scholarly journals Early evolution of the angiosperm clade Asteraceae in the Cretaceous of Antarctica

2015 ◽  
Vol 112 (35) ◽  
pp. 10989-10994 ◽  
Author(s):  
Viviana D. Barreda ◽  
Luis Palazzesi ◽  
Maria C. Tellería ◽  
Eduardo B. Olivero ◽  
J. Ian Raine ◽  
...  
Keyword(s):  
Pollen Grains ◽  
Terrestrial Ecosystems ◽  
Flowering Plants ◽  
Flowering Plant ◽  
Recent Common Ancestor ◽  
Time Interval ◽  
Most Recent Common Ancestor ◽  
The Family ◽  
Dramatic Rise ◽  
Molecular Phylogenetic

The Asteraceae (sunflowers and daisies) are the most diverse family of flowering plants. Despite their prominent role in extant terrestrial ecosystems, the early evolutionary history of this family remains poorly understood. Here we report the discovery of a number of fossil pollen grains preserved in dinosaur-bearing deposits from the Late Cretaceous of Antarctica that drastically pushes back the timing of assumed origin of the family. Reliably dated to ∼76–66 Mya, these specimens are about 20 million years older than previously known records for the Asteraceae. Using a phylogenetic approach, we interpreted these fossil specimens as members of an extinct early diverging clade of the family, associated with subfamily Barnadesioideae. Based on a molecular phylogenetic tree calibrated using fossils, including the ones reported here, we estimated that the most recent common ancestor of the family lived at least 80 Mya in Gondwana, well before the thermal and biogeographical isolation of Antarctica. Most of the early diverging lineages of the family originated in a narrow time interval after the K/P boundary, 60–50 Mya, coinciding with a pronounced climatic warming during the Late Paleocene and Early Eocene, and the scene of a dramatic rise in flowering plant diversity. Our age estimates reduce earlier discrepancies between the age of the fossil record and previous molecular estimates for the origin of the family, bearing important implications in the evolution of flowering plants in general.

scholarly journals The age of flowering plants is unknown

2021 ◽  
Author(s):  
Hervé Sauquet ◽  
Santiago Ramírez-Barahona ◽  
Susana Magallón
Keyword(s):  
Molecular Data ◽  
Flowering Plants ◽  
Molecular Dating ◽  
Flowering Plant ◽  
Recent Common Ancestor ◽  
Crown Group ◽  
Most Recent Common Ancestor ◽  
Research Fields ◽  
History Of ◽  
Future Work

The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ca. 140 Ma (Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both quantitative analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age), the age(s) of emergence of their unique, distinctive features including flowers (morphological age), and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior. Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as unknown (140–270 Ma) and that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.

scholarly journals Molecular evolution of dengue virus types 1 and 4 in Korean travelers

2021 ◽  
Vol 166 (4) ◽  
pp. 1103-1112
Author(s):  
Eun-Ha Hwang ◽  
Green Kim ◽  
Hoyin Chung ◽  
Hanseul Oh ◽  
Jong-Hwan Park ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Positive Selection ◽  
Recent Common Ancestor ◽  
Coding Region ◽  
Genotype I ◽  
Most Recent Common Ancestor ◽  
Evolutionary Features ◽  
Molecular Phylogenetic ◽  
First Time ◽  
Global Travel

AbstractDengue virus (DV) is a mosquito-borne virus that is endemic to many tropical and subtropical areas. Recently, the annual incidence of DV infection has increased worldwide, including in Korea, due to global warming and increased global travel. We therefore sought to characterize the molecular and evolutionary features of DV-1 and DV-4 isolated from Korean overseas travelers. We used phylogenetic analysis based on the full coding region to classify isolates of DV-1 in Korea into genotype I (43251, KP406802), genotype IV (KP406803), and genotype V (KP406801). In addition, we found that strains of DV-4 belonged to genotype I (KP406806) and genotype II (43257). Evidence of positive selection in DV-1 strains was identified in the C, prM, NS2A, and NS5 proteins, whereas DV-4 showed positive selection only in the non-structural proteins NS2A, NS3, and NS5. The substitution rates per site per year were 5.58 × 10-4 and 6.72 × 10-4 for DV-1 and DV-4, respectively, and the time of the most recent common ancestor was determined using the Bayesian skyline coalescent method. In this study, the molecular, phylogenetic, and evolutionary characteristics of Korean DV-1 and DV-4 isolates were evaluated for the first time.

