scholarly journals Phylogenetic Signal and Bias in Paleontology

2021 ◽  
Author(s):  
Robert J Asher ◽  
Martin R Smith
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Tree Of Life ◽  
Morphological Data ◽  
Phylogenetic Resolution ◽  
Phylogeny Estimation ◽  
Better Than

Abstract An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.

scholarly journals DNA Barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae)

Zootaxa ◽  
2007 ◽  
Vol 1423 (1) ◽  
pp. 1-26 ◽  
Author(s):  
JEFFREY H. SKEVINGTON ◽  
CHRISTIAN KEHLMAIER ◽  
GUNILLA STÅHLS
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Base Pairs ◽  
Data Set ◽  
Taxonomic Decision ◽  
Morphological Species

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

Characterisation of the Australian Nacophorini using adult morphology, and phylogeny of the Geometridae based on morphological characters

Zootaxa ◽  
2008 ◽  
Vol 1736 (1) ◽  
pp. 1 ◽  
Author(s):  
CATHERINE J. YOUNG
Keyword(s):  
Phylogenetic Analysis ◽  
Majority Rule ◽  
Morphological Character ◽  
Morphological Characters ◽  
Data Sources ◽  
Morphological Data ◽  
Bootstrap Support ◽  
Consensus Tree ◽  
Molecular Analyses ◽  
Character Set

The Australian Nacophorini and related taxa are described using a matrix of 116 adult morphological characters. Adults of 72 species are illustrated using photographs and electron micrographs. Subsets of the characters are used to conduct a phylogenetic analysis based on cladistic principles. The adult morphological character set was augmented with 17 characters from eggs and 27 from larvae. The resulting phylogeny is poorly resolved but provides support for many of the relationships recovered by previous molecular analyses of the group, including basal derivations for characters of Larentiinae and Sterrhinae relative to those of the rest of Geometridae, and the monophyly of the Geometrinae + Oenochrominae s. str. Combining 28S D2 datawith morphological data produced a matrix of 60 taxa and 590 characters. The majority rule consensus tree produced by the combined morphological and 28S D2 data is almost identical to the majority rule consensus tree produced by the 28S D2 data alone, except that bootstrap support is lower for most nodes. Common clades obtained from the molecular and morphological trees are described in terms of morphological data. On this basis a concept of the Australian Nacophorini includes Lithinini and Australian Archiearinae. Two robust groups within the tribe also are delimited using characters from all data sources. Comparsions are made between the Nearctic and Neotropical Nacophorini on the basis of shared morphological characters. Australian Boarmiini are defined by synapomorphies.

scholarly journals First Report of Podosphaera aphanis Causing Powdery Mildew on Wild Blackberry Species (Rubus spp.) in Mexico

Plant Disease ◽  
2021 ◽  
Author(s):  
Alma Rosa Solano-Báez ◽  
Santos Gerardo Leyva-Mir ◽  
Moises Camacho-Tapia ◽  
Alfonso Arellano Victoria ◽  
Geremias Rodríguez-Bautista ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Powdery Mildew ◽  
Primary Source ◽  
Morphological Characters ◽  
Morphological Data ◽  
Wild Populations ◽  
First Report ◽  
Voucher Specimens ◽  
New Varieties ◽  
Germ Tubes

