW SDSs on chromosome 15. Here, we test the utility of whole genome re-sequencing (WGR) for phylogenomic reconstructions of willows to infer changes between different SDSs. We used more than 1 TB of WGR data from 70 Salix taxa to ascertain single nucleotide polymorphisms on the autosomes, the sex-linked regions (SLRs) and the chloroplast genomes, for phylogenetic and species tree analyses. To avoid bias, we chose reference genomes from both groups, Salix dunnii from clade Salix and S. purpurea from clade Vetrix. Two main largely congruent groups were recovered: the paraphyletic Salix grade and the Vetrix clade. The autosome dataset trees resolved four subclades (C1-C4) in Vetrix. C1 and C2 comprise species from the Hengduan Mountains and adjacent areas and from Eurasia, respectively. Section Longifoliae (C3) grouped within the Vetrix clade but fell into the Salix clade in trees based on the chloroplast dataset analysis. Salix triandra from Eurasia (C4) was revealed as sister to the remaining species of clade Vetrix. In Salix, the polyploid group C5 is paraphyletic to clade Vetrix and subclade C6 is consistent with Argus's subgenus Protitea. Chloroplast datasets separated both Vetrix and Salix as monophyletic, and yielded C5 embedded within Salix. Using only diploid species, both the SLR and autosomal datasets yielded trees with Vetrix and Salix as well-supported clades. WGR data are useful for phylogenomic analyses of willows. The different SDSs may contribute to the isolation of the two major groups, but the reproductive barrier between them needs to be studied.

Disentangling the importance of space and host tree for the beta-diversity of beetles, fungi, and bacteria: Lessons from a large dead-wood experiment

Forestry in Europe changed the tree species composition and reduced dead-wood amount and heterogeneity, and therefore negatively affected saproxylic diversity. Efficient conservation requires knowledge about the importance of the relevant diversity drivers across taxa. We examined the relative importance of space vs. host for saproxylic diversity at a spatial extend of 600 km in Germany. Further, we disentangled effects of among regions, forest stands, host clades, and tree species on saproxylic diversity. This allows inferences for spatial- and host tree-related conservation strategies. Beetle, fungal sporocarp, molecular-derived fungal, and bacterial communities were studied in a large nested dead-wood experiment comprising 11 tree species. We used multiplicative diversity partitioning to assess the diversity of rare, typical, and dominant species. The beta-diversity of beetles and fungal sporocarps was equally explained by space and host, but that of molecular fungi and bacteria mainly by the host. Across taxa, beta-diversity was higher among forest stands than among regions. However, for beetles and fungal sporocarps, differences among regions were also important. Host tree clade and host tree species were important for beetle and host clade for fungal sporocarp beta-diversity. Host tree species was more important than host clade for the beta-diversity of molecular fungi and bacteria. The divergent response of different taxa to space and host calls into question the use of a simple spatially-centered or host-centered strategy. Instead, a high dead-wood tree species diversity on a broad spatial coverage at the national scale in temperate European forests is necessary to maintain rare and abundant species.

Pantropical diversification of padauk trees and relatives was influenced by biome‐switching and long‐distance dispersal

