scholarly journals Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of the relationship of angiosperms and Gnetales

Paleobiology ◽  
2018 ◽  
Vol 44 (3) ◽  
pp. 490-510 ◽  
Author(s):  
Mario Coiro ◽  
Guillaume Chomicki ◽  
James A. Doyle
Keyword(s):  
Phylogenetic Signal ◽  
Plant Evolution ◽  
Morphological Data ◽  
Sensitivity Analyses ◽  
Data Sets ◽  
Seed Plant ◽  
Model Based ◽  
Plant Phylogeny ◽  
Almost All ◽  
Relationship Of

AbstractThe placement of angiosperms and Gnetales in seed plant phylogeny remains one of the most enigmatic problems in plant evolution, with morphological analyses (which have usually included fossils) and molecular analyses pointing to very distinct topologies. Almost all morphology-based phylogenies group angiosperms with Gnetales and certain extinct seed plant lineages, while most molecular phylogenies link Gnetales with conifers. In this study, we investigate the phylogenetic signal present in published seed plant morphological data sets. We use parsimony, Bayesian inference, and maximum-likelihood approaches, combined with a number of experiments with the data, to address the morphological–molecular conflict. First, we ask whether the lack of association of Gnetales with conifers in morphological analyses is due to an absence of signal or to the presence of competing signals, and second, we compare the performance of parsimony and model-based approaches with morphological data sets. Our results imply that the grouping of Gnetales and angiosperms is largely the result of long-branch attraction (LBA), consistent across a range of methodological approaches. Thus, there is a signal for the grouping of Gnetales with conifers in morphological matrices, but it was swamped by convergence between angiosperms and Gnetales, both situated on long branches. However, this effect becomes weaker in more recent analyses, as a result of addition and critical reassessment of characters. Even when a clade including angiosperms and Gnetales is still weakly supported by parsimony, model-based approaches favor a clade of Gnetales and conifers, presumably because they are more resistant to LBA. Inclusion of fossil taxa weakens rather than strengthens support for a relationship of angiosperms and Gnetales. Our analyses finally reconcile morphology with molecules in favoring a relationship of Gnetales to conifers, and show that morphology may therefore be useful in reconstructing other aspects of the phylogenetic history of the seed plants.

scholarly journals Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of the relationship of angiosperms and Gnetales

2017 ◽  
Author(s):  
Mario Coiro ◽  
Guillaume Chomicki ◽  
James A. Doyle
Keyword(s):  
Phylogenetic Signal ◽  
Plant Evolution ◽  
Sensitivity Analyses ◽  
Seed Plant ◽  
Long Branch Attraction ◽  
Model Based ◽  
Plant Phylogeny ◽  
History Of ◽  
Almost All ◽  
Relationship Of

AbstractThe placement of angiosperms and Gnetales in seed plant phylogeny remains one of the most enigmatic problems in plant evolution, with morphological analyses (which have usually included fossils) and molecular analyses pointing to very distinct topologies. Almost all morphology-based phylogenies group angiosperms with Gnetales and certain extinct seed plant lineages, while most molecular phylogenies link Gnetales with conifers. In this study, we investigate the phylogenetic signal present in published seed plant morphological datasets. We use parsimony, Bayesian inference, and maximum likelihood approaches, combined with a number of experiments with the data, to address the morphological-molecular conflict. First, we ask whether the lack of association of Gnetales with conifers in morphological analyses is due to an absence of signal or to the presence of competing signals, and second, we compare the performance of parsimony and model based approaches with morphological datasets. Our results imply that the grouping of Gnetales and angiosperms is largely the result of long branch attraction, consistent across a range of methodological approaches. Thus, there is a signal for the grouping of Gnetales with conifers in morphological matrices, but it was swamped by convergence between angiosperms and Gnetales, both situated on long branches. However, this effect becomes weaker in more recent analyses, as a result of addition and critical reassessment of characters. Even when a clade including angiosperms and Gnetales is still weakly supported by parsimony, model-based approaches favor a clade of Gnetales and conifers, presumably because they are more resistant to long branch attraction. Inclusion of fossil taxa weakens rather than strengthens support for a relationship of angiosperms and Gnetales. Our analyses finally reconcile morphology with molecules in favoring a relationship of Gnetales to conifers, and show that morphology may therefore be useful in reconstructing other aspects of the phylogenetic history of the seed plants.

