scholarly journals Synthesizing and databasing fossil calibrations: divergence dating and beyond

2011 ◽  
Vol 7 (6) ◽  
pp. 801-803 ◽  
Author(s):  
Daniel T. Ksepka ◽  
Michael J. Benton ◽  
Matthew T. Carrano ◽  
Maria A. Gandolfo ◽  
Jason J. Head ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Interdisciplinary Collaboration ◽  
Branch Length ◽  
Molecular Data ◽  
Primary Objective ◽  
Calibration Data ◽  
Fossil Calibration ◽  
Divergence Dating ◽  
Molecular Phylogenetic ◽  
History Of

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3–6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.

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.

A new species of Physaloptera (Nematoda: Spirurida) from Proechimys gardneri (Rodentia: Echimyidae) from the Amazon rainforest and molecular phylogenetic analyses of the genus

2019 ◽  
Vol 94 ◽  
Author(s):  
A. Maldonado ◽  
R.O. Simões ◽  
J. São Luiz ◽  
S.F. Costa-Neto ◽  
R.V. Vilela
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Amazon Rainforest ◽  
Ancestral State ◽  
Intermediate Hosts ◽  
The Status ◽  
Molecular Phylogenetic ◽  
History Of ◽  
A New Species

Abstract Nematodes of the genus Physaloptera are globally distributed and more than 100 species are known. Their life cycle involves insects, including beetles, cockroaches and crickets, as intermediate hosts. This study describes a new species of Physaloptera and reports molecular phylogenetic analyses to determine its relationships within the family Physalopteridae. Physaloptera amazonica n. sp. is described from the stomach of the caviomorph rodent Proechimys gardneri collected in the Amazon rainforest in the state of Acre, Brazil. The species is characterized by the male having the first and second pair of sessile papillae asymmetrically placed, lacking a median papilla-like protuberance between the third pairs of sessile papillae, differentiated by size and shape of the spicules, while females have four uterine branches. For both nuclear 18S rRNA and MT-CO1 gene-based phylogenies, we recovered Turgida sequences forming a clade nested within Physaloptera, thus making Physaloptera paraphyletic to the exclusion of Turgida, suggesting that the latter may have evolved from the former monodelphic ancestral state to a derived polydelphic state, or that some species of Physaloptera may belong to different genera. Relationships between most taxa within Physaloptera were poorly resolved in our phylogenies, producing multifurcations or a star phylogeny. The star-like pattern may be attributed to evolutionary processes where past simultaneous species diversification events took place. Physaloptera amazonica n. sp. formed an independent lineage, separately from the other species of Physaloptera, thus supporting the status of a new species. However, all molecular data suggested a closer relationship with other Neotropical species. In conclusion, we added a new species to this already largely diverse genus Physaloptera, bringing new insights to its phylogenetic relationships. Further analyses, adding more species and markers, should provide a better understanding of the evolutionary history of physalopterids.

Molecular paleobiology of early-branching animals: integrating DNA and fossils elucidates the evolutionary history of hexactinellid sponges

Paleobiology ◽  
2013 ◽  
Vol 39 (1) ◽  
pp. 95-108 ◽  
Author(s):  
Martin Dohrmann ◽  
Sergio Vargas ◽  
Dorte Janussen ◽  
Allen G. Collins ◽  
Gert Wörheide
Keyword(s):  
Fossil Record ◽  
Classification Systems ◽  
Great Promise ◽  
Crown Group ◽  
Data Set ◽  
Fossil Calibration ◽  
Molecular Phylogenetic ◽  
Temporal Succession ◽  
History Of ◽  
Glass Sponges