scholarly journals Simulating trees with millions of species

2020 ◽  
Vol 36 (9) ◽  
pp. 2907-2908 ◽  
Author(s):  
Stilianos Louca
Keyword(s):  
Common Ancestor ◽  
R Package ◽  
Supplementary Information ◽  
Recent Common Ancestor ◽  
Time Interval ◽  
Simulation Tools ◽  
Parametric Bootstrapping ◽  
Most Recent Common Ancestor ◽  
Large Trees ◽  
Efficient Software

Abstract Motivation The birth-death (BD) model constitutes the theoretical backbone of most phylogenetic tools for reconstructing speciation/extinction dynamics over time. Performing simulations of reconstructed trees (linking extant taxa) under the BD model in backward time, conditioned on the number of species sampled at present day and, in some cases, a specific time interval since the most recent common ancestor (MRCA), is needed for assessing the performance of reconstruction tools, for parametric bootstrapping and for detecting data outliers. The few simulation tools that exist scale poorly to large modern phylogenies, which can comprise thousands or even millions of tips (and rising). Results Here I present efficient software for simulating reconstructed phylogenies under time-dependent BD models in backward time, conditioned on the number of sampled species and (optionally) on the time since the MRCA. On large trees, my software is 1000–10 000 times faster than existing tools. Availability and implementation The presented software is incorporated into the R package ‘castor’, which is available on The Comprehensive R Archive Network (CRAN). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Tadpole types of Chinese megophryid frogs (Anura: Megophryidae) and implications for larval evolution

2011 ◽  
Vol 57 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Cheng Li ◽  
Xian-Guang Guo ◽  
Yue-Zhao Wang
Keyword(s):  
Common Ancestor ◽  
Historical Change ◽  
Recent Common Ancestor ◽  
Type B ◽  
Oral Disc ◽  
Most Recent Common Ancestor ◽  
Mitochondrial Cytochrome B ◽  
The Family ◽  
Type C ◽  
Body Shapes

Abstract The larval body shapes and oral discs of 30 frog species from the family Megophryidae from China were examined. Using a phylogenetic framework derived from a Bayesian analysis of published mitochondrial cytochrome b and 16S rRNA gene sequences, we deduced a pattern of historical change among megophryid larval forms. These larvae were categorized into four types according to their body shapes and oral discs: (A) Leptobrachiini type, (B) Lalax type, (C) Brachytarsophrys type, and (D) Megophryini type, of which B and C are novel types. Type A is characterized by a typical oral disc with multiple rows of teeth, representing the tadpole type of the most recent common ancestor of the family Megophryidae. Type B has a typical oral disc with reduced tooth rows, an elongated labium, and integumentary glands. Type C has no labial teeth and a smaller umbelliform oral disc. Type D is characterized by a lack of labial teeth, an enlarged umbelliform oral disc, representing the tadpole of the most recent common ancestor of the subfamily Megophryinae. Our analysis supports the hypothesis that the umbelliform oral disc is apomorphic and also reveals the close association between morphology and microhabitat.

Early divergence of an Azorean endemic species in the moss genus Rhynchostegiella (Brachytheciaceae)

Phytotaxa ◽  
2015 ◽  
Vol 210 (1) ◽  
pp. 60 ◽  
Author(s):  
Alain Vanderpoorten ◽  
Jairo PatiÑo ◽  
Gerard Dirkse ◽  
TOM BLOCKEEL ◽  
Lars Hedenäs
Keyword(s):  
Endemic Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
Recent Common Ancestor ◽  
Width Ratio ◽  
Most Recent Common Ancestor ◽  
Molecular Phylogenetic ◽  
Variable Species ◽  
The One ◽  
A New Species

Using the moss genus Rhynchostegiella (Brachytheciaceae) as a model, we address the question of whether taxonomic shortcomings account for the extremely low rates of endemism reported in the Azorean bryophyte flora. Eight accessions initially assigned to three of the four previously reported species in the Azores were identified as a distinct species using the Generalized Mixed Yule Coalescent method in the context of a molecular phylogenetic analysis of the genus. Rhynchostegiella azorica sp. nov. is therefore described as a new species that is endemic to the Azores. Its morphological features intergrade with those observed in other species, with a seta that ranges from almost smooth to rough; a length to width ratio of the laminal cells that matches the one of the R. curviseta group; but a leaf apex that is typical of the R. tenella group. This suggests that previous reports of four Rhynchostegiella species from Azores are erroneous and that a single, morphologically variable species, R. azorica, occurs in the archipelago. Rhynchostegiella azorica is sister to the remainder of the species of the genus, whose most recent common ancestor was dated at 4–20 Ma. This points to a more ancient origin in comparison with other Macaronesian endemic species of the genus. The unexpected discovery of an Azorean endemic species in Rhynchostegiella suggests that patterns of endemicity in the Azorean bryophyte flora are not well estimated from traditional taxonomic knowledge and point to the necessity of an extensive integrative taxonomic revision.