scholarly journals Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

2017 ◽  
Author(s):  
Ross Mounce
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Scientific Progress ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Phylogenetic Groups ◽  
Use Of Data ◽  
Wide Range ◽  
Cladistic Analyses

In this thesis I attempt to gather together a wide range of cladistic analyses of fossil and extant taxa representing a diverse array of phylogenetic groups. I use this data to quantitatively compare the effect of fossil taxa relative to extant taxa in terms of support for relationships, number of most parsimonious trees (MPTs) and leaf stability. In line with previous studies I find that the effects of fossil taxa are seldom different to extant taxa – although I highlight some interesting exceptions. I also use this data to compare the phylogenetic signal within vertebrate morphological data sets, by choosing to compare cranial data to postcranial data. Comparisons between molecular data and morphological data have been previously well explored, as have signals between different molecular loci. But comparative signal within morphological data sets is much less commonly characterized and certainly not across a wide array of clades. With this analysis I show that there are many studies in which the evidence provided by cranial data appears to be be significantly incongruent with the postcranial data – more than one would expect to see just by the effect of chance and noise alone. I devise and implement a modification to a rarely used measure of homoplasy that will hopefully encourage its wider usage. Previously it had some undesirable bias associated with the distribution of missing data in a dataset, but my modification controls for this. I also take an in-depth and extensive review of the ILD test, noting it is often misused or reported poorly, even in recent studies. Finally, in attempting to collect data and metadata on a large scale, I uncovered inefficiencies in the research publication system that obstruct re-use of data and scientific progress. I highlight the importance of replication and reproducibility – even simple reanalysis of high profile papers can turn up some very different results. Data is highly valuable and thus it must be retained and made available for further re-use to maximize the overall return on research investment.

Generic Delimitations and Relationships of the Cape Genera Capnophyllum, Dasispermum, and Sonderina, the North African Genera Krubera and Stoibrax, and a New Monotypic Genus of the Subfamily Apioideae (Apiaceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 580-594 ◽  
Author(s):  
Anthony R. Magee ◽  
Ben-Erik van Wyk ◽  
Patricia M. Tilney ◽  
Stephen R. Downie
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Monotypic Genus ◽  
North African ◽  
African Species ◽  
Dna Sequence Data ◽  
The North ◽  
Relationship Of

Generic circumscriptions and phylogenetic relationships of the Cape genera Capnophyllum, Dasispermum, and Sonderina are explored through parsimony and Bayesian inference analyses of nrDNA ITS and cpDNA rps16 intron sequences, morphology, and combined molecular and morphological data. The relationship of these genera with the North African genera Krubera and Stoibrax is also assessed. Analyses of both molecular data sets place Capnophyllum, Dasispermum, Sonderina, and the only southern African species of Stoibrax (S. capense) within the newly recognized Lefebvrea clade of tribe Tordylieae. Capnophyllum is strongly supported as monophyletic and is distantly related to Krubera. The monotypic genus Dasispermum and Stoibrax capense are embedded within a paraphyletic Sonderina. This complex is distantly related to the North African species of Stoibrax in tribe Apieae, in which the type species, Stoibrax dichotomum, occurs. Consequently, Dasispermum is expanded to include both Sonderina and Stoibrax capense. New combinations are formalized for Dasispermum capense, D. hispidum, D. humile, and D. tenue. An undescribed species from the Tanqua Karoo in South Africa is also closely related to Capnophyllum and the Dasispermum–Sonderina complex. The genus Scaraboides is described herein to accommodate the new species, S. manningii. This monotypic genus shares the dorsally compressed fruit and involute marginal wings with Capnophyllum, but is easily distinguished by its erect branching habit, green leaves, scabrous umbels, and fruit with indistinct median and lateral ribs, additional solitary vittae in each marginal wing, and parallel, closely spaced commissural vittae. Despite the marked fruit similarities with Capnophyllum, analyses of DNA sequence data place Scaraboides closer to the Dasispermum–Sonderina complex, with which it shares the erect habit, green (nonglaucous) leaves, and scabrous umbels.

