scholarly journals Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3055 ◽  
Author(s):  
Andrea Cau
Keyword(s):  
Bayesian Methods ◽  
Phylogenetic Analyses ◽  
Phylogenetic Inference ◽  
Parsimony Analysis ◽  
Higher Taxa ◽  
Phylogenetic Methods ◽  
Phylogenetic Framework ◽  
Bayesian Methodologies ◽  
High Diversity ◽  
Birth Death

Bayesian phylogenetic methods integrating simultaneously morphological and stratigraphic information have been applied increasingly among paleontologists. Most of these studies have used Bayesian methods as an alternative to the widely-used parsimony analysis, to infer macroevolutionary patterns and relationships among species-level or higher taxa. Among recently introduced Bayesian methodologies, the Fossilized Birth-Death (FBD) model allows incorporation of hypotheses on ancestor-descendant relationships in phylogenetic analyses including fossil taxa. Here, the FBD model is used to infer the relationships among an ingroup formed exclusively by fossil individuals, i.e., dipnoan tooth plates from four localities in the Ain el Guettar Formation of Tunisia. Previous analyses of this sample compared the results of phylogenetic analysis using parsimony with stratigraphic methods, inferred a high diversity (five or more genera) in the Ain el Guettar Formation, and interpreted it as an artifact inflated by depositional factors. In the analysis performed here, the uncertainty on the chronostratigraphic relationships among the specimens was included among the prior settings. The results of the analysis confirm the referral of most of the specimens to the taxaAsiatoceratodus,Equinoxiodus, LavocatodusandNeoceratodus, but reject those toCeratodusandFerganoceratodus. The resulting phylogeny constrained the evolution of the Tunisian sample exclusively in the Early Cretaceous, contrasting with the previous scenario inferred by the stratigraphically-calibrated topology resulting from parsimony analysis. The phylogenetic framework also suggests that (1) the sampled localities are laterally equivalent, (2) but three localities are restricted to the youngest part of the section; both results are in agreement with previous stratigraphic analyses of these localities. The FBD model of specimen-level units provides a novel tool for phylogenetic inference among fossils but also for independent tests of stratigraphic scenarios.

Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit

2020 ◽  
Author(s):  
Benedict King
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Methods ◽  
Diversification Rate ◽  
Evolutionary Relationships ◽  
Data Sets ◽  
Tree Model ◽  
Phylogenetic Methods ◽  
History Of ◽  
Tree Topologies ◽  
Birth Death

Abstract The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several data sets with multiple phylogenetic methods, that topologies produced by tip dating are outliers as compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip dating have better fit to stratigraphy than trees recovered by other methods under both the Gap Excess Ratio (GER) and the Stratigraphic Completeness Index (SCI). This is because trees with better stratigraphic fit are assigned a higher likelihood by the fossilized birth-death tree model. However, the degree to which the tree model favors tree topologies with high stratigraphic fit metrics is modulated by the diversification dynamics of the group under investigation. In particular, when net diversification rate is low, the tree model favors trees with a higher GER compared to when net diversification rate is high. Differences in stratigraphic fit and tree topology between tip dating and other methods are concentrated in parts of the tree with weaker character signal, as shown by successive deletion of the most incomplete taxa from two data sets. These results show that tip dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit an expectation that can be overturned by strong evidence from character data. [fossilized birth-death; fossils; missing data; morphological clock; morphology; parsimony; phylogenetics.]

scholarly journals Phylogenetic analysis of SARS-CoV-2 data is difficult

2020 ◽  
Author(s):  
Benoit Morel ◽  
Pierre Barbera ◽  
Lucas Czech ◽  
Ben Bettisworth ◽  
Lukas Hübner ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Phylogenetic Inference ◽  
Daily Basis ◽  
Extreme Caution ◽  
Data Analyses ◽  
Phylogenetic Methods ◽  
Degree Of Confidence

Abstract Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.

scholarly journals Phylogeny and morphologic evolution of the Ordovician Camerata (Class Crinoidea, Phylum Echinodermata)

2017 ◽  
Vol 91 (4) ◽  
pp. 815-828 ◽  
Author(s):  
Selina R. Cole
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Major Group ◽  
Higher Taxa ◽  
Morphologic Evolution ◽  
Phylogenetic Framework ◽  
Selection For

