scholarly journals Improvements in the fossil record may largely resolve the conflict between morphological and molecular estimates of mammal phylogeny

2018 ◽  
Author(s):  
Robin M. D. Beck ◽  
Charles Baillie
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Fossil Record ◽  
Morphological Character ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Case Scenario ◽  
State Reconstruction ◽  
Consensus View

AbstractMorphological phylogenies of mammals continue to show major conflicts with the robust molecular consensus view of their relationships. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships, particularly for fossil taxa for which, in most cases, molecular data is unlikely to ever become available. We tested this under a hypothetical “best case scenario” by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive molecular phylogeny of mammals, and then seeing what effect inclusion of these predicted ancestors had on unconstrained analyses of morphological data. We found that this resulted in topologies that are highly congruent with the molecular consensus, even when simulating the effect of incomplete fossilisation. Most strikingly, several analyses recovered monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record may be sufficient to largely reconcile morphological and molecular phylogenies of mammals, even with current morphological character sets.

scholarly journals Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny

2018 ◽  
Vol 285 (1893) ◽  
pp. 20181632 ◽  
Author(s):  
Robin M. D. Beck ◽  
Charles Baillie
Keyword(s):  
Maximum Likelihood ◽  
Fossil Record ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Case Scenario ◽  
State Reconstruction ◽  
Consensus View

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical ‘best case scenario’ by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record—specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus—may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

scholarly journals Molecular evidence and marine snake origins

2005 ◽  
Vol 1 (2) ◽  
pp. 227-230 ◽  
Author(s):  
Michael S.Y Lee
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Evidence ◽  
Gene Sequences ◽  
Molecular Analyses ◽  
Marine Origin ◽  
Molecular Tree

A molecular phylogeny was used to refute the marine scenario for snake origins. Nuclear gene sequences suggested that snakes are not closely related to living varanid lizards, thus also apparently contradicting proposed relationships between snakes and marine mosasaurs (usually considered to be varanoids). However, mosasaurs share derived similarities with both snakes and living varanids. A reanalysis of the morphological data suggests that, if the relationships between living taxa are constrained to the proposed molecular tree, with fossil forms allowed to insert in their optimal positions within this framework, mosasaurs cluster with snakes rather than with varanids. Combined morphological and molecular analyses also still unite marine lizards with snakes. Thus, the molecular data do not refute the phylogenetic evidence for a marine origin of snakes.

Molecular phylogeny of the spoonbills (Aves: Threskiornithidae) based on mitochondrial DNA

Zootaxa ◽  
2010 ◽  
Vol 2603 (1) ◽  
pp. 53 ◽  
Author(s):  
R. TERRY CHESSER ◽  
CAROL K. L. YEUNG ◽  
CHENG-TE YAO ◽  
XIU-HUA TIAN ◽  
SHOU-HSIEN LI
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Bayesian Analyses ◽  
Limited Sampling

Spoonbills (genus Platalea) are a small group of wading birds, generally considered to constitute the subfamily Plataleinae (Aves: Threskiornithidae). We reconstructed phylogenetic relationships among the six species of spoonbills using variation in sequences of the mitochondrial genes ND2 and cytochrome b (total 1796 bp). Topologies of phylogenetic trees reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses were virtually identical and supported monophyly of the spoonbills. Most relationships within Platalea received strong support: P. minor and P. regia were closely related sister species, P. leucorodia was sister to the minor-regia clade, and P. alba was sister to the minor-regia-leucorodia clade. Relationships of P. flavipes and P. ajaja were less well resolved: these species either formed a clade that was sister to the four-species clade, or were successive sisters to this clade. This phylogeny is consistent with ideas of relatedness derived from spoonbill morphology. Our limited sampling of the Threskiornithinae (ibises), the putative sister group to the spoonbills, indicated that this group is paraphyletic, in agreement with previous molecular data; this suggests that separation of the Threskiornithidae into subfamilies Plataleinae and Threskiornithinae may not be warranted.

scholarly journals Using ancestral state reconstruction methods for onomasiological reconstruction in multilingual word lists

