Molecular Data Sets and Broad Taxon Sampling in Detecting Morphological Convergence

1994 ◽  
pp. 243-248 ◽  
Author(s):  
M. Blackwell ◽  
J. W. Spatafora
Keyword(s):  
Molecular Data ◽  
Taxon Sampling ◽  
Data Sets ◽  
Morphological Convergence

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.]

scholarly journals Exploring phylogenomic relationships within Myriapoda: should high matrix occupancy be the goal?

2015 ◽  
Author(s):  
Rosa Fernandez ◽  
Gregory D Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
Sister Group ◽  
Molecular Data ◽  
Taxon Sampling ◽  
Molecular Evidence ◽  
Data Sets ◽  
The Family ◽  
Family Level ◽  
Conserved Genes ◽  
Bayesian Mixture ◽  
Bayesian Mixture Models

Myriapods are one of the dominant terrestrial arthropod groups including the diverse and familiar centipedes and millipedes. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes in many species) or on maximizing matrix occupancy (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed forty Illumina transcriptomes representing three myriapod classes (Diplopoda, Chilopoda and Symphyla); twenty-five transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Eight supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at three levels of mean gene occupancy per taxon (50%, 75% and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in two alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but two nodes remained in conflict in the different analyses despite dense taxon sampling at the family level, situating the order Scolopendromorpha as sister group to a morphologically-anomalous grouping of Lithobiomorpha + Geophilomorpha in a subset of analyses. Interestingly, this anomalous result was obtained for all analyses conducted with the most complete matrix (90% of occupancy), being at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) or with the matrices optimizing phylogenegic informativeness and the most conserved genes, but also with previous hypotheses based on morphology, development or other molecular data sets. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.

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.

scholarly journals Muellerella, a lichenicolous fungal genus recovered as polyphyletic within Chaetothyriomycetidae (Eurotiomycetes, Ascomycota)

2019 ◽  
Vol 64 (2) ◽  
pp. 367-381
Author(s):  
Lucia Muggia ◽  
Sergio Pérez-Ortega ◽  
Damien Ertz
Keyword(s):  
Environmental Samples ◽  
Strong Support ◽  
Morphological Diversity ◽  
Molecular Data ◽  
Taxon Sampling ◽  
Phylogenetic Placement ◽  
Monophyletic Lineage ◽  
Black Fungi ◽  
Culture Dependent ◽  
Multilocus Phylogeny

AbstractMolecular data and culture-dependent methods have helped to uncover the phylogenetic relationships of numerous species of lichenicolous fungi, a specialized group of taxa that inhabit lichens and have developed diverse degrees of specificity and parasitic behaviors. The majority of lichenicolous fungal taxa are known in either their anamorphic or teleomorphic states, although their anamorph-teleomorph relationships have been resolved in only a few cases. The pycnidium-forming Lichenodiplis lecanorae and the perithecioid taxa Muellerella atricola and M. lichenicola were recently recovered as monophyletic in Chaetothyriales (Eurotiomycetes). Both genera are lichenicolous on multiple lichen hosts, upon which they show a subtle morphological diversity reflected in the description of 14 species in Muellerella (of which 12 are lichenicolous) and 12 in Lichenodiplis. Here we focus on the teleomorphic genus Muellerella and investigate its monophyly by expanding the taxon sampling to other species occurring on diverse lichen hosts. We generated molecular data for two nuclear and one mitochondrial loci (28S, 18S and 16S) from environmental samples. The present multilocus phylogeny confirms the monophyletic lineage of the teleomorphic M. atricola and M. lichenicola with their L. lecanorae-like anamorphs, but places the rest of the Muellerella species studied in two different monophyletic lineages with strong support. The first, Muellerella spp. 1, is nested within some new lineages of black fungi isolated from different epilithic lichen thalli, while the second, Muellerella spp. 2, is closely related to the Verrucariales. Based on these results, we reappraise the phylogenetic placement of Muellerella and suggest its polyphyly within Chaetothyriomycetidae.

scholarly journals Phylogenetic analysis of large molecular data sets

2017 ◽  
pp. 99
Author(s):  
Pamela S. Soltis ◽  
Douglas E. Soltis
Keyword(s):  
Large Data ◽  
Molecular Data ◽  
Global Optimum ◽  
Large Data Sets ◽  
Phylogeny Reconstruction ◽  
Local Optimum ◽  
Data Sets ◽  
Additional Consideration ◽  
Technological Advances ◽  
The Difference

Technological advances in molecular biology have greatly increased the speed and efficiency of DNA sequencing, making it possible to construct large molecular data sets for phylogeny reconstruction relatively quickly. Despite their potential for improving our understanding of phylogeny, these large data sets also provide many challenges. In this paper, we discuss several of these challenges, including 1) the failure of a search to find the most parsimonious trees (the local optimum) in a reasonable amount of time, 2) the difference between a local optimum and the global optimum, and 3) the existence of multiple classes (islands) of most parsimonious trees. We also discuss possible strategies to improve the' likelihood of finding the most parsimonious tree(s) and present two examples from our work on angiosperm phylogeny. We conclude with a discussion of two alternatives to analyses of entire large data sets, the exemplar approach and compartmentalization, and suggest that additional consideration must be given to issues of data analysis for large data sets, whether morphological or molecular.

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.

