Parallelism and Reversibility in Xylem Evolution a Review

IAWA Journal ◽  
1996 ◽  
Vol 17 (4) ◽  
pp. 351-364 ◽  
Author(s):  
Pieter Baas ◽  
Elisabeth A. Wheeler
Keyword(s):  
Phylogenetic Analyses ◽  
Distribution Patterns ◽  
Seed Plants ◽  
Hydraulic Architecture ◽  
Primitive Angiosperms ◽  
Perforation Plate ◽  
High Incidence ◽  
Fusiform Initials ◽  
Plate Type ◽  
Transformation Series

The irreversibility of the major trends of xylem evolution, such as the origin of vessels in primitive angiosperms with long fusiform initials, and the shifts from scalariform to simple perforations and from tracheids to libriform fibres, has long been accepted by wood anatomists. Parallel development of these and other xylem features is generally accepted, and is suggested by the distribution patterns of the fibre and perforation plate type. Some recent phylogenetic analyses of seed plants suggest that there also have been some reversals in these general trends. The likelihood and extent of parallel origins and reversions of the major trends in xylem specialization are explored here by analysing a number of published hypotheses on the phylogenetic relationships within wood anatomically diverse major clades of angiosperms, and within some individual families. On the basis of these analyses, it appears that for these major Baileyan transformation series, parallelisms were more than twice as common as reversals. Functional adaptations to increased efficiency and safety of hydraulic architecture can largely explain the high incidence of parallelisms in xylem evolution.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

scholarly journals Climate variability impacts on diversification processes in a biodiversity hotspot: a phylogeography of ancient pseudoscorpions in south-western Australia

2019 ◽  
Vol 186 (4) ◽  
pp. 934-949 ◽  
Author(s):  
Danilo Harms ◽  
J Dale Roberts ◽  
Mark S Harvey
Keyword(s):  
Phylogenetic Analyses ◽  
Distribution Patterns ◽  
Biodiversity Hotspot ◽  
Molecular Dating ◽  
Environmental Niche ◽  
Ecological Niche Models ◽  
The South ◽  
Niche Modelling ◽  
South West ◽  
Western Division

Abstract The south-western division of Australia is the only biodiversity hotspot in Australia and is well-known for extreme levels of local endemism. Climate change has been identified as a key threat for flora and fauna, but very few data are presently available to evaluate its impact on invertebrate fauna. Here, we derive a molecular phylogeography for pseudoscorpions of the genus Pseudotyrannochthonius that in the south-west are restricted to regions with the highest rainfall. A dated molecular phylogeny derived from six gene fragments is used for biogeographic reconstruction analyses, spatial mapping, environmental niche-modelling, and to infer putative species. Phylogenetic analyses uncover nine clades with mostly allopatric distributions and often small linear ranges between 0.5 and 130 km. Molecular dating suggests that the origins of contemporary diversity fall into a period of warm/humid Palaeogene climates, but splits in the phylogeny coincide with major environmental shifts, such as significant global cooling during the Middle Miocene. By testing several models of historical biogeography available for the south-west, we determine that Pseudotyrannochthonius is an ancient relict lineage that principally follows a model of allopatric speciation in mesic zone refugia, although there are derivations from this model in that some species are older and distribution patterns more complex than expected. Ecological niche models indicate that drier and warmer future climates will lead to range contraction towards refugia of highest rainfall, probably mimicking past variations that have generated high diversity in these areas. Their conservation management will be crucial for preserving the unique biodiversity heritage of the south-west.

scholarly journals Sixty years from the first disease description, a novel badnavirus associated with chestnut mosaic disease

2020 ◽  
Author(s):  
Armelle Marais ◽  
Sergio Murolo ◽  
Chantal Faure ◽  
Yoann Brans ◽  
Clement Larue ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Epidemiological Studies ◽  
Mosaic Disease ◽  
Open Reading Frames ◽  
Sequence Comparisons ◽  
High Incidence ◽  
The Usa ◽  
Reading Frames

Although the chestnut mosaic disease (ChMD) was described several decades ago, its etiology is still not elucidated. Here, using classical approaches in combination with high throughput sequencing (HTS) techniques, we identify a novel Badnavirus that is a strong etiological candidate for ChMD. Two disease sources from Italy and France were submitted to HTS-based viral indexing. Total RNAs were extracted, ribodepleted and sequenced on an Illumina NextSeq500 (2x150 or 2x 75 nt). In each source, we identified a single contig of about 7.2 kilobases that corresponds to a complete circular viral genome and shares homologies with various badnaviruses. The genomes of the two isolates have an average nucleotide identity of 90.5% with a typical badnaviral genome organization comprising three open reading frames. Phylogenetic analyses and sequence comparisons show that this virus is a novel species for which we propose the name Chestnut mosaic virus (ChMV). Using a newly developed molecular detection test, we systematically detected the virus in symptomatic graft-inoculated indicator plants (chestnut and American oak), as well in chestnut trees presenting typical ChMD symptoms in the field (100% and 87% in France and Italy surveys, respectively). Datamining of publicly available chestnut SRA transcriptomic data allowed the reconstruction of two additional complete ChMV genomes from two Castanea mollissima sources from the USA, as well as ChMV detection in C. dentata from the USA. Preliminary epidemiological studies, performed in France and in Central Eastern Italy, showed that ChMV has a high incidence in some commercial orchards, with a low within-orchard genetic diversity.