2018 ◽  
Vol 8 (1) ◽  
pp. 22-54 ◽  
Author(s):  
Gerhard Jäger ◽  
Johann-Mattis List
Keyword(s):  
Maximum Likelihood ◽  
Ancestral State Reconstruction ◽  
Ancestral State ◽  
State Reconstruction ◽  
Reconstruction Methods ◽  
Lexical Change ◽  
Word Lists ◽  
Automatic Methods ◽  
Test Sets ◽  
Inference Methods

AbstractCurrent efforts in computational historical linguistics are predominantly concerned with phylogenetic inference. Methods for ancestral state reconstruction have only been applied sporadically. In contrast to phylogenetic algorithms, automatic reconstruction methods presuppose phylogenetic information in order to explain what has evolved when and where. Here we report a pilot study exploring how well automatic methods for ancestral state reconstruction perform in the task of onomasiological reconstruction in multilingual word lists, where algorithms are used to infer how the words evolved along a given phylogeny, and reconstruct which cognate classes were used to express a given meaning in the ancestral languages. Comparing three different methods, Maximum Parsimony, Minimal Lateral Networks, and Maximum Likelihood on three different test sets (Indo-European, Austronesian, Chinese) using binary and multi-state coding of the data as well as single and sampled phylogenies, we find that Maximum Likelihood largely outperforms the other methods. At the same time, however, the general performance was disappointingly low, ranging between 0.66 (Chinese) and 0.79 (Austronesian) for the F-Scores. A closer linguistic evaluation of the reconstructions proposed by the best method and the reconstructions given in the gold standards revealed that the majority of the cases where the algorithms failed can be attributed to problems of independent semantic shift (homoplasy), to morphological processes in lexical change, and to wrong reconstructions in the independently created test sets that we employed.

scholarly journals Morphological and phylogenetic evidence for two new species of Russula subg. Heterophyllidia from Guangdong Province of China

MycoKeys ◽  
2021 ◽  
Vol 82 ◽  
pp. 139-157
Author(s):  
Bin Chen ◽  
Jie Song ◽  
Yanliu Chen ◽  
Jinhua Zhang ◽  
Junfeng Liang
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Guangdong Province ◽  
Morphological Characters ◽  
Molecular Data ◽  
Terminal Cell ◽  
Two New Species ◽  
Long Chains

Two new species of Russula subg. Heterophyllidia from Guangdong Province of China were described and illustrated based on morphological characters, and their identity supported by molecular phylogeny. R. luofuensis is morphologically characterized by a grayish yellow to brownish orange pileus center with a purplish gray to grayish magenta margin, a surface that is cracked and broken into small golden-brown patches, subglobose to broadly ellipsoid basidiospores with warts fused in short or long chains and a suprapellis composed of hyphal extremities with inflated, ellipsoid or globose cells and attenuated terminal cell. R. subbubalina is distinguished by the blanched almond to dark salmon pileus that is cracked with age, subglobose to broadly ellipsoid basidiospores with wart fused in short or long chains and frequently connected by line connections, a suprapellis with hyphal ends composed of inflated or ellipsoid cells and attenuated terminal cell, and pileocystidia that are mainly clavate and sometimes with round or ellipsoid appendage. The phylogenetic analyses based on ITS-nrLSU-mtSSU-TEF1 dataset were performed using maximum likelihood and Bayesian analysis. In terms of morphological features and molecular data, the former species belongs to subsect. Virescentinae, whereas the latter comes under subsect. Heterophyllinae.

scholarly journals Peculiar macrophagous adaptations in a new Cretaceous pliosaurid

2015 ◽  
Vol 2 (12) ◽  
pp. 150552 ◽  
Author(s):  
Valentin Fischer ◽  
Maxim S. Arkhangelsky ◽  
Ilya M. Stenshin ◽  
Gleb N. Uspensky ◽  
Nikolay G. Zverkov ◽  
...  
Keyword(s):  
Early Cretaceous ◽  
Fossil Record ◽  
Late Jurassic ◽  
Phylogenetic Analyses ◽  
Consensus Methods ◽  
Ancestral State ◽  
Ecological Diversity ◽  
Apex Predator ◽  
State Reconstruction ◽  
Marine Reptile

