scholarly journals A timeline for terrestrialization: consequences for the carbon cycle in the Palaeozoic

2012 ◽  
Vol 367 (1588) ◽  
pp. 519-536 ◽  
Author(s):  
Paul Kenrick ◽  
Charles H. Wellman ◽  
Harald Schneider ◽  
Gregory D. Edgecombe
Keyword(s):  
Carbon Cycle ◽  
Phylogenetic Trees ◽  
Relative Timing ◽  
Earth Systems ◽  
Organ Systems ◽  
Molecular Phylogenetic ◽  
Magnesium Silicates ◽  
Early Palaeozoic ◽  
Fossil Data ◽  
Time Of Origin

The geochemical carbon cycle is strongly influenced by life on land, principally through the effects of carbon sequestration and the weathering of calcium and magnesium silicates in surface rocks and soils. Knowing the time of origin of land plants and animals and also of key organ systems (e.g. plant vasculature, roots, wood) is crucial to understand the development of the carbon cycle and its effects on other Earth systems. Here, we compare evidence from fossils with calibrated molecular phylogenetic trees (timetrees) of living plants and arthropods. We show that different perspectives conflict in terms of the relative timing of events, the organisms involved and the pattern of diversification of various groups. Focusing on the fossil record, we highlight a number of key biases that underpin some of these conflicts, the most pervasive and far-reaching being the extent and nature of major facies changes in the rock record. These effects probably mask an earlier origin of life on land than is evident from certain classes of fossil data. If correct, this would have major implications in understanding the carbon cycle during the Early Palaeozoic.

scholarly journals 60 million years of co-divergence in the fig–wasp symbiosis

2005 ◽  
Vol 272 (1581) ◽  
pp. 2593-2599 ◽  
Author(s):  
Nina Rønsted ◽  
George D Weiblen ◽  
James M Cook ◽  
Nicolas Salamin ◽  
Carlos A Machado ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Time Frame ◽  
Molecular Dating ◽  
Fig Wasp ◽  
Geological Time ◽  
Molecular Phylogenetic ◽  
Pollinator Specialization ◽  
Phylogenetic Hypotheses ◽  
Fossil Data ◽  
Plant Pollinator

Figs ( Ficus ; ca 750 species) and fig wasps (Agaoninae) are obligate mutualists: all figs are pollinated by agaonines that feed exclusively on figs. This extraordinary symbiosis is the most extreme example of specialization in a plant–pollinator interaction and has fuelled much speculation about co-divergence. The hypothesis that pollinator specialization led to the parallel diversification of fig and pollinator lineages (co-divergence) has so far not been tested due to the lack of robust and comprehensive phylogenetic hypotheses for both partners. We produced and combined the most comprehensive molecular phylogenetic trees to date with fossil data to generate independent age estimates for fig and pollinator lineages, using both non-parametric rate smoothing and penalized likelihood dating methods. Molecular dating of ten pairs of interacting lineages provides an unparalleled example of plant–insect co-divergence over a geological time frame spanning at least 60 million years.

scholarly journals Molecular Phylogenetic Diversity and Biological Characterization of Diaporthe Species Associated with Leaf Spots of Camellia sinensis in Taiwan

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1434
Author(s):  
Hiran A. Ariyawansa ◽  
Ichen Tsai ◽  
Jian-Yuan Wang ◽  
Patchareeya Withee ◽  
Medsaii Tanjira ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Leaf Spot ◽  
Phylogenetic Trees ◽  
Fungal Infections ◽  
Elongation Factor ◽  
Fungal Species ◽  
Tea Leaves ◽  
Phenotypic Characters ◽  
Leaf Spots ◽  
Molecular Phylogenetic