AbstractAimPhenotypes promoting dispersal over ecological timescales may have macroevolutionary consequences, such as long‐distance dispersal and diversification. However, whether dispersal traits explain the distribution of pantropical plant groups remains unclear. Here we reconstruct the biogeographical history of a tree clade to assess whether seed dispersal traits and biome‐switching explain the clade’s pantropical distribution.LocationPantropical.TaxonThe Pterocarpus clade (Leguminosae/Fabaceae).MethodsWe sequenced 303 nuclear loci using target capture and generated a time‐calibrated phylogenomic tree. We also generated a corroborative time‐calibrated phylogenetic tree from data‐mined Sanger‐sequencing data. We then collated distribution data and seed dispersal morphology traits to compare trait‐dependent and trait‐independent biogeographical models, allowing us to infer whether dispersal traits influenced Pterocarpus’ spatio‐temporal evolution. Finally, using the results of these model tests, we estimated the ancestral ranges and biomes of Pterocarpus species to better understand their biogeographical history, and assessed the degree and direction of biome‐switching over the course of their diversification.ResultsWe recovered well‐supported phylogenetic relationships within Pterocarpus, within which there were two subclades – one neotropical and the other palaeotropical. Our divergence date estimates suggested that Pterocarpus diversified from around 12 Ma, during the Miocene. Trait‐dependent biogeographical models were rejected for both range and biome evolution within Pterocarpus, but models including dispersal were supported. Pterocarpus’ ancestral node shared a range across the new‐world and old‐world tropics, followed by divergence into palaeotropical and neotropical clades. Biome‐switching occurred most frequently into rainforest and grassland.Main conclusionsOur analyses suggest that Pterocarpus underwent infrequent cross‐continental dispersal and establishment into novel biomes. While this was minimally impacted by seed dispersal traits, biome‐switching following long‐distance dispersal and climate change have played an important role in diversification within Pterocarpus since the Miocene. Indeed, rare events of long‐distance dispersal likely explain the wide distributions of many pantropical plant species.

Phylogenetic classification and evolution of Early Triassic conodonts

Conodonts are some of the most important biostratigraphic index fossils in the Paleozoic and Triassic because of their rapid evolution and extensive distribution. Here we present a cladistic analysis of Early Triassic conodonts to reexamine the systematic classification and evolutionary relationships of the three related families Anchignathodontidae, Ellisonidae, and Gondolellidae. The tree consists of 38 Early Triassic conodont species with multielement apparatus documented, based on parsimony analysis of 73 discrete morphological characters including 40 P 1 element characters, 4 P 2 element characters, 27 S element characters and 2 M element characters. Based on the phylogenetic time tree, a series of evolutionary lineages are supported: Parafurnishius xuanhanensis – Furnishius triserratus – Platyvillosus regularis ; Scythogondolella mosheri – Scythogondolella milleri ; Discretella – Conservatella – Paullella meeki ; Triassospathodus homeri – Chiosella ; and Triassospathodus symmetricus – Triassospathodus chioensis . Reassignment of Ellisonia agordina to be Hadrodontina agordina is supported while Neospathodus planus should be resigned to the genus Triassospathodus . Meanwhile, Parafurnishius and Furnishius may belong to Gondolellidae rather than Ellisonidae or Ellisonidae may be a polyphyletic group rather than a monophyletic group. The cladogram suggests that Hindeodus , Hadrodontina and Pachycladina are monophyletic, whilst Novispathodus and Triassospathodus are paraphyletic and polyphyletic, respectively. In addition, a P 1 element with a round basal cavity is an important trait to distinguish Novispathodus from Triassospathodus . The cladogram and revised classification provide a robust phylogenetic foundation for further investigations on systematic classification and evolutionary rates of conodonts during the Early Triassic. • A multi-element cladistic tree of 38 conodont species is established. • The tree reexamines the classification and evolution of these 38 species. • Hindeodus , Hadrodontina and Pachycladina are monophyletic. • Novispathodus are paraphyletic and Triassospathodus are polyphyletic. • Neospathodus planus should be resigned to the genus Triassospathodus .

The life cycle in late Paleozoic eryopid temnospondyls: developmental variation, plasticity and phylogeny