During the Middle and Late Jurassic, pliosaurid plesiosaurs evolved gigantic body size and a series of craniodental adaptations that have been linked to the occupation of an apex predator niche. Cretaceous pliosaurids (i.e. Brachaucheninae) depart from this morphology, being slightly smaller and lacking the macrophagous adaptations seen in earlier forms. However, the fossil record of Early Cretaceous pliosaurids is poor, concealing the evolution and ecological diversity of the group. Here, we report a new pliosaurid from the Late Hauterivian (Early Cretaceous) of Russia. Phylogenetic analyses using reduced consensus methods recover it as the basalmost brachauchenine. This pliosaurid is smaller than other derived pliosaurids, has tooth alveoli clustered in pairs and possesses trihedral teeth with complex serrated carinae. Maximum-likelihood ancestral state reconstruction suggests early brachauchenines retained trihedral teeth from their ancestors, but modified this feature in a unique way, convergent with macrophagous archosaurs or sphenacodontoids. Our findings indicate that Early Cretaceous marine reptile teeth with serrated carinae cannot be unequivocally assigned to metriorhynchoid crocodylomorphs. Furthermore, they extend the known diversity of dental adaptations seen in Sauropterygia, the longest lived clade of marine tetrapods.

scholarly journals Mitochondrial DNA Phylogeny of Babblers (Timaliidae)

The Auk ◽  
2003 ◽  
Vol 120 (1) ◽  
pp. 35-54
Author(s):  
Alice Cibois
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Dna Phylogeny ◽  
Traditional Classification ◽  
Phylogenetic Hypotheses

Abstract The systematics of the babblers (Timaliidae) and related members of the Old World insectivorous passerines have been particularly difficult. To clarify our understanding of this group, phylogenetic relationships were constructed using sequences of three mitochondrial genes (cytochrome b, rRNA 12S and 16S). The results indicated that several species traditionally placed among babblers, the shrike babblers (Pteruthius) and the Gray-chested Thrush Babbler (Kakamega poliothorax), are not related to the Timaliidae, but belong to other passerine groups. Furthermore, the phylogenetic hypotheses inferred from molecular data suggest that the babblers assemblage includes two other oscine taxa traditionally considered to be distantly related, Sylvia (Sylviidae) and Zosterops (Zosteropidae). The polyphyly of several babbler genera is discussed, with particular attention to the laughingthrushes (genera Garrulax and Babax) for which the phylogeny is compared to previous hypotheses of relationships. Results from different tests under the maximum-parsimony and maximum-likelihood criteria indicate the rejection of the hypothesis of monophyly for the laughingthrushes group. Thus, the molecular phylogeny challenges the traditional classification of the Timaliidae.

scholarly journals Habrosia (Caryophyllaceae) a monotypic genus endemic to Western Asia

2021 ◽  
Vol 80 (2) ◽  
Author(s):  
Duilio Iamonico
Keyword(s):  
Molecular Phylogeny ◽  
Molecular Data ◽  
Taxonomic Position ◽  
Morphological Data ◽  
Monotypic Genus ◽  
Distribution Map ◽  
Correct Position ◽  
Molecular Tree ◽  
Western Asia ◽  
Molecular Investigation

Habrosia (Sagineae, Caryophyllaceae) is a genus that includes only H. spinuliflora, a species occurring in Iran, Iraq, Syria, Lebanon, and Turkey (Irano-Turanian floristic chorological element). Based on the available molecular data published in 2011, Habrosia appears to be nested in a Minuartia-clade, which includes taxa currently recognized under the genus Sabulina. Consequently, Habrosia should be treated as a genus to be included in Sabulina. However, the molecular tree published in 2011 considered only 9 Sabulina members whereas, according to the current concept, Sabulina is a genus comprising about 65 species. Unfortunately, the molecular phylogeny including a larger Sabulina sample published in 2014 did not include H. spinuliflora and the taxonomic position of Habrosia remains, therefore, uncertain. With the aim of verifying the correct position of Habrosia in the tribe Sagineae with respect to its relationship to Sabulina, a comprehensive molecular investigation based on ITS sequences, linked to detailed morphological data, is presented. The results obtained revealed that Habrosia is not part of Sabulina. A detailed description of H. spinuliflora, its ecological preference, and a distribution map are provided. Eventually, the name Arenaria spinulifolia (basionym of H. spinuliflora) is lectotypified on a specimen preserved at G (barcode G00212963).

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