scholarly journals A molecular method for a qualitative analysis of potentially coding sequences of DNA

2004 ◽  
Vol 64 (3a) ◽  
pp. 383-398
Author(s):  
M. L. Christoffersen ◽  
M. E. Araújo ◽  
M. A. M. Moreira
Keyword(s):  
Amino Acid ◽  
Phylogenetic Analyses ◽  
A Priori ◽  
Morphological Data ◽  
Computer Algorithms ◽  
Protein Coding ◽  
Tree Topologies ◽  
Alternative Amino Acid ◽  
Cladistic Analyses ◽  
Transformation Series

Total sequence phylogenies have low information content. Ordinary misconceptions are that character quality can be ignored and that relying on computer algorithms is enough. Despite widespread preference for a posteriori methods of character evaluation, a priori methods are necessary to produce transformation series that are independent of tree topologies. We propose a stepwise qualitative method for analyzing protein sequences. Informative codons are selected, alternative amino acid transformation series are analyzed, and most parsimonious transformations are hypothesized. We conduct four phylogenetic analyses of philodryanine snakes. The tree based on all nucleotides produces least resolution. Trees based on the exclusion of third positions, on an asymmetric step matrix, and on our protocol, produce similar results. Our method eliminates noise by hypothesizing explicit transformation series for each informative protein-coding amino acid. This approaches qualitative methods for morphological data, in which only characters successfully interpreted in a phylogenetic context are used in cladistic analyses. The method allows utilizing character information contained in the original sequence alignment and, therefore, has higher resolution in inferring a phylogenetic tree than some traditional methods (such as distance methods).

scholarly journals Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae

2004 ◽  
Vol 359 (1450) ◽  
pp. 1495-1508 ◽  
Author(s):  
J. E. Richardson ◽  
L. W. Chatrou ◽  
J. B. Mols ◽  
R. H. J. Erkens ◽  
M. D. Pirie
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Plastid Dna ◽  
Distribution Patterns ◽  
Historical Biogeography ◽  
Rate Heterogeneity ◽  
Long Distance ◽  
Fossil Calibration ◽  
Dispersal Capability

Annonaceae are a pantropically distributed family found predominantly in rainforests, so they are megathermal taxa, whereas Rhamnaceae are a cosmopolitan family that tend to be found in xeric regions and may be classified as mesothermal. Phylogenetic analyses of these families are presented based on rbcL and trn L–F plastid DNA sequences. Likelihood ratio tests revealed rate heterogeneity in both phylogenetic trees and they were therefore made ultrametric using non–parametric rate smoothing and penalized likelihood. Divergence times were then estimated using fossil calibration points. The historical biogeography of these families that are species rich in different biomes is discussed and compared with other published reconstructions. Rhamnaceae and most lineages within Annonaceae are too young to have had their distribution patterns influenced by break–up of previously connected Gondwanan landmasses. Contrasts in the degree of geographical structure between these two families may be explained by differences in age and dispersal capability. In both groups, long–distance dispersal appears to have played a more significant role in establishing modern patterns than had previously been assumed. Both families also contain examples of recent diversification of species–rich lineages. An understanding of the processes responsible for shaping the distribution patterns of these families has contributed to our understanding of the historical assembly of the biomes that they occupy.

Underestimated anuran radiations in the high Andes: five new species and a new genus of Holoadeninae, and their phylogenetic relationships (Anura: Craugastoridae)

2017 ◽  
Vol 182 (1) ◽  
pp. 129-172 ◽  
Author(s):  
Ignacio De la Riva ◽  
Juan C Chaparro ◽  
Santiago Castroviejo-Fisher ◽  
José M Padial
Keyword(s):  
New Species ◽  
Species Diversity ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Distribution Patterns ◽  
Southern Peru ◽  
The Andes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Taxonomic Research