scholarly journals Vegetative and reproductive innovations of early land plants: implications for a unified phylogeny

2000 ◽  
Vol 355 (1398) ◽  
pp. 769-793 ◽  
Author(s):  
Karen Sue Renzaglia ◽  
R. Joel Duff ◽  
Daniel L. Nickrent ◽  
David J. Garbary
Keyword(s):  
Phylogenetic Signal ◽  
Phenotypic Variability ◽  
Land Plant ◽  
Land Plants ◽  
Total Evidence ◽  
Data Sets ◽  
Data Set ◽  
Plant Phylogeny ◽  
Male Gametes ◽  
Early Land

As the oldest extant lineages of land plants, bryophytes provide a living laboratory in which to evaluate morphological adaptations associated with early land existence. In this paper we examine reproductive and structural innovations in the gametophyte and sporophyte generations of hornworts, liverworts, mosses and basal pteridophytes. Reproductive features relating to spermatogenesis and the architecture of motile male gametes are overviewed and evaluated from an evolutionary perspective. Phylogenetic analyses of a data set derived from spermatogenesis and one derived from comprehensive morphogenetic data are compared with a molecular analysis of nuclear and mitochondrial small subunit rDNA sequences. Although relatively small because of a reliance on water for sexual reproduction, gametophytes of bryophytes are the most elaborate of those produced by any land plant. Phenotypic variability in gametophytic habit ranges from leafy to thalloid forms with the greatest diversity exhibited by hepatics. Appendages, including leaves, slime papillae and hairs, predominate in liverworts and mosses, while hornwort gametophytes are strictly thalloid with no organized external structures. Internalization of reproductive and vegetative structures within mucilage–filled spaces is an adaptive strategy exhibited by hornworts. The formative stages of gametangial development are similar in the three bryophyte groups, with the exception that in mosses apical growth is intercalated into early organogenesis, a feature echoed in moss sporophyte ontogeny. A monosporangiate, unbranched sporophyte typifies bryophytes, but developmental and structural innovations suggest the three bryophyte groups diverged prior to elaboration of this generation. Sporophyte morphogenesis in hornworts involves non–synchronized sporogenesis and the continued elongation of the single sporangium, features unique among archegoniates. In hepatics, elongation of the sporophyte seta and archegoniophore is rapid and requires instantaneous wall expandability and hydrostatic support. Unicellular, spiralled elaters and capsule dehiscence through the formation of four regular valves are autapomorphies of liverworts. Sporophytic sophistications in the moss clade include conducting tissue, stomata, an assimilative layer and an elaborate peristome for extended spore dispersal. Characters such as stomata and conducting cells that are shared among sporophytes of mosses, hornworts and pteridophytes are interpreted as parallelisms and not homologies. Our phylogenetic analysis of three different data sets is the most comprehensive to date and points to a single phylogenetic solution for the evolution of basal embryophytes. Hornworts are supported as the earliest divergent embryophyte clade with a moss/liverwort clade sister to tracheophytes. Among pteridophytes, lycophytes are monophyletic and an assemblage containing ferns, Equisetum and psilophytes is sister to seed plants. Congruence between morphological and molecular hypotheses indicates that these data sets are tracking the same phylogenetic signal and reinforces our phylogenetic conclusions. It appears that total evidence approaches are valuable in resolving ancient radiations such as those characterizing the evolution of early embryophytes. More information on land plant phylogeny can be found at: http://www.science.siu.edu/landplants/index.html.

scholarly journals Description of a New Scaled Species of Ptychostomella (Gastrotricha: Macrodasyida) from the Brazilian Coast and a Cladistics Analysis of the Genus