Abstract. Eryopid temnospondyls were large apex predators in Carboniferous and Permian stream and lake habitats. The eryopid life cycle is exemplified by Onchiodon labyrinthicus from Niederhäslich (Saxony, Germany), which is represented by numerous size classes from small larvae to heavily ossified adults. Morphometric and principal component analyses provide new insights into ontogenetic changes in O. labyrinthicus, and comparison with adults of other eryopids documents phylogenetic patterns in the occupation of morphospace. Compared with small specimens of Sclerocephalus spp., immature O. labyrinthicus occupies a neighboring but much larger space, corresponding to a broader range of variation. Adults of Actinodon frossardi map with some juveniles of O. labyrinthicus, whereas other juveniles of the latter lie close to adults of O. thuringiensis, Glaukerpeton avinoffi and Osteophorus roemeri. Morphospace occupation of adult eryopids is partly consistent with cladistic tree topology, which gives the following branching pattern: Actinodon frossardi forms the basalmost eryopid, followed by Osteophorus roemeri, Glaukerpeton avinoffi and the genus Onchiodon (O. labyrinthicus + O. thuringiensis); then Clamorosaurus nocturnus; and finally the monophyletic genus Eryops. The presumably juvenile skull of Eryops anatinus falls well outside the domains of both adult eryopids and immature O. labyrinthicus, showing a unique combination of juvenile and adult features. Instead, Onchiodon langenhani and the Ruprechtice specimens referred to O. labyrinthicus map within the domain of immature O. labyrinthicus. Raised levels of variation in O. labyrinthicus coincide with evidence of a stressed habitat, in which limiting factors were fluctuating salinity, absence of fishes, enhanced competition and seasonal algal blooms. The documented broad variation was possibly caused by developmental plasticity responding to fluctuations in lake hydrology and nutrients in this small, short-lived water body.

First Report of Golovinomyces orontii Causing Hydrangea macrophylla Powdery Mildew in Qinghai-Tibet Plateau, China.

Hydrangea macrophylla (Thunb.) Ser. (Hydrangeaceae) is the most popular hydrangea species grown in home gardens and landscapes in China. Plants of H. macrophylla with symptoms of powdery mildew were found in a commercial wholesale nursery in Huzhu, Haidong (36°49'11.87" N, 101°57'03.36″E, alt. 2490 m), in May 2020, with disease incidence reaching 80%. Symptoms included yellowing and necrosis of leaves. Upon microscopic observation, masses of conidia and mycelium were observed covering the symptomatic tissues. Fungal isolates displayed nipple-shaped hyphal appressoria, often poorly developed, conidiophores erect, arising laterally or from the upper surface of hyphal mother cells, and positioned almost centrally or towards one end of the cells, up to about 160 μm long (n = 30), with foot cells straight or flexuous, 32 to 86 × 8 to 13 μm (n = 50), followed by one to three shorter cells about 11 to 24 × 10 to 15 μm (n = 50), forming catenescent conidia in usually predominantly chains, conidia doliiform to limoniform, hyaline, 24 to 35 × 13 to 25μm (n = 50). Conidial germination was of the Euoidium type. Chasmothecia were not observed. To confirm fungal classification, single spores were isolated and cultured on detached leaf bioassay following the protocol described in Farinas et al. (2019). Total DNA was extracted directly from single-spore cultures using a Chelex extraction method (Walsh et al. 1991). The rDNA internal transcribed spacer (ITS) regions were amplified by polymerase chain reaction (PCR) utilizing the universal primer pairs ITS1/ITS4 (White et al. 1990). The sequences (726-727 bp) were deposited in GenBank (accessions no. MT568633, MT757924 and MT757925). The ITS sequences showed 99.9-100% identity with a sequence of Golovinomyces orontii reported on Papaver rhoeas (AB769466) in Switzerland. Based on the ITS rDNA phylogenetic tree, the sequences retrieved from the specimen clustered within a strongly supported clade with G. orontii (AB769466), confirming the identity of the pathogen (Takamatsu 2013). Cladistic trees were constructed using the neighbor-joining method with the Kimura 2-parameter substitution model in MEGA 6.0. Branch robustness was assessed via bootstrap analysis with 1,000 replicates. To confirm pathogenicity, eight H. macrophylla plants were sprayed until run-off with a suspension containing 1 × 105 conidia/ml. Four plants were used for fulfilling Koch's postulates and four plants were used as mock-inoculated controls sprayed only with sterile distilled water. Inoculated and non-inoculated plants were covered with plastic bags separately and maintained overnight in a greenhouse at 25 ± 2°C and 50 to 60% relative humidity. Typical powdery mildew colonies developed on inoculated plants 10 to 15 days after inoculation, which were morphologically identical to those originally observed on the diseased plats, whereas the control plants remained symptomless. To our knowledge, this is the first report of powdery mildew caused by G. orontii on H. macrophylla in Qinghai-Tibet Plateau, China (Braun and Cook 2012).

