scholarly journals Molecular Phylogenies Map to Biogeography Better than Morphological Ones

2021 ◽  
Author(s):  
Jack Oyston ◽  
Mark Wilkinson ◽  
Marcello Ruta ◽  
Matthew Wills
Keyword(s):  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Data Sources ◽  
Morphological Data ◽  
Data Sets ◽  
Independent Data ◽  
Molecular Phylogenies ◽  
Better Than ◽  
Molecular Trees

Abstract Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Most current phylogenies of extant taxa are inferred from molecules, and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has never been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographical distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees, we show that molecular trees are, on average, significantly more biogeographically congruent than their morphological counterparts. We also report an increase in the biogeographical congruence of phylogenies over research time. We find no significant differences in stratigraphical congruence between morphological and molecular trees. These findings have implications for understanding homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses, and the difficulty of analysing fossil groups for which molecular data are unavailable.

Echinoderm phylogeny: how congruent are morphological and molecular estimates?

1997 ◽  
Vol 3 ◽  
pp. 337-355 ◽  
Author(s):  
Andrew B. Smith
Keyword(s):  
Cladistic Analysis ◽  
Molecular Data ◽  
Data Matrix ◽  
Morphological Data ◽  
Initial Assessment ◽  
Molecular Evidence ◽  
Data Sets ◽  
Independent Data ◽  
Robust Solution ◽  
Single Data

Single data sets, whether derived from morphological or molecular evidence, provide one-off estimates of the correct phylogeny. Their reliability can only be gauged by statistical approaches such as bootstrapping or clade decay, but these test only whether there are sufficient characters in the data matrix to justify the groupings identified. They do not test whether the characters themselves are reliable. Consequently, confidence in the correctness of phylogenetic interpretations comes primarily from discovering the same (or statistically indistinguishable) patterns from independent data sets.Congruence studies are most advanced for echinoids, where four independent data sets (two morphological and two molecular) provide strong corroboration for a single phylogenetic scheme. Analysis of all four data sets combined generates a highly robust hypothesis of relationships. The situation is very different for asteroids. Two analyses based on morphological data have reached very different conclusions. Three independent molecular data sets also have been compiled, but none has a statistically reliable signal concerning higher taxon relationships. Even combining all three molecular data sets fails to generate a statistically robust solution, implying that the major lines of asteroids diverged rapidly from one another. For ophiuroids, both morphological and molecular data generate topologies that for the most part lack statistical robustness. There is currently no cladistic analysis of holothurian relationships based on morphological data, and only a few taxa have been sequenced. The molecular data is, however, congruent and does permit an initial assessment of relationships. Nothing definite can be deduced about crinoid relationships since even fewer molecular sequences are known and morphological analysis remains sketchy.Class-level relationships derived from two morphological and two molecular data sets also show considerable congruence, though a single definitive solution has yet to emerge.

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.

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.

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

New species of Crella (Pytheas) Topsent, 1890 and Crellomima Rezvoi, 1925 (Crellidae, Poecilosclerida, Demospongiae) from Chilean shallow and Argentinean deep waters, with a synthesis on the known phylogenetic relationships of crellid sponges

Zootaxa ◽  
2021 ◽  
Vol 5052 (3) ◽  
pp. 353-379
Author(s):  
JULIO C.C. FERNANDEZ ◽  
MARIANELA GASTALDI ◽  
GERMÁN ZAPATA-HERNÁNDEZ ◽  
LUIS M. PARDO ◽  
FABIANO L. THOMPSON ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Molecular Data ◽  
Southern Chile ◽  
Deep Waters ◽  
Molecular Phylogenetic ◽  
Molecular Phylogenies ◽  
Taxonomic Studies ◽  
Phylogenetic Affinities

Here, we describe four new species of Crellidae Dendy, 1922 and discuss characters and relationships from published molecular phylogenies including crellid sponges. New species proposed are Crella (Pytheas) chiloensis Fernandez, Gastaldi, Pardo & Hajdu, sp. nov., from southern Chile (15 m depth), C. (P.) desventuradae Fernandez, Gastaldi, Zapata-Hernández & Hajdu, sp. nov., from Desventuradas Archipelago (10–20 m depth), Crella (P.) santacruzae Fernandez, Gastaldi, Thompson & Hajdu, sp. nov., from deep waters off Argentina (750 m depth) and Crellomima sigmatifera Fernandez, Gastaldi & Hajdu, sp. nov., from the Chilean fjords region (ca. 20 m depth). These new species are set apart from each other and from known species mainly due to aspects of their spiculation. Chelae microscleres and acanthostyles supply characters that might be used to infer phylogenetic relationships and to verify the monophyly of Crella Gray, 1867 and Crellidae, which has seemingly been contradicted by preliminary molecular data available in the systematics’ literature. Our own interpretation of phylogenetic affinities, in the light of morphological characters from previous taxonomic studies, argues for a classification reassessment of materials (vouchers) included in these molecular phylogenies, especially in the case of Crella incrustans (Carter, 1885). We argue that currently available molecular phylogenetic outcomes for crellid sponges are not supportive of the polyphyly of Crella and Crellidae.  