Reconciliation of paleontological and molecular phylogenetic evidence holds great promise for a better understanding of the temporal succession of cladogenesis and character evolution, especially for taxa with a fragmentary fossil record and uncertain classification. In zoology, studies of this kind have largely been restricted to Bilateria. Hexactinellids (glass sponges) readily lend themselves to test such an approach for early-branching (non-bilaterian) animals: they have a long and rich fossil record, but for certain taxa paleontological evidence is still scarce or ambiguous. Furthermore, there is a lack of consensus for taxonomic interpretations, and discrepancies exist between neontological and paleontological classification systems. Using conservative fossil calibration constraints and the largest molecular phylogenetic data set assembled for this group, we infer divergence times of crown-group Hexactinellida in a Bayesian relaxed molecular clock framework. With some notable exceptions, our results are largely congruent with interpretations of the hexactinellid fossil record, but also indicate long periods of undocumented evolution for several groups. This study illustrates the potential of an integrated molecular/paleobiological approach to reconstructing the evolution of challenging groups of organisms.

scholarly journals Tuber Fulgens Quél. A New Record for Turkish Truffles

2020 ◽  
Vol 8 (11) ◽  
pp. 2472-2475
Author(s):  
Ilgaz Akata ◽  
Mustafa Sevindik ◽  
Ergin Şahin
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Large Subunit ◽  
Morphological Data ◽  
Lsu Rdna ◽  
High Sequence Similarity ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
History Of ◽  
First Time

Tuber samples were collected from Kırklareli province on the 10th of August 2020 and they are identified by implementing both traditional methods and molecular phylogenetic analysis using the rDNA sequences including Internal Transcribed Spacer (ITS) and 28S Ribosomal Large Subunit (LSU) regions. By taking into account the high sequence similarity between the collected samples (ANK Akata 7351) and the truffle species Tuber fulgens Quél. the collected specimen was regarded as T. fulgens and the morphological data also consolidated this finding. As a result, T. fulgens was reported for the first time from Turkey. A short description of the newly reported species is given along with its macro and microphotographs, and spore images taken by a scanning electron microscope (SEM). Additionally, ITS and LSU rDNA based evolutionary history of the specimen is provided with phylogenetic trees.

scholarly journals Dactylogyridae 2021: Seeing the forest through the (phylogenetic) trees

2021 ◽  
Author(s):  
Nikol Kmentová ◽  
Armando J. Cruz-Laufer ◽  
Antoine Pariselle ◽  
Karen Smeets ◽  
Tom Artois ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Molecular Data ◽  
Model Organisms ◽  
Multiple Sequence ◽  
Evolutionary Patterns ◽  
Playing Field ◽  
Current State ◽  
Molecular Phylogenetic ◽  
Host Parasite

Dactylogyridae is one of the most studied families of parasitic flatworms with more than 1000 species and 166 genera described to date including ecto-, meso-, and endoparasites. Dactylogyrid monogeneans have been used as model organisms for host-parasite macroevolutionary and biogeographical studies due to the scientific and economic importance of some of their host lineages. Consequently, an array of phylogenetic research into different dactylogyrid lineages has been produced over the past years but the last family-wide study was published over a decade ago. Here, we provide a new phylogeny of Dactylogyridae including representatives of all the genera with available molecular data. First, we discuss morphological, host range, biogeographical, and freshwater-marine patterns. Second, we provide an overview of the current state of the systematics of the family, and its subfamilies and genera. Third, we elaborate on the implications of taxonomic, citation, and confirmation bias in past studies. We found two well-supported main lineages which we assigned to the subfamilies Dactylogyrinae and Ancyrocephalinae. The subfamilies further include 11 well-supported clades whose members share only few diagnostic morphological features. Our study highlights the discrepancy between morphological similarities and molecular phylogenetic relationships in some dactylogyrid lineages. Environmental changes might have induced morphological adaptation, e.g. changes in the attachment organ in response to marine-freshwater habitat switches or reduction of eyespots related to water turbidity. Moreover, synonymisation of some of the para- or polyphyletic genera is proposed. We conclude that a strong taxonomic bias further limits knowledge on biogeographical evolutionary patterns that can be inferred from these results. Finally, we propose addressing potential citation and confirmation biases through a ‘level playing field’ multiple sequence alignment as provided by this study.