<p class="ZootaxaTitle">New concepts and methods for phylogenetic taxonomy and nomenclature in zoology, exemplified by a new ranked cladonomy of recent amphibians (Lissamphibia)

Although currently most taxonomists claim to adhere to the concept of ‘phylogenetic taxonomy’, in fact most of the zoological classifications currently published are only in part ‘phylogenetic’ but include also phenetic or gradist approaches, in their arbitrary choices of the nodes formally recognised as taxa and in their attribution of ranks to these taxa. We here propose a new approach to ‘phylogenetic taxonomy and nomenclature’, exemplified by a phylogenetic classification or cladonomy of the extant amphibians (subclass Lissamphibia of the class Amphibia) derived from a supermatrix-based phylogenetic analysis using 4060 amphibian species, i.e. about half of the 8235 species recognised on 31 October 2020. These taxa were represented by a mean of 3029 bp (range: 197–13849 bp) of DNA sequence data from a mean of 4 genes (range: 1‒15). The cladistic tree thus generated was transferred into a classification according to a new taxonomic and nomenclatural methodology presented here, which allows a bijective or isomorphic relationship between the phylogenetic hypothesis and the classification through a rigorous use of suprageneric ranks, in which their hierarchy mirrors the structure of the tree. Our methodology differs from all previous ones in several particulars: [1] whereas the current International Code of Zoological Nomenclature uses only three ‘groups of names’ (species, genus and family), we recognise four nominal-series (species, genus, family and class); [2] we strictly follow the Code for the establishment of the valid nomen (scientific name) of taxa in the three lower nominal-series (however, in a few situations, we suggest improvements to the current Rules of the Code); [3] we provide precise and unambiguous Criteria for the assignment of suprageneric nomina to either the family- or the class-series, excluding nomina proposed expressly under unranked or pseudoranked nomenclatural systems; [4] in the class-series, for which the Code provides only incomplete Rules concerning availability, we provide precise, complete and unambiguous Criteria for the nomenclatural availability, taxonomic allocation and nomenclatural validity and correctness of nomina; [5] we stress the fact that nomenclatural ranks do not have biological definitions or meanings and that they should never be used in an ‘absolute’ way (e.g., to express degrees of genetic or phenetic divergence between taxa or hypothesised ages of cladogeneses) but in a ‘relative’ way: two taxa which are considered phylogenetically as sister-taxa should always be attributed to the same nomenclatural rank, but taxa bearing the same rank in different ‘clades’ are by no means ‘equivalent’, as the number of ranks depends largely on the number of terminal taxa (species) and on the degree of phylogenetic resolution of the tree; [6] because of this lack of ‘equivalence’, some arbitrary criteria are necessary to fix a starting point for assigning a given suprageneric rank to some taxa, from which the ranks of all other taxa will automatically derive through a simple implementation of the hierarchy of ranks: for this purpose we chose the rank family and we propose a ‘Ten Criteria Procedure’ allowing to fix the position of this rank in any zoological classification. As a result of the implementation of this set of Criteria, we obtained a new ranked classification of extant lissamphibians using 25 suprageneric ranks below the rank class (11 class-series and 14 family-series ranks), and including 34 class-series and 573 family-series taxa, and where the 575 genera we recognise are referred to 69 families and 87 subfamilies. We provide new nomina and diagnoses for 10 class-series taxa, 171 family-series taxa, 14 genus-series taxa and 1 species. As many new species of amphibians are permanently described, this classification and its nomenclature will certainly have to change many times in the future but, using the clear, explicit, complete, automatic and unambiguous methodology presented here, these changes will be easy to implement, and will not depend on subjective and arbitrary choices as it has too often been the case in the last decades. We suggest that applying this methodology in other zoological groups would improve considerably the homogeneity, clarity and usefulness of zoological taxonomy and nomenclature.

RAD-sequencing reveals patterns of diversification and hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees.

A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide single nucleotide polymorphism data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are today largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression has occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now coexist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role that introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.