Camellia sinensis is one of the major crops grown in Taiwan and has been widely cultivated around the island. Tea leaves are prone to various fungal infections, and leaf spot is considered one of the major diseases in Taiwan tea fields. As part of a survey on fungal species causing leaf spots on tea leaves in Taiwan, 19 fungal strains morphologically similar to the genus Diaporthe were collected. ITS (internal transcribed spacer), tef1-α (translation elongation factor 1-α), tub2 (beta-tubulin), and cal (calmodulin) gene regions were used to construct phylogenetic trees and determine the evolutionary relationships among the collected strains. In total, six Diaporthe species, including one new species, Diaporthe hsinchuensis, were identified as linked with leaf spot of C. sinensis in Taiwan based on both phenotypic characters and phylogeny. These species were further characterized in terms of their pathogenicity, temperature, and pH requirements under laboratory conditions. Diaporthe tulliensis, D. passiflorae, and D. perseae were isolated from C. sinensis for the first time. Furthermore, pathogenicity tests revealed that, with wound inoculation, only D. hongkongensis was pathogenic on tea leaves. This investigation delivers the first assessment of Diaporthe taxa related to leaf spots on tea in Taiwan.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

scholarly journals Evolutionary Dynamics of rDNA Clusters in Chromosomes of Five Clam Species Belonging to the Family Veneridae (Mollusca, Bivalvia)

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Concepción Pérez-García ◽  
Ninoska S. Hurtado ◽  
Paloma Morán ◽  
Juan J. Pasantes
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Dynamics ◽  
5S Rdna ◽  
Gene Clusters ◽  
Ruditapes Philippinarum ◽  
Ruditapes Decussatus ◽  
Rdna Cluster ◽  
Single Chromosome ◽  
Molecular Phylogenetic ◽  
Chromosomal Changes

The chromosomal changes accompanying bivalve evolution are an area about which few reports have been published. To improve our understanding on chromosome evolution in Veneridae, ribosomal RNA gene clusters were mapped by fluorescentin situhybridization (FISH) to chromosomes of five species of venerid clams (Venerupis corrugata,Ruditapes philippinarum,Ruditapes decussatus,Dosinia exoleta, andVenus verrucosa). The results were anchored to the most comprehensive molecular phylogenetic tree currently available for Veneridae. While a single major rDNA cluster was found in each of the five species, the number of 5S rDNA clusters showed high interspecies variation. Major rDNA was either subterminal to the short arms or intercalary to the long arms of metacentric or submetacentric chromosomes, whereas minor rDNA signals showed higher variability. Major and minor rDNAs map to different chromosome pairs in all species, but inR. decussatusone of the minor rDNA gene clusters and the major rDNA cluster were located in the same position on a single chromosome pair. This interspersion of both sequences was confirmed by fiber FISH. Telomeric signals appeared at both ends of every chromosome in all species. FISH mapping data are discussed in relation to the molecular phylogenetic trees currently available for Veneridae.

Can the Cambrian explosion be inferred through molecular phylogeny?

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 15-25
Author(s):  
Hervé Philippe ◽  
Anne Chenuil ◽  
André Adoutte
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Phylogenetic Reconstruction ◽  
Cambrian Explosion ◽  
Bootstrap Support ◽  
Time Interval ◽  
Short Time Interval ◽  
Data Set ◽  
Molecular Phylogenetic ◽  
Animal Phyla

Most of the major invertebrate phyla appear in the fossil record during a relatively short time interval, not exceeding 20 million years (Myr), 540-520 Myr ago. This rapid diversification is known as the `Cambrian explosion'. In the present paper, we ask whether molecular phylogenetic reconstruction provides confirmation for such an evolutionary burst. The expectation is that the molecular phylogenetic trees should take the form of a large unresolved multifurcation of the various animal lineages. Complete 18S rRNA sequences of 69 extant representatives of 15 animal phyla were obtained from data banks. After eliminating a major source of artefact leading to lack of resolution in phylogenetic trees (mutational saturation of sequences), we indeed observe that the major lines of triploblast coelomates (arthropods, molluscs, echinoderms, chordates...) are very poorly resolved i.e. the nodes defining the various clades are not supported by high bootstrap values. Using a previously developed procedure consisting of calculating bootstrap proportions of each node of the tree as a function of increasing amount of nucleotides (Lecointre, G., Philippe, H. Le, H. L. V. and Le Guyader, H. (1994) Mol. Phyl. Evol., in press) we obtain a more informative indication of the robustness of each node. In addition, this procedure allows us to estimate the number of additional nucleotides that would be required to resolve confidently the currently uncertain nodes; this number turns out to be extremely high and experimentally unfeasible. We then take this approach one step further: using parameters derived from the above analysis, assuming a molecular clock and using palaeontological dates for calibration, we establish a relationship between the number of sites contained in a given data set and the time interval that this data set can confidently resolve (with 95% bootstrap support). Under these assumptions, the presently available 18S rRNA database cannot confidently resolve cladogenetic events separated by less than about 40 Myr. Thus, at the present time, the potential resolution by the palaeontological approach is higher than that by the molecular one.

