scholarly journals Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets

2020 ◽  
Author(s):  
Johannes S Neumann ◽  
Rob Desalle ◽  
Apurva Narechania ◽  
Bernd Schierwater ◽  
Michael Tessler
Keyword(s):  
A Priori ◽  
Genomic Data ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Taxon Sampling ◽  
Data Sets ◽  
Analysis Tool ◽  
Character Weighting ◽  
The Impact

Abstract There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000–400,000 characters in size with $\sim $15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their “equivalent” under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10$\times $ in both likelihood and parsimony can in some cases “flip” which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically “swamp out” morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of “flipping points” (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.]

The impact of multiple molecular and morphological data sets on the phylogenetic reconstruction of subtribe Neurachninae (Poaceae: Panicoideae: Paniceae)

2021 ◽  
Author(s):  
E. J. Thompson ◽  
Melodina Fabillo
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Plastid Markers ◽  
Morphological And Molecular Data ◽  
The Impact ◽  
Selection Of

The taxonomy of Neurachninane has been unstable, with its member genera consisting of Ancistrachne, Calyptochloa, Cleistochloa, Dimorphochloa, Neurachne, Paraneurachne and Thyridolepis, changing since its original circumscription that comprised only the latter three genera. Recent studies on the phylogeny of Neurachninae have focused primarily on molecular data. We analysed the phylogeny of Neurachninae on the basis of molecular data from seven molecular loci (plastid markers: matK, ndhF, rbcL, rpl16, rpoC2 and trnLF, and ribosomal internal transcribed spacer, ITS) and morphological data from 104 morphological characters, including new taxonomically informative micromorphology of upper paleas. We devised an impact assessment scoring (IAS) protocol to aid selection of a tree for inferring the phylogeny of Neurachninae. Combining morphological and molecular data resulted in a well resolved phylogeny with the highest IAS value. Our findings support reinstatement of subtribe Neurachninae in its original sense, Neurachne muelleri and Dimorphochloa rigida. We show that Ancistrachne, Cleistochloa and Dimorphochloa are not monophyletic and Ancistrachne maidenii, Calyptochloa, Cleistochloa and Dimorphochloa form a new group, the cleistogamy group, united by having unique morphology associated with reproductive dimorphism.

Revision of Autolytinae (Syllidae: Polychaeta)

Zootaxa ◽  
2004 ◽  
Vol 680 (1) ◽  
pp. 1 ◽  
Author(s):  
ARNE NYGREN
Keyword(s):  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Nominal Species ◽  
Strict Consensus Tree ◽  
Incertae Sedis ◽  
Nomina Dubia ◽  
Morphological And Molecular Data ◽  
Combined Data

Autolytinae is revised based on available types, and newly collected specimens. Out of 170 nominal species, 18 are considered as incertae sedis, 43 are regarded as junior synonyms, and 25 are referred to as nomina dubia. The relationships of Autolytinae is assessed from 51 morphological characters and 211 states for 76 ingroup-taxa, and 460 molecular characters from mitochondrial 16S rDNA and nuclear 18S rDNA for 31 ingroup-taxa; outgroups include 12 non-autolytine syllid polychaetes. Two analyses are provided, one including morphological data only, and one with combined morphological and molecular data sets. The resulting strict consensus tree from the combined data is chosen for a reclassification. Three main clades are identified: Procerini trib. n., Autolytini Grube, 1850, and Epigamia gen. n. Proceraea Ehlers, 1864 and Myrianida Milne Edwards, 1845 are referred to as nomen protectum, while Scolopendra Slabber, 1781, Podonereis Blainville, 1818, Amytis Savigny, 1822, Polynice Savigny, 1822, and Nereisyllis Blainville, 1828 are considered

Cladistic relationships among higher groups of Heteroptera: congruence between morphological and molecular data sets

1993 ◽  
Vol 24 (2) ◽  
pp. 121-137 ◽  
Author(s):  
Ward C. Wheeler ◽  
Ranhy Bang ◽  
Randall T. Schuh
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Sister Group Relationship ◽  
Molecular Evidence ◽  
Data Sets ◽  
Nuclear Rdna ◽  
History Of ◽  
Morphological And Molecular Data