Cladistic and quantitative shape analyses of five new syntopic Sarsamphiascus (Copepoda, Harpacticoida): problems and solutions for diosaccin systematics and taxonomy

Five new species of the genus Sarsamphiascus Huys, 2009 were collected from a small Korean beach, which is a record for the number of syntopic copepod congeners. They differ in numerous macro-morphological characters, some of which extend generic boundaries, and are classified in two species groups. Diossacins are widely regarded as taxonomically problematic, and the new discovery presents an opportunity to test characters commonly used in their systematics through a cladistic analysis. Another aim is to test with landmark-based geometric morphometrics the extent of inter- and intraspecific variability of characters with reported significant variation but commonly used in diosaccin taxonomy. The cladistic analysis, based on 14 binary characters, reveals at least three distinct clades among five new species, which, in addition to significant size differences, probably facilitates their syntopy. Some characters previously used to distinguish species groups in Sarsamphiascus, and to distinguish this genus from other diosaccins, are exposed as symplesiomorphies, suggesting that some of these groups might not be monophyletic. Studies of alternative characters are suggested, including cuticular organs on somites, which are surveyed for the first time in this genus. Principal component analysis (PCA) of nine landmarks on the female fifth leg exopod reveals that 70% of variability can be explained by the first two eigenvectors and that in morphospace there is no overlap between Korean species, despite a significant intraspecific variability. Discriminant function analysis with cross-validation shows highly significant results, both in parametric tests and after 10,000 permutation runs, correctly classifying all specimens for all species pairs and suggesting the fifth leg exopod as an ideal taxonomic character here. Evolutionary integration of the morphometric data is tested by plotting PCA scores onto the cladistic tree; randomized permutation test suggests an absence of statistically significant phylogenetic signal. http://www.zoobank.org/urn:lsid:zoobank.org:pub:31913865-E23D-4E76-97B0-2F6D791E717A

Allometry rather than abiotic drivers explains biomass allocation among leaves, stems and roots of Artemisia across a large environmental gradient in China

Abstract Biomass allocation patterns reflect the adaptive strategies of plants growing in different environments, which is a central issue in comparative plant ecology and evolution. However, the factors underpinning specific allocation patterns across organs and the existence of general rules governing allocation remain contentious. Optimal partitioning theory (OPT) states that plants can respond to resource availability by allocating relatively more biomass to the organ that captures the most limiting resources to optimize growth. In contrast, allometric partitioning theory (APT) postulates that biomass allocation among organs is a power function of plant size independently of environmental variation. As phylogenetic and growth form constraints (e.g. formation of inert heartwood in tree clades) may also affect biomass allocation, comparison among and within closely related taxa of rather similar growth form may enable a more direct testing of which of these two theories prevails. To test whether OPT or APT was prevalent at wide geographical scale, we investigated biomass allocation patterns among leaves, stems and roots of 1,022 plants of 62 Artemisia species (Asteraceae) collected along broad climate (annual mean temperature range: −4.9 to 18.0°C, annual mean precipitation range: 193–1,668 mm) and soil gradients (soil carbon content range: 1.6–15.4 kg C m−2) in central and eastern China. There were strong allometric relationships among leaf mass (ML), stem mass (MS) and root mass (MR) at both interspecific and intraspecific levels. Moreover, the interspecific and intraspecific patterns were not different from general patterns for pooled plants, that is, ML/MR and ML/MS, but not MS/MR, generally decreased with plant size. However, the three organ mass ratios were not responsive to broad climatic or soil gradients after the effect of plant size was removed. Synthesis. Our results generally support APT instead of OPT, suggesting that Artemisia plants have evolved an allometric strategy rather than relying on adjustment of allocation among organs to adapt to the broadly varying environments at the regional scale. For follow‐up research, we hypothesize that the strong allometric constraints on biomass allocation should depend on strong physiological adaptive responses of the different organs of Artemisia to environmental gradients.

Global assessment of genetic paradigms of Pvmdr1 mutations in chloroquine-resistant Plasmodium vivax isolates.