Lifeforms as criterion for species delimitation: Are Aristida adscensionis and A. coerulescens (Aristidoideae, Poaceae) two species?

Phytotaxa ◽  
2019 ◽  
Vol 393 (1) ◽  
pp. 67 ◽  
Author(s):  
MIKE THIV ◽  
J. ALFREDO REYES-BETANCORT ◽  
ORI FRAGMAN-SAPIR
Keyword(s):  
Morphometric Analysis ◽  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Life Forms ◽  
Clear Separation ◽  
Taxonomic Treatment ◽  
Molecular Phylogenetic ◽  
The Mediterranean

The distinction of the perennial Aristida coerulescens from the annual A. adscensionis and its taxonomic treatment has been subject of long discussions. We here include accessions from the Mediterranean and Macaronesia for molecular phylogenetic analyses and conducted a morphometric analysis. A lineage of A. adscensionis, A. coerulescens and A. effusa is well supported in phylogenetic trees. Moreover, a group of Mediterranean, Macaronesia and Arabian A. coerulescens and A. adscensionis is revealed where both taxa are intermingled. A morphological analysis of traditionally used spikelet characters did not indicate a clear separation of both taxa. We therefore conclude that A. coerulescens should best be treated as synonym of A. adscensionis. The differential character of annual and perennial life forms seems to be plastic in this taxon indicating rapid shifts between these two strategies. 

scholarly journals Penicillin-Binding Protein Typing, Antibiotic Resistance Gene Identification, and Molecular Phylogenetic Analysis of Meropenem-Resistant Streptococcus pneumoniae Serotype 19A-CC3111 Strains in Japan

2019 ◽  
Vol 63 (9) ◽  
Author(s):  
Satoshi Nakano ◽  
Takao Fujisawa ◽  
Yutaka Ito ◽  
Bin Chang ◽  
Yasufumi Matsumura ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Amino Acid ◽  
Phylogenetic Trees ◽  
Binding Protein ◽  
Antibiotic Resistance Gene ◽  
Multidrug Resistant ◽  
Penicillin Binding Protein ◽  
Motif Analysis ◽  
Molecular Phylogenetic ◽  
Susceptible Clone

ABSTRACT Since the introduction of pneumococcal conjugate vaccines, the prevalence of non-meropenem-susceptible pneumococci has been increasing in Japan. In an earlier study, we demonstrated that multidrug-resistant serotype 15A-ST63 in Japan has a specific pbp1a sequence (pbp1a-13) that could promote meropenem resistance. To trace the origin of pbp1a, we analyzed isolates of serotype 19A-CC3111, which is the most prevalent non-meropenem-susceptible clone in Japan. We analyzed a total of 119 serotype 19A-CC3111 strains recovered in Japan using whole-genome sequencing. Of the 119 isolates, 53 (44.5%) harbored pbp1a-13, indicating that the clone may be the primary reservoir of the pbp1a type and that the pbp1a region may be horizontally transferred between different serotype strains. The single acquisition of pbp1a-13 seemed to cause only penicillin resistance and not multidrug resistance; a combination of penicillin-binding protein (PBP) recombination in the pbp2b and/or pbp2x region(s) with acquisition of pbp1a-13 caused multidrug resistance. Conserved amino acid motif analysis suggested that the pbp1a 370SXXK, pbp2b 448SXN, and pbp2x 337SXXN motifs were the candidates for amino acid substitutions increasing the MICs of meropenem, cefotaxime, and penicillin. We identified a specific clone that was correlated with multidrug resistance, although no correlation was observed between phylogenetic trees generated using core genomes and those generated with only the cps locus. All tested isolates were highly erythromycin resistant, and most harbored mefE within macrolide efflux genetic assembly (MEGA) elements and ermB within Tn917, which was inserted within Tn916 and exhibited a structure identical to that of Tn2017.