AbstractThe monophyly of the 7 infraorders of Heteroptera and history of higher group concepts and interrelationships within the Heteroptera are briefly reviewed. Data from 31 morphological characters are combined with 669 bases of 18S nuclear rDNA for 29 taxa, including several outgroups to the Heteroptera, to produce a phylogeny based on the total available evidence. The molecular data alone and in conjunction with morphological data indicate that: the Homoptera are probably not monophyletic; the Auchenorrhyncha are the sister group of Coleorrhyncha + Heteroptera ; the Enicocephalomorpha are the sister group of remaining Heteroptera; the Dipsocoromorpha are the sister group of remaining Heteroptera; the Gerromorpha are the sister group of remaining Heteroptera; the Nepomorpha are the sister group of remaining Heteroptera; the Leptopodomorpha are the sister group of the Cimicomorpha + Pentatomomorpha. The molecular evidence corroborates the morphologically based theory of a sister group relationship between Aradoidea and trichophoran Pentatomomorpha. This scheme deviates from that previously published by Schuh, in which the Leptopodomorpha were treated as the sister group of the Nepomorpha.

Molecular relationships of the Australian Ennominae (Lepidoptera: Geometridae) and implications for the phylogeny of the Geometridae from molecular and morphological data

Zootaxa ◽  
2006 ◽  
Vol 1264 (1) ◽  
pp. 1 ◽  
Author(s):  
CATHERINE J. YOUNG
Keyword(s):  
A Priori ◽  
Nuclear Gene ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Protein Coding ◽  
Outgroup Species ◽  
Phylogenetic Framework ◽  
Molecular Relationships

Molecular data from the 28S D2 ribosomal nuclear gene fragment were utilised to construct a phylogeny for the Australian Ennominae. Sequences were obtained from 68 geometrid and 5 outgroup species. Sequences from a smaller subset of 17 species also were analysed using the nuclear protein-coding gene EF-1a. Species were sampled from all major subfamilies of the Geometridae as no a priori assumptions could be made confidently about possible sister groups to the Australian Ennominae.The major findings from these analyses were as follows:(a) Drepanidae are a sister group to Geometridae;(b) Larentiinae are derived basally within the Geometridae; the Sterrhinae are the penultimate basally derived group;(c) Oenochrominae s. str. are closely related to the Geometrinae.(d) Ennominae are not monophyletic;(e) Tasmanian Archiearinae are misplaced in the Archiearinae and have close affinities to Australian Nacophorini (Ennominae);(f) Australian Nacophorini are not monophyletic.These results are at odds with traditionally held beliefs on the origins of Geometridae but are in broad agreement with and elaborate on the findings of Abraham et al. (2001). The implications of these findings in relation to key morphological characters are discussed using the proposed phylogenetic framework.

scholarly journals The Strepsiptera-Odyssey: the history of the systematic placement of an enigmatic parasitic insect order

Entomologia ◽  
2013 ◽  
pp. e4 ◽  
Author(s):  
H. Pohl ◽  
R.G. Beutel
Keyword(s):  
Single Copy ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Genes ◽  
Morphological Data ◽  
Data Sets ◽  
Protein Coding ◽  
Insect Order ◽  
Close Relationship ◽  
History Of

The history of the phylogenetic placement of the parasitic insect order Strepsiptera is outlined. The first species was described in 1793 by P. Rossi and assigned to the hymenopteran family Ichneumonidae. A position close to the cucujiform beetle family Rhipiphoridae was suggested by several earlier authors. Others proposed a close relationship with Diptera or even a group Pupariata including Diptera, Strepsiptera and Coccoidea. A subordinate placement within the polyphagan series Cucujiformia close to the wood-associated Lymexylidae was favored by the coleopterist R.A. Crowson. W. Hennig considered a sistergroup relationship with Coleoptera as the most likely hypothesis but emphasized the uncertainty. Cladistic analyses of morphological data sets yielded very different placements, alternatively as sistergroup of Coleoptera, Antliophora, or all other holometabolan orders. Results based on ribosomal genes suggested a sistergroup relationship with Diptera (Halteria concept). A clade Coleopterida (Strepsiptera and Coleoptera) was supported in two studies based on different combinations of protein coding nuclear genes. Analyses of data sets comprising seven or nine genes (7 single copy nuclear genes), respectively, yielded either a subordinate placement within Coleoptera or a sistergroup relationship with Neuropterida. Several early hypotheses based on a typological approach − affinities with Diptera, Coleoptera, a coleopteran subgroup, or Neuropterida − were revived using either a Hennigian approach or formal analyses of morphological characters or different molecular data sets. A phylogenomic approach finally supported a sistergroup relationship with monophyletic Coleoptera.