AbstractDespite recent efforts to accelerate exploration and species description, the diversity of high Andean frogs remains highly underestimated. We report high levels of species diversity in direct-developing frogs or terraranas inhabiting the wet puna and adjacent cloud forests of the Amazonian versant of the Andes in Bolivia and Peru. Descriptive evidence of external morphology, distribution patterns and molecular phylogenetic analyses support the existence of nine unnamed species in two clades, which represents a 30% increase in species diversity for those clades. The relationships of these species and their relatives in Holoadeninae are tested using nuclear and mitochondrial genes for 159 terminals representing the 11 genera in this subfamily and 25 species of previously unknown relationships. Our results corroborate species monophyly in all but three cases and support the monophyly of all Holoadeninae genera, albeit the position of some differs between analyses. We propose a new genus (Microkayla gen. nov.) for the clade containing all Bolivian species formerly in Psychrophrynella plus five species from southern Peru. The new genus is monophyletic and supported by anatomical synapomorphies. Psychrophrynella is re-diagnosed and redefined to include three species from the Andes of southern Peru. We discuss the taxonomic instability associated with Noblella and Psychrophrynella due to the fact that the type species of both genera share a number of traits that support a close relationship. We also name and describe three new species of Bryophryne and two of Microkayla from Peru, provide baseline data for the future description of four Bolivian species of Microkayla, and describe the unknown mating calls of two species. Our results support that the grasslands of the Amazonian versant of the Andes harbour a large diversity of species with small altitudinal and horizontal distributions that replace each other along a latitudinal axis. These species belong to different lineages whose closest relatives are forest species, often from distant parts of the continent. These patterns suggest that high Andean environments were colonized several times independently by species with forest ancestors and which radiated into a multitude of species with remarkably similar ecomorphologies. The extent of these radiations remains obscured by a still rudimentary knowledge of species diversity due to insufficient fieldwork and taxonomic research.

Is Morphology Really at Odds with Molecules in Estimating Fern Phylogeny?

2009 ◽  
Vol 34 (3) ◽  
pp. 455-475 ◽  
Author(s):  
Harald Schneider ◽  
Alan R. Smith ◽  
Kathleen M. Pryer
Keyword(s):  
Phylogenetic Relationships ◽  
Vascular Plants ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Spore Wall ◽  
Morphological Evidence ◽  
Bayesian Posterior Probability ◽  
Seed Plants ◽  
Dna Sequence Data ◽  
Reproductive Characters

Using a morphological dataset of 136 vegetative and reproductive characters, we infer the tracheophyte phylogeny with an emphasis on early divergences of ferns (monilophytes). The dataset comprises morphological, anatomical, biochemical, and some DNA structural characters for a taxon sample of 35 species, including representatives of all major lineages of vascular plants, especially ferns. Phylogenetic relationships among vascular plants are reconstructed using maximum parsimony and Bayesian inference. Both approaches yield similar relationships and provide evidence for three major lineages of extant vascular plants: lycophytes, ferns, and seed plants. Lycophytes are sister to the euphyllophyte clade, which comprises the fern and seed plant lineages. The fern lineage consists of five clades: horsetails, whisk ferns, ophioglossoids, marattioids, and leptosporangiate ferns. This lineage is supported by characters of the spore wall and has a parsimony bootstrap value of 76%, although the Bayesian posterior probability is only 0.53. Each of the five fern clades is well supported, but the relationships among them lack statistical support. Our independent phylogenetic analyses of morphological evidence recover the same deep phylogenetic relationships among tracheophytes as found in previous studies utilizing DNA sequence data, but differ in some ways within seed plants and within ferns. We discuss the extensive independent evolution of the five extant fern clades and the evidence for the placement of whisk ferns and horsetails in our morphological analyses.

Stem anatomy of Apioideae (Apiaceae): effects of habit and reproductive strategy

IAWA Journal ◽  
2021 ◽  
pp. 1-20
Author(s):  
Kamil E. Frankiewicz ◽  
Alexei A. Oskolski ◽  
Jean-Pierre Reduron ◽  
Łukasz Banasiak ◽  
Jorge-Alfredo Reyes-Betancort ◽  
...  
Keyword(s):  
Reproductive Strategy ◽  
Fibre Length ◽  
Vessel Diameter ◽  
Tissue Type ◽  
Vessel Element ◽  
Ground Tissue ◽  
Stem Anatomy ◽  
Perforation Plate ◽  
Close Relatives ◽  
Plate Type

Abstract Apioideae is the biggest and the most diverse of four subfamilies recognised within Apiaceae. Except for a few, likely derived, woody clades, most representatives of this subfamily are herbaceous. In the present study, we assessed stem anatomy of 87, mostly therophytic and hemicryptophytic, species from at least 20 distinct lineages of Apioideae, and juxtaposed them with 67 species from our previous anatomical projects also focused on this subfamily. Comparing our data with the literature, we found that wood anatomy does not allow for a distinction between apioids and their close relatives (Azorelloideae, Saniculoideae), but more distantly related Mackinlayoideae differ from Apioideae in their perforation plate type. Vessel element and fibre length, and vessel diameter were positively correlated with plant height: phenomena already reported in literature. Similar pattern was retrieved for vertical intervessel pit diameter. Wood ground tissue in apioids ranges from entirely fibrous to parenchymatous. The shortening of internodes seems to favour the formation of parenchymatic ground tissue, whereas the early shift to flowering promotes the deposition of fibrous wood in monocarpic species. These results support a hypothesis on interdependence among internode length, reproductive strategy, and wood ground tissue type.