Chloroquine (CQ) is generally prescribed as the front-line antimalarial drug of choice to treat Plasmodium vivax infections; however, some clinical CQ-resistant P. vivax isolates have been indigenously reported around the world during the last decade. In this study, P. vivax isolates (n=52) were obtained from autochthonous samples in southeast Iran during 2015-2017. The genomic DNA of samples was extracted, amplified (nested PCR) and sequenced by targeting the multidrug-resistance 1 gene. To verify the global genetic diversity of CQ-resistant P. vivax strains, the sequences of Pvmdr1 originating from Asia and the Americas were retrieved. A total of 46 haplotypes were grouped into three distinct geographical haplogroups. The haplotype diversity and occurrence rates of Pvmdr1 976F/1076L mutations indicate that the efficacy of CQ is being compromised in Mexico, China, Nicaragua, Thailand, Brazil (2016), Ethiopia, Mauritania (2012) and southwest India in the near future. The cladistic phylogenetic tree showed that Pvmdr1 sequences isolated from the southeast Asian clade has a partial sister relationship with the American clade. The current findings will serve as a basis to develop appropriate malaria control strategies and public health policies in symptomatic imported malaria cases or plausible CQ-resistant P. vivax strains.

First Report of Powdery Mildew Caused by Podosphaera elsholtziae on Dracocephalum tanguticum in China

Dracocephalum tanguticum Maxim. is endemic to the Qinghai Tibetan Plateau. It has been widely used in Tibetan traditional medicine to treat pneumonia and respiratory inflammation, but powdery mildew has seriously affected the quality of the plants and reduced the economic value. In August 2017, severe powdery mildew was observed on D. tanguticum in Huangnan (35.31°N, 101.93°E, altitude 3,300 m), China. Voucher specimens were deposited in the Herbarium of Plant Pathology at Qinghai University under accession number QHU2017043. This powdery mildew fungus is morphologically characterized as follows. Mycelium was observed on the entire surface of the leaves and stem, and more than 70% of leaf areas were affected; hyphae hyaline, thin-walled, smooth, 3 to 6 µm wide; hyphal appressoria nipple shaped; conidia ellipsoid-ovoid to doliiform, 22 to 30 × 12 to 17µm; chasmothecia amphigenous, scattered to gregarious, dark brown, globose or subglobose, 67 to 83 µm in diameter; peridium cells irregular shaped, 8 to 37 µm in diameter; appendages usually few, mostly fewer than six, arising from the lower half, myceloid, simple, usually unbranched, 0.3 to 2 times as long as the chasmothecial diameter, 3 to 7 µm wide, brown below and paler toward the tip, septate, wall thin, smooth; ascus broadly ellipsoid-ovoid, sessile or with a very short stalk, 60 to 71 × 50 to 58 µm, six- to eight-spored; ascospores broad ellipsoid-ovoid or subglobose, 11 to 18 × 8 to 15 µm, colorless. This fungus was identified as Podosphaera elsholtziae based on the morphology of its asexual and sexual morphs (Braun and Cook 2012). To confirm the identification, the internal transcribed spacer (ITS) region were amplified. Genomic DNA was extracted from chasmothecia using Chelex-100 (Hirata and Takamatsu 1996; Walsh et al. 1991). The ITS5/P3 and PM5/ITS4 primers were used to amplify the ITS region by nested polymerase chain reaction, and the cloned fragments were sequenced. The ITS region sequences were deposited in GenBank (accession no. MK402076). A BLAST search analysis of the two sequences revealed 99% identity with P. elsholtziae infecting Ajuga reptans Linn. in Japan. Based on the ITS rDNA phylogenetic tree, the sequences retrieved from the specimen clustered within the same clade (bootstrap value 97%) with P. elsholtziae (AB026142). Cladistic trees were constructed using the maximum parsimony method with the Kimura two-parameter substitution model in MEGA 5.0. Branch robustness was assessed via bootstrap analysis with 1,000 replicates. Phylogenetic analysis data agreed with morphological characteristics (Takamatsu et al. 1999, 2009). Pathogenicity tests were performed by rubbing infected leaves onto healthy leaves and stems of four D. tanguticum seedlings. Four healthy seedlings were kept separately as a noninoculated control. Inoculated and noninoculated plants were maintained in a greenhouse at 22 to 25°C. Inoculated plants developed signs and symptoms after 17 days, whereas control plants remained symptomless. The morphology of the fungus on inoculated leaves was identical to that originally observed on diseased plants. To our knowledge, this is the first report of powdery mildew caused by P. elsholtziae on D. tanguticum worldwide.