scholarly journals Phylogenetic Relationships Within the Family Potyviridae: Wheat Streak Mosaic Virus and Brome Streak Mosaic Virus Are Not Members of the Genus Rymovirus

1998 ◽  
Vol 88 (8) ◽  
pp. 782-787 ◽  
Author(s):  
Drake C. Stenger ◽  
Jeffrey S. Hall ◽  
Il-Ryong Choi ◽  
Roy French
Keyword(s):  
Mosaic Virus ◽  
Type Species ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Wheat Streak Mosaic Virus ◽  
Recent Common Ancestor ◽  
Amino Acid Residues ◽  
Most Recent Common Ancestor ◽  
The Family ◽  
Eriophyid Mites

The complete nucleotide sequence of wheat streak mosaic virus (WSMV) has been determined based on complementary DNA clones derived from the 9,384-nucleotide (nt) RNA of the virus. The genome of WSMV has a 130-nt 5′ leader and 149-nt 3′-untranslated region and is polyadenylated at the 3′ end. WSMV RNA encodes a single polyprotein of 3,035 amino acid residues and has a deduced genome organization typical for a member of the family Potyviridae (5′-P1/HC-Pro/P3/6K1/CI/6K2/VPg-NIa/NIb/CP-3′). Because WSMV shares with ryegrass mosaic virus (RGMV) the biological property of transmission by eriophyid mites, WSMV has been assigned to the genus Rymovirus, of which RGMV is the type species. Phylogenetic analyses were conducted with complete polyprotein or NIb protein sequences of 11 members of the family Potyviridae, including viruses of monocots or dicots and viruses transmitted by aphids, whiteflies, and mites. WSMV and the monocot-infecting, mite-transmitted brome streak mosaic virus (BrSMV) are sister taxa and share a most recent common ancestor with the whitefly-transmitted sweet potato mild mottle virus, the type species of the proposed genus “Ipomovirus.” In contrast, RGMV shares a most recent common ancestor with aphid-transmitted species of the genus Potyvirus. These results indicate that WSMV and BrSMV should be classified within a new genus of the family Potyviridae and should not be considered species of the genus Rymovirus.

Towards uncovering evolution of lineage-specific calcium oxalate crystal patterns in Piperales

Botany ◽  
2015 ◽  
Vol 93 (3) ◽  
pp. 159-169 ◽  
Author(s):  
Harry T. Horner ◽  
Marie-Stéphanie Samain ◽  
Sarah T. Wagner ◽  
Stefan Wanke
Keyword(s):  
Calcium Oxalate ◽  
Recent Common Ancestor ◽  
Calcium Oxalate Crystal ◽  
Character Reconstruction ◽  
Most Recent Common Ancestor ◽  
Molecular Phylogenetic ◽  
Crystal Type ◽  
Phylogenetic Hypotheses ◽  
Crystal Sand ◽  
Ancestral Character Reconstruction

Piperales is among the largest and most diverse angiosperm orders (>4000 species), occurring broadly in tropical and temperate habitats. Twenty-four of the species from 12 genera, representing all lineages of Piperales, except the holoparasitic Hydnoraceae, display a mixture of leaf calcium oxalate crystal types found in previous studies of the two genera of Piperaceae subfamily Piperoideae (Peperomia Ruiz & Pav. and Piper L.). Crystal macropatterns, a result of varying leaf anatomies and diverse habitats, are investigated in a comparative way by using clearings and recent molecular phylogenetic hypotheses to trace crystal types and macropattern evolution. Ancestral character reconstruction reveals that the most recent common ancestor of Piperales had either crystal sand or druses or both and that prisms, raphides, and styloids are derived from the ancestral crystal type(s). These results are also recovered for both the ancestors of the perianth-less and the perianth-bearing Piperales. Raphides or druses are found in the two other subfamilies of Piperaceae (Verhuellioideae and Zippelioideae). Asaraceae and Lactoridaceae display crystal sand, whereas Aristolochia L. (Aristolochiaceae) species display mainly druses. Our crystal investigation, combined with ancestral character reconstruction, suggests that styloids, raphides, and prisms are derived within Piperales from crystal sand or druses.

