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 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 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 The effects of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold on pseudoextinction analyses of extant placental orders

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257338
Author(s):  
Peggy L. Brady ◽  
Mark S. Springer
Keyword(s):  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Molecular Scaffolds ◽  
Data Set ◽  
Molecular Scaffold ◽  
Hypothetical Ancestor

Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.

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.

Xylodon bambusinus and X. xinpingensis spp. nov. (Hymenochaetales) from southern China

Phytotaxa ◽  
2021 ◽  
Vol 511 (3) ◽  
Author(s):  
XIANG MA ◽  
CHANG-LIN ZHAO
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Growth Habit ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Two New Species ◽  
Thin Walled ◽  
Inference Methods

Two new species, Xylodon bambusinus and X. xinpingensis, are proposed based on morphological and molecular evidences. Both species share the annual growth habit, resupinate basidiomata and monomitic hyphal system with clamped, colorless generative hyphae, smooth, thin-walled basidiospores, but X. bambusinus is characterized by the smooth to tuberculate hymenial surface, presence of capitate and fusiform cystidia, broad ellipsoid basidiospores, while X. xinpingensis by the reticulate hymenophore with cream hymenial surface, and subglobose basidiospores (4.5–6 × 3.5–5 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on molecular data of ITS and ITS+nLSU sequences showed that X. bambusinus was sister to X. subclavatus, while X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus. The nLSU dataset revealed that X. bambusinus grouped with X. asperus and X. brevisetus with lower supports, and that X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus and then with X. rimosissimus without supports. Both morphological and molecular evidences confirmed the placement of two new species in Xylodon. Description and figures from the new species and a key to the known species of Xylodon from China are presented.

scholarly journals The phylogenetic position of the solitary zoanthid genus Sphenopus (Cnidaria: Hexacorallia)

2012 ◽  
Vol 81 (1) ◽  
pp. 43-54 ◽  
Author(s):  
James D. Reimer ◽  
Meifang Lin ◽  
Takuma Fujii ◽  
David J.W. Lane ◽  
Bert W. Hoeksema
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Solid Substrate ◽  
Ancestral State Reconstruction ◽  
Phylogenetic Position ◽  
Ancestral State ◽  
State Reconstruction ◽  
Unique Character ◽  
The Family ◽  
Southern Taiwan

The zoanthid genus Sphenopus (Cnidaria: Anthozoa: Zoantharia), like many other brachycnemic zoanthids, is found in shallow subtropical and tropical waters, but is uniquely unitary (solitary, monostomatous), azooxanthellate, and free-living. With sparse knowledge of its phylogenetic position, this study examines the phylogenetic position of Sphenopus within the family Sphenopidae utilizing specimens from southern Taiwan and Brunei collected in 1999-2011, and furthermore analyzes the evolution of its unique character set via ancestral state reconstruction analyses. Phylogenetic analyses surprisingly show Sphenopus to be phylogenetically positioned within the genus Palythoa, which is colonial (polystomatous), zooxanthellate, and attached to solid substrate. Ancestral state reconstruction strongly indicates that the unique characters of Sphenopus have evolved recently within Palythoa and only in the Sphenopuslineage. These results indicate that zoanthid body plans can evolve with rapidity, as in some other marine invertebrates, and that the traditional definitions of zoanthid genera may need reexamination.

A new species of Physaloptera (Nematoda: Spirurida) from Proechimys gardneri (Rodentia: Echimyidae) from the Amazon rainforest and molecular phylogenetic analyses of the genus

2019 ◽  
Vol 94 ◽  
Author(s):  
A. Maldonado ◽  
R.O. Simões ◽  
J. São Luiz ◽  
S.F. Costa-Neto ◽  
R.V. Vilela
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Amazon Rainforest ◽  
Ancestral State ◽  
Intermediate Hosts ◽  
The Status ◽  
Molecular Phylogenetic ◽  
History Of ◽  
A New Species

Abstract Nematodes of the genus Physaloptera are globally distributed and more than 100 species are known. Their life cycle involves insects, including beetles, cockroaches and crickets, as intermediate hosts. This study describes a new species of Physaloptera and reports molecular phylogenetic analyses to determine its relationships within the family Physalopteridae. Physaloptera amazonica n. sp. is described from the stomach of the caviomorph rodent Proechimys gardneri collected in the Amazon rainforest in the state of Acre, Brazil. The species is characterized by the male having the first and second pair of sessile papillae asymmetrically placed, lacking a median papilla-like protuberance between the third pairs of sessile papillae, differentiated by size and shape of the spicules, while females have four uterine branches. For both nuclear 18S rRNA and MT-CO1 gene-based phylogenies, we recovered Turgida sequences forming a clade nested within Physaloptera, thus making Physaloptera paraphyletic to the exclusion of Turgida, suggesting that the latter may have evolved from the former monodelphic ancestral state to a derived polydelphic state, or that some species of Physaloptera may belong to different genera. Relationships between most taxa within Physaloptera were poorly resolved in our phylogenies, producing multifurcations or a star phylogeny. The star-like pattern may be attributed to evolutionary processes where past simultaneous species diversification events took place. Physaloptera amazonica n. sp. formed an independent lineage, separately from the other species of Physaloptera, thus supporting the status of a new species. However, all molecular data suggested a closer relationship with other Neotropical species. In conclusion, we added a new species to this already largely diverse genus Physaloptera, bringing new insights to its phylogenetic relationships. Further analyses, adding more species and markers, should provide a better understanding of the evolutionary history of physalopterids.

scholarly journals The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

2015 ◽  
Vol 46 (3) ◽  
pp. 269-290 ◽  
Author(s):  
Ian J. Kitching ◽  
C. Lorna Culverwell ◽  
Ralph E. Harbach
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Set ◽  
Generic Status ◽  
Strong Signal ◽  
Phylogenetic Studies ◽  
Data Support

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

Molecular characterisation of, and new data on, two populations of Xiphinema ingens Luc & Dalmasso, 1964 (Nematoda: Longidoridae) from Iran

Nematology ◽  
2015 ◽  
Vol 17 (2) ◽  
pp. 125-138
Author(s):  
Sohrab Mirzaei ◽  
Ebrahim Pourjam ◽  
Majid Pedram
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Morphological Variation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
28S Rdna ◽  
Molecular Characterisation ◽  
Morphometric Data ◽  
Two Populations

Two populations of Xiphinema ingens were recovered and characterised based on morphological, morphometric and molecular data. Interesting morphological variation was observed on the nature of differentiation in uterus of females between both populations, i.e. one population had only a pseudo-Z-organ in the shape of globular bodies, whilst the second population had a similar pseudo-Z-organ but also had crystalloids which varied in size and number and were located near the pseudo-Z-globules or sometimes at some distance from them towards the vagina. Variation was also observed in the shape of tail of juveniles within each population as well as between two recovered populations. Both populations had the same range of morphometric data and formed a fully supported clade in both Bayesian inference (BI) and maximum likelihood (ML) methods of phylogenetic analyses using partial sequences of 28S rDNA D2-D3 and ITS1 regions. The two populations of X. ingens formed a clade with another Xiphinema species native to Iran (X. castilloi) in 28S and two species, X. macroacanthum and X. bernardi, in ITS1 trees.

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