No longer shipwrecked—Selkirkia (Boraginaceae) back on the mainland with generic rearrangements in South American “Omphalodes” based on molecular data

Phytotaxa ◽  
2016 ◽  
Vol 270 (4) ◽  
pp. 231 ◽  
Author(s):  
NORBERT HOLSTEIN ◽  
JULIANA CHACÓN ◽  
HARTMUT H. HILGER ◽  
MAXIMILIAN WEIGEND
Keyword(s):  
Type Species ◽  
Molecular Data ◽  
Taxon Sampling ◽  
South American ◽  
South American Species ◽  
European Species ◽  
The North ◽  
Genus 2 ◽  
Eurasian Species ◽  
Group 1

The genus Omphalodes (Boraginaceae) has recently been shown to be polyphyletic. Two distantly related lineages have already been segregated into the genera Memoremea (Central Europe) and Nihon (East Asia), respectively. We expanded the taxon sampling in the Omphalodeae and confirm that the genus is still paraphyletic to the two monotypic genera Selkirkia from the Juan Fernández Islands off the coast of Chile and Myosotidium from Chatham Island off the coast of New Zealand, plus two South American species currently assigned to Cynoglossum, and one species recently segregated from the latter genus as Mapuchea. Four clades are retrieved in a narrowly delimited Omphalodes group: 1) Iberodes, the annual southwestern European species of Omphalodes s.l. that have been recently segregated into this genus, 2) Omphalodes s.str., perennial western Eurasian species (including the type species of the genus), 3) the North American species of Omphalodes, and 4) the southern hemispheric Myosotidium as sister to a monophyletic group with Mapuchea plus the two other South American species of “Cynoglossum” and the island shrub Selkirkia berteroi. We argue that the taxa of this latter clade are best placed into an expanded genus Selkirkia. Selkirkia then represents a morphologically coherent entity with glochidiate nutlets. Its considerable difference in vegetative morphology to Myosotidium is easily explained by the highly divergent habitats the respective plants occupy. Lectotypifications, illustrations, and descriptions are provided for Myosotidium and the species of the expanded genus Selkirkia.

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

scholarly journals Gene Expression Does Not Support the Developmental Hourglass Model in Three Animals with Spiralian Development

2019 ◽  
Vol 36 (7) ◽  
pp. 1373-1383 ◽  
Author(s):  
Longjun Wu ◽  
Kailey E Ferger ◽  
J David Lambert
Keyword(s):  
Gene Expression ◽  
Large Fraction ◽  
Molecular Data ◽  
Development Stage ◽  
Data Sets ◽  
Rna Seq ◽  
Developmental Evolution ◽  
Phylotypic Stage ◽  
Hourglass Model ◽  
Almost All

Abstract It has been proposed that animals have a pattern of developmental evolution resembling an hourglass because the most conserved development stage—often called the phylotypic stage—is always in midembryonic development. Although the topic has been debated for decades, recent studies using molecular data such as RNA-seq gene expression data sets have largely supported the existence of periods of relative evolutionary conservation in middevelopment, consistent with the phylotypic stage and the hourglass concepts. However, so far this approach has only been applied to a limited number of taxa across the tree of life. Here, using established phylotranscriptomic approaches, we found a surprising reverse hourglass pattern in two molluscs and a polychaete annelid, representatives of the Spiralia, an understudied group that contains a large fraction of metazoan body plan diversity. These results suggest that spiralians have a divergent midembryonic stage, with more conserved early and late development, which is the inverse of the pattern seen in almost all other organisms where these phylotranscriptomic approaches have been reported. We discuss our findings in light of proposed reasons for the phylotypic stage and hourglass model in other systems.

scholarly journals Phylogenetic position and taxonomy of Cycloseris explanulata and C. wellsi (Scleractinia: Fungiidae): lost mushroom corals find their way home

2012 ◽  
Vol 81 (3) ◽  
pp. 125-146 ◽  
Author(s):  
Francesca Benzoni ◽  
Roberto Arrigoni ◽  
Fabrizio Stefani ◽  
Bastian T. Reijnen ◽  
Simone Montano ◽  
...  
Keyword(s):  
Molecular Study ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Distribution Data ◽  
Data Sets ◽  
Free Living ◽  
New Findings ◽  
The Family ◽  
Ecological Implications ◽  
History Of

The scleractinian species Psammocora explanulata and Coscinaraea wellsi were originally classified in the family Siderastreidae, but in a recent morpho-molecular study it appeared that they are more closely related to each other and to the Fungiidae than to any siderastreid taxon. A subsequent morpho-molecular study of the Fungiidae provided new insights regarding the phylogenetic relationships within that family. In the present study existing molecular data sets of both families were analyzed jointly with those of new specimens and sequences of P. explanulata and C. wellsi. The results indicate that both species actually belong to the Cycloseris clade within the family Fungiidae. A reappraisal of their morphologic characters based on museum specimens and recently collected material substantiate the molecular results. Consequently, they are renamed Cycloseris explanulata and C. wellsi. They are polystomatous and encrusting like C. mokai, another species recently added to the genus, whereas all Cycloseris species were initially thought to be monostomatous and free-living. In the light of the new findings, the taxonomy and distribution data of C. explanulata and C. wellsi have been updated and revised. Finally, the ecological implications of the evolutionary history of the three encrusting polystomatous Cycloseris species and their free-living monostomatous congeners are discussed.

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