Ecological niche divergence associated with species and populations differentiation in Erythrophleum (Fabaceae, Caesalpinioideae)

Background and aims – The isolation of populations inside forest refugia during past climate changes has widely been hypothesized as a major driver of tropical plant diversity. Environmental conditions can also influence patterns of diversity by driving divergent selection leading to local adaptation and, potentially, ecological speciation. Genetic and phylogenetic approaches are frequently used to study the diversification of African tree clades. However, the environmental space occupied by closely related species or intra-specific gene pools is barely quantified, though needed to properly test hypotheses on diversification processes.Methods – Using species distribution models, we determined the bioclimatic constraints on the distribution of closely related species and intra-specific gene pools. Our study model, Erythrophleum (Fabaceae – Caesalpinioideae), is a tropical tree genus widespread across Africa, and vastly investigated for genetics. Here, we combined the available phylogenetic data with information on niche divergence to explore the role of ecology into diversification at the species and gene pool levels.Key results – Ecological speciation through climate has probably played a key role in the evolution of the Erythrophleum species. The differential climatic niche of the species indicated adaptive divergence along rainfall gradients, that have probably been boosted by past climate fluctuations. At the gene pool level, past climate changes during the Pleistocene have shaped genetic diversity, though within Erythrophleum suaveolens, adaptive divergence also occurred.Conclusions – We believe that ecological speciation is a key mechanism of diversification for tropical African tree species, since such climatic niche partition exist among many other genera. Modelling the environmental niche of closely related taxa, and testing for niche differentiation, combined with divergence dates offered new insights on the process of diversification.

Flora of Pernambuco, Brazil: Tabebuia alliance and tribe Jacarandeae (Bignoniaceae)

Abstract: Bignoniaceae is a Pantropical plant family that includes 82 genera and 830 species of trees, lianas, and shrubs. The Tabebuia alliance (14 genera and 147 species) and tribe Jacarandeae (2 genera and 50 species) are both Neotropical and represent the largest clades of trees and shrubs in the family. Here, we present a taxonomic treatment for these two clades for the state of Pernambuco, Brazil. Overall, we documented 23 species distributed in seven genera, i.e., Cybistax Mart. ex Meisn., Godmania Hemsl., Jacaranda Juss., Handroanthus Mattos, Sparattosperma Mart. ex Meisner, Tabebuia Gomes ex DC., and Zeyheria Mart. Six taxa are new records for the state, i.e., Cybistax antisyphilitica (Mart.) Mart., Handroanthus capitatus (Bureau & K. Schum) Mattos, Handroanthus umbellatus (Sond.) Mattos, Jacaranda cuspidifolia Mart., Sparattosperma catingae A.H. Gentry, and Tabebuia stenocalyx Sprague & Stapf. Furthermore, S. catingae, previously thought to be endemic to the Caatinga of Bahia, was documented for the first time in the Atlantic Forest domain. We present identification keys and taxonomic descriptions for all genera and species, as well as provide illustrations and information on the geographic distribution, habitat, and phenology for all species.

First Report of Powdery Mildew Caused by Erysiphe macleayae on Corydalis edulis in China