Wild blackberry species (Rubus spp. L.; Rosaceae) represents an invaluable source of genes for the generation of new varieties, but also serve as a primary source of disease inoculum. During April of 2020, symptoms of powdery mildew were observed on four populations of wild blackberry species located in the states of Chiapas (16°59'11"N, 92°59'07"W; 16°47'08"N, 92°31'05"W) and Michoacán (19°37'17"N, 100°08'59"W; 19°29'25"N, 101°32'54"W), Mexico. Signs of the pathogen were white powdery masses mainly on the top of new shoots. Symptoms included yellowing, necrosis, and early defoliation of the plants. Hyphae were tin-walled, hyaline, smooth, and 4.0–9.0 mm wide. Appressoria were indistinct -to- nipple-shaped. Conidiophores (n=30, 75–225 × 10.5–13.5 μm) were straight, and unbranched with cylindrical foot cells (n=30, 31.5–158 × 8–13.5 μm), straight, somewhat widening upwards, followed by 1–3 shorter cells. Conidia (n=100; 25.5–38.5 × 9.5–22.5 μm) were catenulate, ellipsoid-ovoid -to- doliiform, containing fibrosin bodies (in 3% KOH). Germ tubes (n=30, 13.5–40.5 × 4.5 μm) emerged laterally, and were unbranched with slightly swollen tips. Chasmothecia were not found. Morphological characters of the fungus in all samples corresponded to the previous descriptions of Podosphaera aphanis by Braun and Cook (2012) and Stevanovi´c et al. (2020). Voucher specimens were deposited in the Department of Agricultural Parasitology Herbarium at the Chapingo Autonomous University under accessions UACH421, UACH423, UACH425, UACH426. To confirm the species identification, the internal transcribed spacer (ITS) of one sample was amplified using the primers ITS5 (White et al. 1990) and P3 (Kusaba and Tsuge, 1995) and sequenced. The sequence was deposited in GenBank (accession number MW988591). A phylogenetic analysis using Bayesian inference and maximum likelihood was performed (Hernández-Restrepo et al. 2018) and included other Podosphaera species (Takamatsu et al. 2010). The sequence from the isolate UACH426 clustered with the strain MUMH1871 of P. aphanis forming a definite clade and remained as a sister taxon of P. pannosa. Pathogenicity was verified through inoculation by gently dusting conidia from one powdery mildew patch onto leaves of five healthy blackberry plants of each specie. The same number of noninoculated plants served as controls. All plants were maintained in a greenhouse at 25–30°C with 75% relative humidity. All inoculated plants developed powdery mildew symptoms after 12 days, whereas no symptoms were observed on noninoculated plants. The fungus recovered from the inoculated plants was morphologically identical to that originally observed on diseased blackberry plants, demonstrating the pathogenicity of the fungus. Based on morphological data and phylogenetic analysis, the fungus was identified as P. aphanis. This fungus has been reported to cause powdery mildew on blackberry plants in Serbia (Stevanovi´c et al. 2020). This is the first report of P. aphanis causing powdery mildew on wild backberry species in Mexico according to Farr and Rossman (2021). The primary source of inoculum of powdery mildew for commercial plantings is wild blackberry plants from noncultivated areas and may warrant control of wild populations.

scholarly journals Markov models provide many solutions for appropriate modeling of inapplicable morphological characters in phylogenetics

2021 ◽  
Author(s):  
Sergei Tarasov
Keyword(s):  
Phylogenetic Analysis ◽  
Markov Models ◽  
Main Type ◽  
Morphological Characters ◽  
Bayesian Framework ◽  
Morphological Data ◽  
New Models

AbstractThis paper describes new models for coding inapplicable characters for phylogenetic analysis with morphological data. I show that these new solutions fall into two categories that require use of different Markov models. Their implementation in the Bayesian framework using popular software RevBayes (Höhna et al., 2016) is provided. A combination of the new models and previous solutions (Tarasov, 2019) is capable to model all main type of dependencies between morphological characters.

scholarly journals Craniodental morphology and phylogeny of marsupials

2021 ◽  
Author(s):  
Robin M. D. Beck ◽  
Robert Voss ◽  
Sharon Jansa
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Future Research ◽  
Data Types ◽  
Wide Range ◽  
Morphological And Molecular Data ◽  
Dense Sampling

The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with relatively limited sampling of Recent and fossil taxa, and many studies based on analyses of molecular data that include a dense sampling of Recent taxa, but relatively few that combine both data types. Another dichotomy in the marsupial phylogenetic literature is between studies that focus on New World taxa, others that focus on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna, based on combined analyses of morphology and molecular sequences, for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 species representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) taxa represented by well-preserved fossils, and 5 outgroups (non-marsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3 and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., †Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., †Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology, including descriptions and illustrations of some features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters, and improved methods of phylogenetic analysis.