scholarly journals Phylogenetic relationships among extinct and extant turtles: the position of Pleurodira and the effects of the fossils on rooting crown-group turtles

2010 ◽  
Vol 79 (3) ◽  
pp. 93-106 ◽  
Author(s):  
Juliana Sterli
Keyword(s):  
Phylogenetic Relationships ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Separate Analysis ◽  
Crown Group ◽  
Rapid Radiation ◽  
Present Contribution ◽  
Origin And Evolution

The origin and evolution of the crown-group of turtles (Cryptodira + Pleurodira) is one of the most interesting topics in turtle evolution, second perhaps only to the phylogenetic position of turtles among amniotes. The present contribution focuses on the former problem, exploring the phylogenetic relationships of extant and extinct turtles based on the most comprehensive phylogenetic dataset of morphological and molecular data analyzed to date. Parsimony analyses were conducted for different partitions of data (molecular and morphological) and for the combined dataset. In the present analysis, separate analyses of the molecular data always retrieve Pleurodira allied to Trionychia. Separate analysis of the morphological dataset, by contrast, depicts a more traditional arrangement of taxa, with Pleurodira as the sister group of Cryptodira, being Chelonioidea the most basal cryptodiran clade. The simultaneous analysis of all available data retrieves all major extant clades as monophyletic, except for Cryptodira given that Pleurodira is retrieved as the sister group of Trionychia. The paraphyly of Cryptodira is an unorthodox result, and is mainly caused by the combination of two factors. First, the molecular signal allies Pleurodira and Trionychia. Second, the morphological data with extinct taxa locates the position of the root of crown-group Testudines in the branch leading to Chelonioidea. This study highlights major but poorly explored topics of turtle evolution: the alternate position of Pleurodira and the root of crown turtles. The diversification of crown turtles is characterized by the presence of long external branches and short internal branches (with low support for the internal nodes separating the major clades of crown turtles), suggesting a rapid radiation of this clade. This rapid radiation is also supported by the fossil record, because soon after the appearance of the oldest crown-group turtles (Middle-Late Jurassic of Asia) the number and diversity of turtles increases remarkably. This evolutionary scenario of a rapid diversification of modern turtles into the major modern lineages is likely the reason for the difficulty in determining the interrelationships and the position of the root of crown-group turtles.

Phylogenetic relationships and classification of the Malagasy pseudoxyrhophiine snake genera Geodipsas and Compsophis based on morphological and molecular data

Zootaxa ◽  
2007 ◽  
Vol 1517 (1) ◽  
pp. 53-62 ◽  
Author(s):  
FRANK GLAW ◽  
ZOLTÁN T. NAGY ◽  
MIGUEL VENCES
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Close Relationships ◽  
Original Description ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Phylogenetic ◽  
Species Groups ◽  
Morphological And Molecular Data

Based on a specimen found at Montagne d'Ambre in northern Madagascar morphologically agreeing with Compsophis albiventris Mocquard, 1894, we report on the rediscovery of this enigmatic snake genus and species and its molecular phylogenetic relationships. Compsophis albiventris, considered to be the only representative of its genus and unreported since its original description, bears strong morphological similarities to species of Geodipsas Boulenger, 1896. A molecular phylogeny based on DNA sequences of three mitochondrial and nuclear genes (complete cytochrome b, fragments of 16S rRNA and c-mos) in Compsophis albiventris and three Geodipsas species corroborated close relationships between C. albiventris and Geodipsas boulengeri, and showed that the genera Compsophis and Geodipsas together form a monophyletic unit. Despite the general similarities, morphological data and chromatic features support the existence of two species groups, corresponding to Compsophis and Geodipsas. We consequently consider Geodipsas as a subgenus of Compsophis and transfer all species currently in Geodipsas into the genus Compsophis.

scholarly journals Phylogenetic relationships of the neon tetras Paracheirodon spp. (Characiformes: Characidae: Stethaprioninae), including comments on Petitella georgiae and Hemigrammus bleheri

2020 ◽  
Vol 18 (2) ◽  
Author(s):  
Pedro Senna Bittencourt ◽  
Valéria Nogueira Machado ◽  
Bruce Gavin Marshall ◽  
Tomas Hrbek ◽  
Izeni Pires Farias
Keyword(s):  
Phylogenetic Relationships ◽  
Species Complex ◽  
Molecular Data ◽  
Morphological Data ◽  
Sister Taxon ◽  
Taxonomic History ◽  
Relationship Of

ABSTRACT Neon tetras (Paracheirodon spp.) are three colorful characid species with a complicated taxonomic history, and relationships among the species are poorly known. Molecular data resolved the relationships among the three neon tetras, and strongly supported monophyly of the genus and its sister taxon relationship to Brittanichthys. Additionally, the sister-taxon relationship of the rummy-nose tetras Hemigrammus bleheri and Petitella georgiae was strongly supported by molecular and morphological data. Therefore, we propose to transfer the rummy-nose tetras H. bleheri and H. rhodostomus to the genus Petitella. Furthermore, Petitella georgiae is likely to be a species complex comprised of at least two species.

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