scholarly journals Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

2018 ◽  
Vol 5 (4) ◽  
pp. 171707 ◽  
Author(s):  
Aaron A. Heiss ◽  
Martin Kolisko ◽  
Fleming Ekelund ◽  
Matthew W. Brown ◽  
Andrew J. Roger ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Deep Level ◽  
Molecular Data ◽  
Heterotrophic Flagellates ◽  
Interpretation Errors ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Morphological And Molecular Data ◽  
Phylogenomic Analyses ◽  
Almost All

Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, a group of small heterotrophic flagellates that resemble Excavata by morphology, but branch with Amorphea in most phylogenomic analyses. However, just one malawimonad, Malawimonas jakobiformis , has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a morphological and phylogenomic study of a new deep-branching malawimonad, Gefionella okellyi n. gen. n. sp. Electron microscopy revealed all canonical features of ‘typical excavates’, including flagellar vanes (as an opposed pair, unlike M. jakobiformis but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage Collodictyon , separate from a Metamonada+Discoba clade. However, support for this topology weakened when more sophisticated evolutionary models were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were excluded. Analyses of ‘–FS/LB’ datasets instead suggested a relationship between malawimonads and metamonads. The ‘malawimonad+metamonad signal’ in morphological and molecular data argues against a strict Metamonada+Discoba clade (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade should therefore not be assumed when inferring deep-level evolutionary history in eukaryotes.

scholarly journals The evolution of pathogenic trypanosomes

1999 ◽  
Vol 15 (4) ◽  
pp. 673-684 ◽  
Author(s):  
Jamie R. Stevens ◽  
Wendy C. Gibson
Keyword(s):  
Trypanosoma Brucei ◽  
Ribosomal Rna ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Recent Progress ◽  
Molecular Data ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
History Of ◽  
Vertebrate Hosts

In the absence of a fossil record, the evolution of protozoa has until recently largely remained a matter for speculation. However, advances in molecular methods and phylogenetic analysis are now allowing interpretation of the "history written in the genes". This review focuses on recent progress in reconstruction of trypanosome phylogeny based on molecular data from ribosomal RNA, the miniexon and protein-coding genes. Sufficient data have now been gathered to demonstrate unequivocally that trypanosomes are monophyletic; the phylogenetic trees derived can serve as a framework to reinterpret the biology, taxonomy and present day distribution of trypanosome species, providing insights into the coevolution of trypanosomes with their vertebrate hosts and vectors. Different methods of dating the divergence of trypanosome lineages give rise to radically different evolutionary scenarios and these are reviewed. In particular, the use of one such biogeographically based approach provides new insights into the coevolution of the pathogens, Trypanosoma brucei and Trypanosoma cruzi, with their human hosts and the history of the diseases with which they are associated.

scholarly journals A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3354 ◽  
Author(s):  
Timur G. Simdyanov ◽  
Laure Guillou ◽  
Andrei Y. Diakin ◽  
Kirill V. Mikhailov ◽  
Joseph Schrével ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Wide Distribution ◽  
Phylogenetic Study ◽  
Molecular Evidence ◽  
Molecular Phylogenetic ◽  
Phylogenetic Lineages