Allozyme Evidence for the Phylogeny of Giant New Caledonian Geckos (Squamata: Diplodactylidae: Rhacodactylus), with Comments on the Status of R. leachianus henkeli

1997 ◽  
Vol 45 (3) ◽  
pp. 317 ◽  
Author(s):  
D. A. Good ◽  
A. M. Bauer ◽  
R. A. Sadlier
Keyword(s):  
Phylogenetic Analysis ◽  
Morphological Characters ◽  
Total Evidence ◽  
Morphological Data ◽  
Branching Pattern ◽  
Phenetic Analysis ◽  
Allozyme Data ◽  
The Status ◽  
Distance Data ◽  
Nei's Genetic Distance

The phylogenetic analysis of allozyme characters within the New Caledonian giant geckos, genus Rhacodactylus, yields a pattern of relationships that is largely congruent with that derived from morphological data. A ‘total evidence’ approach, incorporating 13 allozyme and 29 morphological characters, yields a single most-parsimonious tree with the pattern: R. auriculatus ((R. leachainus (R. ciliatus, R. chahoua)) (R. sarasinorum, R. trachyrhynchus)). A phenetic analysis based on Nei’s genetic distance data results in a similar branching pattern. The genus Pseudothecadactylus is tentatively regarded as valid because allozyme data conflict strongly with morphological data that suggest that these geckos evolved from within Rhacodactylus. Allozymes and available morphological data do not support the recognition of the recently described subspecies R. leachianus henkeli.

Lactarius cucurbitoides (Russulales, Basidiomycota), a new species from South Korea supported by molecular and morphological data

Phytotaxa ◽  
2015 ◽  
Vol 205 (3) ◽  
pp. 168 ◽  
Author(s):  
Hyun Lee ◽  
Myung Soo Park ◽  
Paul Eunil Jung ◽  
Jonathan J. Fong ◽  
Seung-Yoon Oh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Closely Related Species ◽  
The Status ◽  
A New Species

A new species belonging to Lactarius subg. Plinthogalus was discovered during a long-term project on the diversity of Korean Lactarius. This species is proposed here as Lactarius cucurbitoides. The status of L. cucurbitoides as a new species is supported by molecular data and morphological features. Phylogenetic analysis based on internal transcribed spacer (ITS) sequences shows that L. cucurbitoides is closely related to L. subplinthogalus, L. friabilis, and L. oomsisiensis, with pairwise distances of 2.8–4.3%. Morphological characters of L. cucurbitoides that distinguish it from these closely related species are a pale yellow to pale orange colored pileus and non-discoloration of white latex. The new species is described and illustrated in the present paper.

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.

Combining morphological and molecular data resolves the phylogeny of Squilloidea (Crustacea : Malacostraca)

2019 ◽  
Author(s):  
Cara Van Der Wal ◽  
Shane T. Ahyong ◽  
Simon Y. W. Ho ◽  
Luana S. F. Lins ◽  
Nathan Lo
Keyword(s):  
Phylogenetic Analysis ◽  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Mantis Shrimp ◽  
Generic Groups ◽  
Morphological And Molecular Data

The mantis shrimp superfamily Squilloidea, with over 185 described species, is the largest superfamily in the crustacean order Stomatopoda. To date, phylogenetic relationships within this superfamily have been comprehensively analysed using morphological data, with six major generic groupings being recovered. Here, we infer the phylogeny of Squilloidea using a combined dataset comprising 75 somatic morphological characters and four molecular markers. Nodal support is low when the morphological and molecular datasets are analysed separately but improves substantially when combined in a total-evidence phylogenetic analysis. We obtain a well resolved and strongly supported phylogeny that is largely congruent with previous estimates except that the Anchisquilloides-group, rather than the Meiosquilla-group, is the earliest-branching lineage in Squilloidea. The splits among the Anchisquilloides- and Meiosquilla-groups are followed by those of the Clorida-, Harpiosquilla-, Squilla- and Oratosquilla-groups. Most of the generic groups are recovered as monophyletic, with the exception of the Squilla- and Oratosquilla-groups. However, many genera within the Oratosquilla-group are not recovered as monophyletic. Further exploration with more extensive molecular sampling will be needed to resolve relationships within the Oratosquilla-group and to investigate the adaptive radiation of squilloids. Overall, our results demonstrate the merit of combining morphological and molecular datasets for resolving phylogenetic relationships.

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