AbstractThe subclass Camerata (Crinoidea, Echinodermata) is a major group of Paleozoic crinoids that represents an early divergence in the evolutionary history and morphologic diversification of class Crinoidea, yet phylogenetic relationships among early camerates remain unresolved. This study conducted a series of quantitative phylogenetic analyses using parsimony methods to infer relationships of all well-preserved Ordovician camerate genera (52 taxa), establish the branching sequence of early camerates, and test the monophyly of traditionally recognized higher taxa, including orders Monobathrida and Diplobathrida. The first phylogenetic analysis identified a suitable outroup for rooting the Ordovician camerate tree and assessed affinities of the atypical dicyclic family Reteocrinidae. The second analysis inferred the phylogeny of all well-preserved Ordovician camerate genera. Inferred phylogenies confirm: (1) the Tremadocian genera Cnemecrinus and Eknomocrinus are sister to the Camerata; (2) as historically defined, orders Monobathrida and Diplobathrida do not represent monophyletic groups; (3) with minimal revision, Monobathrida and Diplobathrida can be re-diagnosed to represent monophyletic clades; (4) family Reteocrinidae is more closely related to camerates than to other crinoid groups currently recognized at the subclass level; and (5) several genera in subclass Camerata represent stem taxa that cannot be classified as either true monobathrids or true diplobathrids. The clade containing Monobathrida and Diplobathrida, as recognized herein, is termed Eucamerata to distinguish its constituent taxa from more basally positioned taxa, termed stem eucamerates. The results of this study provide a phylogenetic framework for revising camerate classification, elucidating patterns of morphologic evolution, and informing outgroup selection for future phylogenetic analyses of post-Ordovician camerates.

scholarly journals Species Diversity of the Pleurostomatid Ciliate Genus Amphileptus (Ciliophora, Haptoria), With Notes on the Taxonomy and Molecular Phylogeny of Three Species

2021 ◽  
Vol 8 ◽  
Author(s):  
Lei Wu ◽  
Jiqiu Li ◽  
Alan Warren ◽  
Xiaofeng Lin
Keyword(s):  
Species Diversity ◽  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Phylogenetic Methods ◽  
Wide Range ◽  
Rdna Sequence Data ◽  
Molecular Phylogenetic ◽  
Intensive Sampling ◽  
High Diversity

Amphileptus is one of the largest genera of pleurostomatid ciliates and its species diversity has been reported in various habitats all over the world. In the present work, we review its biodiversity based on data with reliable morphological records. Our work confirms that there are 50 valid Amphileptus species, some of which have a wide range of salinity adaptability and diverse lifestyles. This genus has a high diversity in China but this might be because of the relatively intensive sampling. Phylogenetic analyses based on SSU rDNA sequence data verify the non-monophyly of the genus Amphileptus. Furthermore, two new and one poorly known Amphileptus species, namely A. shenzhenensis sp. n., A. cocous sp. n., and A. multinucleatusWang, 1934, from coastal habitats of southern China were investigated using morphological and molecular phylogenetic methods. These three species are highly similar based on their contractile vacuoles and macronuclear nodules. However, they can be discriminated by details of their living morphology and somatic kineties. We also propose two new combinations, Amphileptus polymicronuclei (Li, 1990) comb. n. (original combination Hemiophrys polymicronucleiLi, 1990) and Amphileptus salimicus (Burkovsky, 1970b) comb. n. (original combination Hemiophrys salimicaBurkovsky, 1970b).

scholarly journals Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants

2017 ◽  
Author(s):  
Marek L. Borowiec ◽  
Christian Rabeling ◽  
Seán G. Brady ◽  
Brian L. Fisher ◽  
Ted R. Schultz ◽  
...  
Keyword(s):  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Phylogenetic Inference ◽  
Death Process ◽  
Compositional Heterogeneity ◽  
Data Set ◽  
Key Species ◽  
Divergence Dating ◽  
Birth Death

AbstractKnowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the world’s most species-rich clade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the ant tree of life and the relationships among the so-called poneroid subfamilies. Here we assemble a new data set to attempt a resolution of these two problems and carry out divergence dating, focusing on the age of the root node of crown Formicidae. For the phylogenetic analyses we included data from 110 ant species, including the key species Martialis heureka. We focused taxon sampling on non-formicoid lineages of ants to gain insight about deep nodes in the ant phylogeny. For divergence dating we retained a subset of 62 extant taxa and 42 fossils in order to approximate diversified sampling in the context of the fossilized birth-death process. We sequenced 11 nuclear gene fragments for a total of ~7.5 kb and investigated the DNA sequence data for the presence of among-taxon compositional heterogeneity, a property known to mislead phylogenetic inference, and for its potential to affect the rooting of the ant phylogeny. We found sequences of the Leptanillinae and several outgroup taxa to be rich in adenine and thymine (51% average AT content) compared to the remaining ants (45% average). To investigate whether this heterogeneity could bias phylogenetic inference we performed outgroup removal experiments, analysis of compositionally homogeneous sites, and a simulation study. We found that compositional heterogeneity indeed appears to affect the placement of the root of the ant tree but has limited impact on more recent nodes. We put forward a novel hypothesis regarding the rooting of the ant phylogeny, in which Martialis and the Leptanillinae together constitute a clade that is sister to all other ants. After correcting for compositional heterogeneity this emerges as the best-supported hypothesis of relationships at deep nodes in the ant tree. The results of our divergence dating under the fossilized birth-death process and diversified sampling suggest that the crown Formicidae originated during the Albian or Aptian ages of the Lower Cretaceous (103–124 Ma). In addition, we found support for monophyletic poneroids comprising the subfamilies Agroecomyrmecinae, Amblyoponinae, Apomyrminae, Paraponerinae, Ponerinae, and Proceratiinae, and well-supported relationships among these subfamilies except for the placement of Proceratiinae and (Amblyoponinae + Apomyrminae). Our phylogeny also highlights the non-monophyly of several ant genera, including Protanilla and Leptanilla in the Leptanillinae, Proceratium in the Proceratiinae, and Cryptopone, Euponera, and Mesoponera within the Ponerinae.

scholarly journals Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 545
Author(s):  
Gédéon Prince Manouana ◽  
Paul Alvyn Nguema-Moure ◽  
Mirabeau Mbong Ngwese ◽  
C.-Thomas Bock ◽  
Peter G. Kremsner ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Preventive Measures ◽  
Phylogenetic Analyses ◽  
Enteric Viruses ◽  
Study Cohort ◽  
Viral Agent ◽  
A Genome ◽  
Stool Samples ◽  
Pcr Techniques ◽  
High Diversity

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

scholarly journals Loose Ends in the Cortinarius Phylogeny: Five New Myxotelamonoid Species Indicate a High Diversity of These Ectomycorrhizal Fungi with South American Nothofagaceae

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 420
Author(s):  
María Eugenia Salgado Salomón ◽  
Carolina Barroetaveña ◽  
Tuula Niskanen ◽  
Kare Liimatainen ◽  
Matthew E. Smith ◽  
...  
Keyword(s):  
New Species ◽  
Current Knowledge ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Global Scale ◽  
South American ◽  
Edible Fungi ◽  
Rdna Its ◽  
Morphological And Molecular Data ◽  
High Diversity

This paper is a contribution to the current knowledge of taxonomy, ecology and distribution of South American Cortinarius (Pers.) Gray. Cortinarius is among the most widely distributed and species-rich basidiomycete genera occurring with South American Nothofagaceae and species are found in many distinct habitats, including shrublands and forests. Due to their ectomycorrhizal role, Cortinarius species are critical for nutrient cycling in forests, especially at higher latitudes. Some species have also been reported as edible fungi with high nutritional quality. Our aim is to unravel the taxonomy of selected Cortinarius belonging to phlegmacioid and myxotelamonioid species based on morphological and molecular data. After widely sampling Cortinarius specimens in Patagonian Nothofagaceae forests and comparing them to reference collections (including holotypes), we propose five new species of Cortinarius in this work. Phylogenetic analyses of concatenated rDNA ITS-LSU and RPB1 sequences failed to place these new species into known Cortinarius sections or lineages. These findings highlight our knowledge gaps regarding the fungal diversity of South American Nothofagaceae forests. Due to the high diversity of endemic Patagonian taxa, it is clear that the South American Cortinarius diversity needs to be discovered and described in order to understand the evolutionary history of Cortinarius on a global scale.

scholarly journals Micromorphological, anatomical and molecular study of Hedera species (Araliaceae) in Iran