scholarly journals Jumping through the hoops: the challenges of daffodil (Narcissus) classification

2019 ◽  
Vol 190 (4) ◽  
pp. 389-404 ◽  
Author(s):  
Kálmán Könyves ◽  
John David ◽  
Alastair Culham
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Plastid Dna ◽  
Microsatellite Data ◽  
Population Sampling ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Nuclear Microsatellite ◽  
Congruent Group ◽  
First Time

Abstract Hoop-petticoat daffodils are a morphologically congruent group comprised of two distinct lineages in molecular phylogenetic trees of Narcissus. It is possible that the morphological similarity is a product of both historic and current low-level gene flow between these lineages. For the first time, we report population sampling from across the entire range of distribution covering the Iberian Peninsula and Morocco. In total, 455 samples were collected from 59 populations. Plastid DNA sequences of matK and ndhF were generated alongside 11 microsatellite loci to permit comparison between plastid and nuclear lineage histories. The plastid DNA phylogenetic tree was highly congruent with previous molecular studies and supported the recognition of these two lineages of hoop-petticoat daffodils as separate sections. Assignment of samples to sections sometimes differed between plastid DNA and (nuclear) microsatellite data. In these cases, the taxa had previously been the focus of dissent in taxonomic placement based on morphology. These discrepancies could be explained by hybridization and introgression among the two lineages during the evolution of hoop-petticoat daffodils, and shows that placement of species in sections is dependent on the source of data used. This study underlines the complex evolutionary history of Narcissus and highlights the discrepancies between floral morphology and phylogeny, which provides a continuing challenge for the systematics of Narcissus.

On the taxonomic status of the genus Dichodon (Caryophyllaceae: tribe Alsineae): morphological and molecular evidence reassessed

Phytotaxa ◽  
2018 ◽  
Vol 360 (3) ◽  
pp. 220 ◽  
Author(s):  
ZAHRA ARABI ◽  
FARROKH GHAHREMANINEJAD ◽  
RICHARD K. RABELER ◽  
IRINA SOKOLOVA ◽  
GÜNTHER HEUBL ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Strong Support ◽  
Taxonomic Status ◽  
Molecular Evidence ◽  
Herbarium Specimens ◽  
Arctic Regions ◽  
Morphological Studies ◽  
The Status ◽  
Molecular Phylogenetic ◽  
New Synonymy

The status of the genus Dichodon has long been debated, and its taxonomic position in tribe Alsineae has been changed during the time from a section or subgenus in Cerastium to genus sister to Holosteum. This group comprises important members of wet meadows in alpine and subalpine vegetation of Europe, arctic regions, and SW-Asia plus one species known as a weed in N-America, and a further one occuring in mountains of Taiwan. In order to clarify the taxonomic questions concerning this group and its species delimitation, we constructed phylogenetic trees, selecting several species belonging to tribe Alsineae as representatives of major lineages of this tribe as well as several accessions of Dichodon. Morphological studies focused more intensively on members of Dichodon using herbarium specimens and direct field examinations. The results confirm those of recent molecular phylogenetic studies, indicating Dichodon as a monophyletic genus sister to Holosteum and not Cerastium. In addition, the obtained cladograms support five distinct groups in Dichodon corresponding to five species of this genus we recognize in Iran, the focal area of this study. Seed micromorphology provides strong support for the recognition of Dichodon as a separate genus, but it is not informative at species and subspecies ranks due to constancy of most of seed characters within the genus. As part of this study, a new species—Dichodon alborzensis—is described, D. kotschyi is reported in Iran for the first time, and Cerastium schischkinii is placed in synonymy (new synonymy) under D. kotschyi.

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