Background Gregarines are a group of early branching Apicomplexa parasitizing invertebrate animals. Despite their wide distribution and relevance to the understanding the phylogenesis of apicomplexans, gregarines remain understudied: light microscopy data are insufficient for classification, and electron microscopy and molecular data are fragmentary and overlap only partially. Methods Scanning and transmission electron microscopy, PCR, DNA cloning and sequencing (Sanger and NGS), molecular phylogenetic analyses using ribosomal RNA genes (18S (SSU), 5.8S, and 28S (LSU) ribosomal DNAs (rDNAs)). Results and Discussion We present the results of an ultrastructural and molecular phylogenetic study on the marine gregarine Ancora sagittata from the polychaete Capitella capitata followed by evolutionary and taxonomic synthesis of the morphological and molecular phylogenetic evidence on eugregarines. The ultrastructure of Ancora sagittata generally corresponds to that of other eugregarines, but reveals some differences in epicytic folds (crests) and attachment apparatus to gregarines in the family Lecudinidae, where Ancora sagittata has been classified. Molecular phylogenetic trees based on SSU (18S) rDNA reveal several robust clades (superfamilies) of eugregarines, including Ancoroidea superfam. nov., which comprises two families (Ancoridae fam. nov. and Polyplicariidae) and branches separately from the Lecudinidae; thus, all representatives of Ancoroidea are here officially removed from the Lecudinidae. Analysis of sequence data also points to possible cryptic species within Ancora sagittata and the inclusion of numerous environmental sequences from anoxic habitats within the Ancoroidea. LSU (28S) rDNA phylogenies, unlike the analysis of SSU rDNA alone, recover a well-supported monophyly of the gregarines involved (eugregarines), although this conclusion is currently limited by sparse taxon sampling and the presence of fast-evolving sequences in some species. Comparative morphological analyses of gregarine teguments and attachment organelles lead us to revise their terminology. The terms “longitudinal folds” and “mucron” are restricted to archigregarines, whereas the terms “epicystic crests” and “epimerite” are proposed to describe the candidate synapomorphies of eugregarines, which, consequently, are considered as a monophyletic group. Abolishing the suborders Aseptata and Septata, incorporating neogregarines into the Eugregarinida, and treating the major molecular phylogenetic lineages of eugregarines as superfamilies appear as the best way of reconciling recent morphological and molecular evidence. Accordingly, the diagnosis of the order Eugregarinida Léger, 1900 is updated.

First molecular phylogeny of Agrilus (Coleoptera: Buprestidae), the largest genus on Earth, with DNA barcode database for forestry pest diagnostics

2018 ◽  
Vol 109 (2) ◽  
pp. 200-211 ◽  
Author(s):  
I. Kelnarova ◽  
E. Jendek ◽  
V.V. Grebennikov ◽  
L. Bocak
Keyword(s):  
Species Identification ◽  
Northern Hemisphere ◽  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Intraspecific Variability ◽  
Molecular Data ◽  
Rapid Identification ◽  
Species Group ◽  
Molecular Phylogenetic ◽  
Multiple Species

AbstractAll more than 3000 species of Agrilus beetles are phytophagous and some cause economically significant damage to trees and shrubs. Facilitated by international trade, Agrilus species regularly invade new countries and continents. This necessitates a rapid identification of Agrilus species, as the first step for subsequent protective measures. This study provides the first DNA reference library for ~100 Agrilus species from the Northern Hemisphere based on three mitochondrial markers: cox1–5′ (DNA barcode fragment), cox1–3′, and rrnL. All 329 Agrilus records available in the Barcode of Life Database format, including specimen images and geo data, are released through a public dataset ‘Agrilus1 329’ available at: dx.doi.org/10.5883/DS-AGRILUS1. All Agrilus species were identified using adult morphology and by using molecular phylogenetic trees, as well as distance- and tree-based algorithms. Most DNA-based species limits agree well with the morphology-based identification. Our results include cases of high intraspecific variability and multiple species para- and polyphyly. DNA barcoding is a powerful species identification tool in Agrilus, although it frequently fails to recover morphologically-delimited Agrilus species-group. Even though the current three-gene database covers only ~3% of the known Agrilus diversity, it contains representatives of all principal lineages from the Northern Hemisphere and represents the most extensive dataset built for DNA-delimited species identification within this genus so far. Molecular data analyses can rapidly and cost-effectively identify an unknown sample, including immature stages and/or non-native taxa, or species not yet formally named.

Sign in / Sign up

Export Citation Format

Share Document