scholarly journals Patterns of Natural Selection on Mitochondrial Protein-Coding Genes in Lungless Salamanders: Relaxed Purifying Selection and Presence of Positively Selected Codon Sites in the Family Plethodontidae

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Ryosuke Kakehashi ◽  
Atsushi Kurabayashi
Keyword(s):  
Mitochondrial Protein ◽  
Purifying Selection ◽  
Recent Common Ancestor ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Most Recent Common Ancestor ◽  
Plethodontid Salamander ◽  
Branch Model ◽  
The Family ◽  
Oxygen Requirements

There are two distinct lungless groups in caudate amphibians (salamanders and newts) (the family Plethodontidae and the genus Onychodactylus, from the family Hynobiidae). Lunglessness is considered to have evolved in response to environmental and/or ecological adaptation with respect to oxygen requirements. We performed selection analyses on lungless salamanders to elucidate the selective patterns of mitochondrial protein-coding genes associated with lunglessness. The branch model and RELAX analyses revealed the occurrence of relaxed selection (an increase of the dN/dS ratio = ω value) in most mitochondrial protein-coding genes of plethodontid salamander branches but not in those of Onychodactylus. Additional branch model and RELAX analyses indicated that direct-developing plethodontids showed the relaxed pattern for most mitochondrial genes, although metamorphosing plethodontids had fewer relaxed genes. Furthermore, aBSREL analysis detected positively selected codons in three plethodontid branches but not in Onychodactylus. One of these three branches corresponded to the most recent common ancestor, and the others corresponded with the most recent common ancestors of direct-developing branches within Hemidactyliinae. The positive selection of mitochondrial protein-coding genes in Plethodontidae is probably associated with the evolution of direct development.

scholarly journals Plastid phylogenomic insights into relationships of all flowering plant families

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Hong-Tao Li ◽  
Yang Luo ◽  
Lu Gan ◽  
Peng-Fei Ma ◽  
Lian-Ming Gao ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Strong Support ◽  
Terrestrial Ecosystems ◽  
Nuclear Data ◽  
Molecular Data ◽  
Flowering Plants ◽  
Flowering Plant ◽  
Bootstrap Support ◽  
Plant Phylogeny ◽  
Phylogenomic Analyses

Abstract Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. Results Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. Conclusions We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.

The embyology and relationship of the Byblidaceae

1996 ◽  
Vol 9 (2) ◽  
pp. 243 ◽  
Author(s):  
JG Conran
Keyword(s):  
Pollen Grains ◽  
Anther Wall ◽  
Linear Tetrad ◽  
Polygonum Type ◽  
Phylogenetic Studies ◽  
The Family ◽  
Molecular Phylogenetic ◽  
The Subject ◽  
Relationship Of ◽  
Antipodal Cells

The relationships of the Byblidaceae have been the subject of a number of recent molecular phylogenetic studies where their traditional relationships with the Roridulaceae and other members of the Rosidae have been overturned in favour of affinities with the Asteridae, in particular to the Lentibulariaceae in the Lamiales. Although the embryological relationships between these families were the subject of an earlier study, the data for the Byblidaceae were incomplete. The family has tetrasporangiate, bilocular anthers with a glandular bi-nucleate tapetum. Formation of the anther wall appears to be of the Dicotyledonous type, and the anthers have ephemeral middle layers and apical fibrous thickenings. Simultaneous microsporogenesis results in tetrahedral tetrads of bi-nucleate pollen grains. The ovules are anatropous, unitegmic and tenuinucellate. Megasporogenesis is direct from the archesporal cell, which in Byblis liniflora Salisb. divides to produce a linear tetrad from which a chalazal megaspore is derived (contrary to a report of a micropylar megaspore in B. gigantea Lindl.). Megagametogenesis conforms to the Polygonum type, and the antipodal cells are persistent. The endosperm is ab initio Cellular and there are well developed micropylar and chalazal haustoria. Embryogenesis appears to conform to the Onagrad type noted for several of the other members of the Lamiales s.l., including the Lentibulariaceae, to which the Byblidaceae have been related in recent molecular studies.

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