Corydalis edulis Maxim. is a common ornamental plant in China. It is also an important Chinese medicinal herb for its antipyretic action and the ability to flush out toxic materials. In October 2016, severe powdery mildew infections were observed on C. edulis in Mengdatianchi (35.82°N, 102.69°E), China. Voucher specimens were deposited in the Herbarium of Plant Pathology at Qinghai University under accession no. QH2016001. This powdery mildew is morphologically characterized as follows. Mycelium amphigenous, thin, effuse or in irregular patches, often around leaf veins, sometimes covering the entire surface, white, evanescent to persistent; hyphae sparingly branched, thin-walled. Hyphal appressoria well-developed, lobed, 3 to 8 µm diam. Conidiophores erect, arising from the top and mostly toward one end of the mother cell, 40 to 150 µm long, foot-cells straight to often curved-sinuous, 25 to 120 μm long and 6 to 10 µm wide, followed by 1 to 3 cells shorter than or about as long as the foot cell. Conidia ellipsoid-ovoid, 25 to 60 × 10 to 29 μm, length/width ratio 1.8 to 3.4. Chasmothecia 70 to 100 μm diam., solitary or in groups, with dark brown mycelioid, unbranched appendages, 0.5 to 7 times as long as the chasmothecial diameter, 5 to 9 µm wide, septate, thin-walled, brown at the base and paler toward the apex. Asci 2 to 5 per chasmothecium, saccate-clavate, subsessile to short-stalked, 40 to 75 × 25 to 60 μm, and 2- to 5-spored. Ascospores ellipsoid-ovoid, rarely slightly curved, 18 to 38 × 12 to 18 μm, often with oil drops, colorless to yellowish. This fungus was identified as Erysiphe macleayae based on the morphology of its asexual and sexual morphs (Braun and Cook 2012). To confirm identification, the 28S rDNA and ITS region were amplified. The ITS5/p3 and PM5/ITS4 primers were used to amplify the ITS region by nested PCR. Primers LSU1/LSU2 were used to amplify the 28S rDNA, and the cloned fragments were sequenced. The 28S rDNA and ITS region sequences were deposited in GenBank (accession nos. KX817183 and KX817184). A BLAST search analysis of the two sequences revealed 100% identity with E. macleayae infecting Macleaya cordata (Willd.) R.Br. in Japan. Based on the ITS rDNA phylogenetic tree, the sequences retrieved from the Chinese specimen clustered within a strongly supported clade (bootstrap value 100%) with E. macleayae (AB016048). Cladistic trees were constructed using the neighbor-joining method with the Kimura 2-parameter substitution model in MEGA 5.0. Branch robustness was assessed via bootstrap analysis with 1,000 replicates. Phylogenetic analysis data agree with morphological characters (Takamatsu et al. 1999, 2009). For Koch’s postulate, inoculated and noninoculated plants were maintained separately in different rooms of a greenhouse at 20 to 24°C. Inoculated plants developed signs and symptoms after 12 days, whereas control plants remained symptomless. The morphology of the fungus on inoculated leaves was identical to that originally observed on diseased plants. To our knowledge, this is the first report of powdery mildew caused by E. macleayae on C. edulis worldwide. Infection of Corydalis by E. macleayae is very unusual since this powdery mildew species naturally occurs on Chelidonium majus, Meconopsis cambrica, and Macleaya spp. In inoculation experiments, it could be demonstrated that E. macleayae from Chelidonium majus was able to infect Argemone, Glaucium, and Papaver spp. (Pastircakova et al. 2016). The present record of this species on C. edulis supports a wider host range of E. macleayae among papaveraceous genera.

Secondary succession and fire disturbance promote dominance of a late-diverging tree lineage in a lowland Neotropical forest

Background: Variation in the distribution and abundance of woody plants as consequence of disturbances such as fire may be explained by lineage age.Aims: We tested whether lowland tropical tree lineages that colonise secondary forests are more late-diverging than clades from old-growth forests, and whether tree phylogenetic beta diversity from old-growth to secondary forests is higher in burned than non-burned secondary forests.Methods: We sampled tree communities in old-growth forests and in secondary forests with distinct disturbance histories (burned and unburned). We calculated mean family age in each plot, and tested for differences among forest types using ANOVA. A phylogenetic fuzzy-weighting procedure was employed to generate a matrix describing the abundance of tree clades per plot, which was then analysed using a principal coordinate analysis.Results: Most clades found in old-growth forests were underrepresented in secondary forests, which have been heavily colonised by a single species from a young lineage that is not found in old-growth forests. Phylogenetic beta diversity was higher between unburned secondary forests and old-growth forests than between burned secondary forests and old-growth forests.Conclusions: The capacity of Neotropical trees to colonise secondary forests and persist after fire disturbance may be related to the age of distinct lineages.