2020 ◽  
Vol 63 (2) ◽  
pp. 91-101
Author(s):  
Elham Amini ◽  
Fatemeh Nasrollahi ◽  
Ali Sattarian ◽  
Mahboobeh Haji Moradkhani ◽  
Sohrab Boozarpour ◽  
...  
Keyword(s):  
North Africa ◽  
Phylogenetic Analyses ◽  
Molecular Study ◽  
Molecular Characteristics ◽  
Nrdna Its ◽  
Anticlinal Wall ◽  
Data Set ◽  
Phylogenetic Methods ◽  
Extant Species ◽  
Qualitative Characters

Hedera, with 12 extant species, is a genus of evergreen climbers native to Europe, north Africa, and south Asia. In this study, the micromorphological, anatomical structure and molecular evidences of 11 populations from two species of Hedera (H. helix and H. pastuchovii) have been considered to evaluate the relationships in Hedera. In total, seven quantitative and qualitative characters of pollen were selected and measured. Based on this study, the anticlinal wall and surface sculpturing of seed support for separation of two species of Hedera. Micromorphology of epidermis illustrated two types of epidermal cells: puzzle-shaped and polygonal cells. Using nuclear (nrDNA ITS) marker, we reconstructed phylogenetic relationships within two species of Hedera. This data set was analyzed by phylogenetic methods including Bayesian inference, maximum likelihood, and maximum parsimony. In phylogenetic analyses, all members of two species formed a well-supported clade (PP = 1; ML/BS = 100/100) and divided into two major clades (A and B). Neighbor Net diagram demonstrated separation of the studied populations. The results showed that these taxa differ in taxonomically important micromorphological, anatomical and molecular characteristics and these data provide reliable evidence for separation of these two species.

A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata)

1995 ◽  
Vol 347 (1320) ◽  
pp. 213-234 ◽  
Keyword(s):  
Data Base ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Total Evidence ◽  
Morphological Data ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Molecular Sequences ◽  
Higher Taxa ◽  
Stem Group

Phylogenedc reladonships of higher taxa of echinoids have been invesdgated using a 163 character morphological data base and molecular sequences from large and small subunit (LSU and SSU) ribosomal RNA (rRNA) genes. The complete ssu rRNA gene has been sequenced for 21 taxa, with representatives from nine of the 14 extant orders of Echinoidea. Partial LSU sequences, representing the first 400 base pairs (b.p.) from the 5' end were also sequenced for three taxa to complement an existing data base of ten taxa. The two molecular sequences provided a total of 371 variable sites, of which 143 were phylogenetically informative (compared to 145 phylogenetically informative sites from morphological data). Morphological, LSU and SSU data have been analysed separately and together. Morphological and ssu sequence data generate topologies that are not significantly in conflict (under Templeton’s test), but the strong signal pairing arbaciids with clypeasteroids in the LSU derived tree marks the LSU sequence data as anomalous for this taxon. A ‘ total evidence’ approach derived a tree very similar in topology to that derived from morphological data. Rooted on the stem group echinoid Archaeocidaris , our total evidence tree suggested relationships of higher taxa as follows: Gidaroida Phormosomatidae Echinothuriidae Diadematidae Spatangoida Clypeasteroida, Cassiduloida Calycina, Arbacioida Stomopneustidae Glyphocidaridae Temnopleuridae Echinometridae Echinidae, Strongylocentridae. Phylogenetic analyses run both with and without key fossil taxa yielded slightly different topologies. It is important to include fossil taxa in a phylogenetic analysis where there are long stem-group branches or where the crown group is highly derived.

Herpetological higher taxa nomina. 7. Lissamphibia Gadow, 1898

Bionomina ◽  
2021 ◽  
Vol 21 (1) ◽  
pp. 73-83
Author(s):  
ALAIN DUBOIS ◽  
THIERRY FRÉTEY
Keyword(s):  
Phylogenetic Relationships ◽  
Rank Order ◽  
Phylogenetic Analyses ◽  
Higher Taxa ◽  
The One

A taxon encompassing all recent taxa of amphibians and their close fossil relatives is highly supported as holophyletic in all recent phylogenetic analyses of amphibians. Under the Duplostensional Nomenclatural System, among twenty nomina available for this taxon, only one, Lissamphibia Gadow, 1898, qualifies as a sozodiaphonym and appears to be the one that should be used for this taxon, traditionally referred to the rank order. However, because of the current uncertainties in the phylogenetic relationships among basal amphibians, the allocation of this nomen to this taxon is still questionable. If it turned out to apply in fact to another, more comprehensive, taxon, its stabilisation under its current acceptation should be realised through an act of archoidy.

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