scholarly journals Integrative systematics untangles the evolutionary history of Stenochrus (Schizomida: Hubbardiidae), a neglected junkyard genus of North American short-tailed whipscorpions

2020 ◽  
Vol 130 (3) ◽  
pp. 458-479
Author(s):  
Rodrigo Monjaraz-Ruedas ◽  
Oscar F Francke ◽  
Lorenzo Prendini
Keyword(s):  
Mitochondrial Gene ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Present Contribution ◽  
Gene Markers ◽  
The Usa ◽  
Morphological And Molecular Data ◽  
Integrative Systematics

Abstract Until recently, the Nearctic short-tailed whipscorpion genus, StenochrusChamberlin, 1922, included 27 species distributed primarily in Mexico, the USA and Central America. Morphological disparity among its species, associated with their adaptation to diverse habitats, raised the question as to whether Stenochrus was monophyletic. The phylogenetic relationships among short-tailed whipscorpions have only recently begun to be explored, and the monophyly of Stenochrus had never been tested. The present contribution provides the first phylogeny of Stenochrus and related genera, based on 61 morphological characters and 2991 aligned DNA nucleotides from two nuclear and two mitochondrial gene markers, for 73 terminal taxa. Separate and simultaneous analyses of the morphological and molecular data sets were conducted with Bayesian Inference, Maximum Likelihood, and parsimony with equal and implied weighting. Terminals represented only by morphological data (‘orphans’) were included in some analyses for evaluation of their phylogenetic positions. As previously defined, Stenochrus sensuReddell & Cokendolpher (1991, 1995) was consistently polyphyletic and comprised eight monophyletic clades, justifying its reclassification into eight genera including Heteroschizomus Rowland, 1973, revalidated from synonymy with Stenochrus by Monjaraz-Ruedas et al. (2019). Rowland & Reddell’s (1980)mexicanus and pecki species groups were consistently paraphyletic. Orphans grouped with the most morphologically similar taxa.

Survey Data Quality in Analyzing Harmonized Indicators of Protest Behavior: A Survey Data Recycling Approach

2021 ◽  
pp. 000276422110216
Author(s):  
Kazimierz M. Slomczynski ◽  
Irina Tomescu-Dubrow ◽  
Ilona Wysmulek
Keyword(s):  
Data Processing ◽  
Data Quality ◽  
Survey Data ◽  
A Priori ◽  
Data Sets ◽  
New Approach ◽  
Survey Quality ◽  
Survey Error ◽  
Ex Post ◽  
The Impact

This article proposes a new approach to analyze protest participation measured in surveys of uneven quality. Because single international survey projects cover only a fraction of the world’s nations in specific periods, researchers increasingly turn to ex-post harmonization of different survey data sets not a priori designed as comparable. However, very few scholars systematically examine the impact of the survey data quality on substantive results. We argue that the variation in source data, especially deviations from standards of survey documentation, data processing, and computer files—proposed by methodologists of Total Survey Error, Survey Quality Monitoring, and Fitness for Intended Use—is important for analyzing protest behavior. In particular, we apply the Survey Data Recycling framework to investigate the extent to which indicators of attending demonstrations and signing petitions in 1,184 national survey projects are associated with measures of data quality, controlling for variability in the questionnaire items. We demonstrate that the null hypothesis of no impact of measures of survey quality on indicators of protest participation must be rejected. Measures of survey documentation, data processing, and computer records, taken together, explain over 5% of the intersurvey variance in the proportions of the populations attending demonstrations or signing petitions.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

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.

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