scholarly journals Comprehensive surveillance data suggest a prominent role of parvovirus B19 infection in Belarus and the presence of a third subtype within subgenotype 1a

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marina A. Yermalovich ◽  
Alina M. Dronina ◽  
Galina V. Semeiko ◽  
Elena O. Samoilovich ◽  
Vladislav V. Khrustalev ◽  
...  
Keyword(s):  
Clinical Presentation ◽  
Parvovirus B19 ◽  
Phylogenetic Analyses ◽  
Erythema Infectiosum ◽  
High Incidence ◽  
Molecular Investigation ◽  
Common Clinical Presentation ◽  
Parvovirus B19 Infection ◽  
Comprehensive Surveillance

AbstractHuman parvovirus B19 (B19V) infection is not notifiable in Belarus and its most common clinical presentation erythema infectiosum (EI) is often difficult to distinguish from other exanthematous diseases. The objective of this study was to provide comprehensive data about EI epidemiology in Belarus based on the serological and molecular investigation of samples from measles and rubella discarded cases collected between 2005 and 2019. Overall, 4919 sera were investigated for IgM antibodies against B19V and the positive cases were analysed according to year, season and age. B19V DNA was amplified by PCR in a total of 238 sera from all over the country, and sequenced for phylogenetic analyses. B19V infection was confirmed in 1377 (27.8%) measles and rubella discarded cases. Two high incidence periods and a seasonal increase of EI between mid-February to mid-July were identified. Children from 4 to 6 and from 7 to 10 years of age represented the largest groups of patients (22.51% and 22.66% of all cases, respectively), followed by adults between 20 and 29 years of age (14.23%). Among the 238 B19Vs sequenced, one belonged to subgenotype 3b and 237 to subgenotype 1a with 81 (34.2%) clustering with subtypes 1a1 and 153 (64.6%) with 1a2. Three strains (1.2%) formed an additional, well-supported cluster suggesting the presence of another subtype of 1a, tentatively named 1a3. The epidemiological and molecular analyses highlighted not only the prominent role of B19V in exanthematous diseases in Belarus, but also suggested a previously underestimated diversity of subgenotype 1a sequences with a third subtype 1a3.

scholarly journals Superoxide Dismutase Multigene Family from a Primitive Chondrostean Sturgeon, Acipenser baerii: Molecular Characterization, Evolution, and Antioxidant Defense during Development and Pathogen Infection

Antioxidants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 232
Author(s):  
Chan-Hee Kim ◽  
Eun Jeong Kim ◽  
Yoon Kwon Nam
Keyword(s):  
Phylogenetic Analyses ◽  
Transcriptional Response ◽  
Distribution Patterns ◽  
Structural Features ◽  
Antioxidant Defenses ◽  
Tissue Type ◽  
Vertebrate Lineage ◽  
Acipenser Baerii ◽  
Copper Zinc ◽  
Different Response

Three distinct superoxide dismutases (SODs)—copper/zinc-SOD (SOD1), manganese-SOD (SOD2), and extracellular copper/zinc-SOD (SOD3)—were identified from a primitive chondrostean fish, Acipenser baerii, enabling the comparison of their transcriptional regulation patterns during development, prelarval ontogeny, and immune stimulation. Each A. baerii SOD isoform (AbSOD) shared conserved structural features with its vertebrate orthologs; however, phylogenetic analyses hypothesized a different evolutionary history for AbSOD3 relative to AbSOD1 and AbSOD2 in the vertebrate lineage. The AbSOD isoforms showed different tissue distribution patterns; AbSOD1 was predominantly expressed in most tissues. The expression of the AbSOD isoforms showed isoform-dependent dynamic modulation according to embryonic development and prelarval ontogenic behaviors. Prelarval microinjections revealed that lipopolysaccharide only induced AbSOD3 expression, while Aeromonas hydrophila induced the expression of AbSOD2 and AbSOD3. In fingerlings, the transcriptional response of each AbSOD isoform to bacterial infection was highly tissue-specific, and the three isoforms exhibited different response patterns within a given tissue type; AbSOD3 was induced the most sensitively, and its induction was the most pronounced in the kidneys and skin. Collectively, these findings suggest isoform-dependent roles for the multigene SOD family in antioxidant defenses against the oxidative stress associated with development and immune responses in these endangered sturgeon fish.

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