Taxonomy ◽  
2021 ◽  
Vol 1 (4) ◽  
pp. 278-289
Author(s):  
Thiago Q. Araújo ◽  
André R. S. Garraffoni
Keyword(s):  
Phylogenetic Signal ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Morphological Data ◽  
North Coast ◽  
Brazilian Coast ◽  
The North ◽  
Lateral Body ◽  
Relationship Of ◽  
Internal Relationship

A new species of marine Gastrotricha from the north coast of São Paulo state, Brazil, is described. Adults of Ptychostomella sebastiana sp. nov. are unique in that they possess a pair of dorsolateral “rod-like” cephalic sensory organs and subrectangular scales covering the lateral body surfaces. A cladistic analysis was performed to investigate the internal relationship of the representatives of the taxa based on morphological data. Our analysis supported the monophyly of the taxon Ptychostomella, but its internal phylogenetic relationships are not well established due to the low phylogenetic signal of morphological characters used in the present study.

scholarly journals Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae

2020 ◽  
Vol 69 (4) ◽  
pp. 613-622 ◽  
Author(s):  
Rong Zhang ◽  
Yin-Huan Wang ◽  
Jian-Jun Jin ◽  
Gregory W Stull ◽  
Anne Bruneau ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Strong Support ◽  
Molecular Data ◽  
Data Sets ◽  
Plastome Evolution ◽  
The Family ◽  
Phylogenetic Resolution ◽  
History Of ◽  
Phylogenomic Analyses ◽  
Almost All

Abstract Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae’s thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding data sets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family’s complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone. [Leguminosae; maximum likelihood; phylogenetic conflict; plastome; recalcitrant relationships; stochasticity; systematic error.]

scholarly journals Phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed plant “tree of life”

2020 ◽  
Author(s):  
Yongzeng Zhang ◽  
Tao Deng ◽  
Lu Sun ◽  
Jacob B Landis ◽  
Michael J Moore ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Random Distribution ◽  
Phylogenetic Signal ◽  
Plant Secondary Metabolites ◽  
Distribution Patterns ◽  
Plant Evolution ◽  
Seed Plants ◽  
Seed Plant ◽  
Multiple Origins ◽  
Selective Forces

Abstract To evaluate phylogenetic patterns of the distribution and evolution of plant secondary metabolites (PSMs), we selected 8 classes of PSMs and mapped them onto an updated phylogenetic tree including 437 families of seed plants. Significant phylogenetic signal was detected in 17 of the 18 tested seed plant clades for at least one of the 8 PSM classes using the D statistic. Phylogenetic signal, nevertheless, indicated weak clustering of PSMs compared to a random distribution across all seed plants. The observed signal suggests strong diversifying selection during seed plant evolution and/or relatively weak evolutionary constraints on the evolution of PSMs. In the survey of the current phylogenetic distributions of PSM, we found that multiple origins of PSM biosynthesis due to external selective forces for diverse genetic pathways may have played important roles. In contrast, a single origin of PSM seems rather uncommon. The distribution patterns for PSMs observed in this study may also be useful in the search for natural compounds for medicinal purposes.

scholarly journals A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data

2020 ◽  
Author(s):  
Nicolás Mongiardino Koch ◽  
Jeffrey R Thompson
Keyword(s):  
Large Scale ◽  
Sea Urchins ◽  
Phylogenetic Signal ◽  
Total Evidence ◽  
Morphological Data ◽  
Data Sets ◽  
Crown Group ◽  
Data Set ◽  
Paleontological Data ◽  
Time Calibration

Abstract Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.]

scholarly journals Character congruence and phylogenetic signal in molecular and morphological data sets: a case study in the living Iguanas (Squamata, Iguanidae)

1996 ◽  
Vol 13 (8) ◽  
pp. 1087-1105 ◽  
Author(s):  
J. W. Sites ◽  
S. K. Davis ◽  
T. Guerra ◽  
J. B. Iverson ◽  
H. L. Snell
Keyword(s):  
Phylogenetic Signal ◽  
Morphological Data ◽  
Data Sets
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