Total evidence and sensitivity phylogenetic analyses of egg‐brooding frogs (Anura: Hemiphractidae)

Cladistics ◽  
2020 ◽  
Author(s):  
Lourdes Y. Echevarría ◽  
Ignacio De la Riva ◽  
Pablo J. Venegas ◽  
Fernando J.M. Rojas‐Runjaic ◽  
Iuri R. Dias ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Total Evidence ◽  
Egg Brooding

A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata)

1995 ◽  
Vol 347 (1320) ◽  
pp. 213-234 ◽  
Keyword(s):  
Data Base ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Total Evidence ◽  
Morphological Data ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Molecular Sequences ◽  
Higher Taxa ◽  
Stem Group

Phylogenedc reladonships of higher taxa of echinoids have been invesdgated using a 163 character morphological data base and molecular sequences from large and small subunit (LSU and SSU) ribosomal RNA (rRNA) genes. The complete ssu rRNA gene has been sequenced for 21 taxa, with representatives from nine of the 14 extant orders of Echinoidea. Partial LSU sequences, representing the first 400 base pairs (b.p.) from the 5' end were also sequenced for three taxa to complement an existing data base of ten taxa. The two molecular sequences provided a total of 371 variable sites, of which 143 were phylogenetically informative (compared to 145 phylogenetically informative sites from morphological data). Morphological, LSU and SSU data have been analysed separately and together. Morphological and ssu sequence data generate topologies that are not significantly in conflict (under Templeton’s test), but the strong signal pairing arbaciids with clypeasteroids in the LSU derived tree marks the LSU sequence data as anomalous for this taxon. A ‘ total evidence’ approach derived a tree very similar in topology to that derived from morphological data. Rooted on the stem group echinoid Archaeocidaris , our total evidence tree suggested relationships of higher taxa as follows: Gidaroida Phormosomatidae Echinothuriidae Diadematidae Spatangoida Clypeasteroida, Cassiduloida Calycina, Arbacioida Stomopneustidae Glyphocidaridae Temnopleuridae Echinometridae Echinidae, Strongylocentridae. Phylogenetic analyses run both with and without key fossil taxa yielded slightly different topologies. It is important to include fossil taxa in a phylogenetic analysis where there are long stem-group branches or where the crown group is highly derived.

scholarly journals Phylogenetic Incongruence among Oncogenic Genital Alpha Human Papillomaviruses

2005 ◽  
Vol 79 (24) ◽  
pp. 15503-15510 ◽  
Author(s):  
Apurva Narechania ◽  
Zigui Chen ◽  
Rob DeSalle ◽  
Robert D. Burk
Keyword(s):  
Phylogenetic Analyses ◽  
Similarity Measures ◽  
Human Papillomaviruses ◽  
Open Reading Frames ◽  
Total Evidence ◽  
Early Gene ◽  
Tree Length ◽  
Species Groups ◽  
E6 And E7 ◽  
Evolutionary Paths

ABSTRACT The human papillomaviruses (HPVs) have long been thought to follow a monophyletic pattern of evolution with little if any evidence for recombination between genomes. On the basis of this model, both oncogenicity and tissue tropism appear to have evolved once. Still, no systematic statistical analyses have shown whether monophyly is the rule across all HPV open reading frames (ORFs). We conducted a taxonomic analysis of 59 mucosal/genital HPVs using whole-genome and sliding-window similarity measures; maximum-parsimony, neighbor-joining, and Bayesian phylogenetic analyses; and localized incongruence length difference (LILD) analyses. The algorithm for the LILD analyses localized incongruence by calculating the tree length differences between constrained and unconstrained nodes in a total-evidence tree across all HPV ORFs. The process allows statistical evaluation of every ORF/node pair in the total-evidence tree. The most significant incongruence was observed at the putative high-risk (i.e., cancer-associated) node, the common oncogenic ancestor for alpha HPV species 9 (e.g., HPV type 16 [HPV16]), 11, 7 (e.g., HPV18), 5, and 6. Although these groups share early-gene homology, including high degrees of similarity among E6 and E7, groups 9 and 11 diverge from groups 7, 5, and 6 with respect to L2 and L1. The HPV species groups primarily associated with cervical and anogenital cancers appear to follow two distinct evolutionary paths, one conferred by the early genes and another by the late genes. The incongruence in the genital HPV phylogeny could have occurred from an early recombination event, an ecological niche change, and/or asymmetric genome convergence driven by intense selection. These data indicate that the phylogeny of the oncogenic HPVs is complex and that their evolution may not be monophyletic across all genes.

Total evidence phylogeny of the North American harvestman family Stygnopsidae (Opiliones : Laniatores : Grassatores) reveals hidden diversity

2017 ◽  
Vol 31 (3) ◽  
pp. 317 ◽  
Author(s):  
Jesús A. Cruz-López ◽  
Oscar F. Francke
Keyword(s):  
Bayesian Inference ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
The North ◽  
Protein Encoding ◽  
The Status ◽  
Taxonomic Changes

Systematic relationships among Laniatores have received considerable attention during the past few years. Many significant taxonomic changes have been proposed, particularly in the superfamily Gonyleptoidea. As part of this superfamily, the basalmost Stygnopsidae is the least known family. In order to propose the first total evidence phylogeny of the family, we produced four datasets: three molecular markers – partial nuclear 28S, mitochondrial ribosomal 16S, mitochondrial protein-encoding cytochrome c oxidase subunit I; and 72 morphological characters. With these data, we performed three different phylogenetic analyses: (1) Bayesian Inference with molecular data, and (2) Bayesian Inference and (3) Maximum Likelihood using combined data. Our results are congruent: a monophyletic Stygnopsidae subdivided into two major clades: Stygnopsinae and Karosinae, subfam. nov. The following genera are redefined: Stygnopsis, Hoplobunus and Serrobunus stat. rev. The following taxa are described: Iztlina venefica, gen. nov., sp. nov. and Tonalteca, gen. nov. Additionally, the following changes are proposed: Serrobunus queretarius (Šilhavý, 1974), comb. nov., Stygnopsis apoalensis (Goodnight & Goodnight, 1973), comb. nov., Stygnopsis mexicana (Roewer, 1915), comb. nov., Stygnopsis oaxacensis (Goodnight & Goodnight, 1973), comb. nov., and Tonalteca spinooculorum (Goodnight & Goodnight, 1973), comb. nov. We also discuss the status of the genera Isaeus stat. rev. and Mexotroglinus. Finally, we discuss the evolution of male genitalia and convergence of selected homoplastic diagnostic characters.

New cyanobacterium Nodosilinea svalbardensis sp. nov. (Prochlorotrichaceae, Synechococcales) isolated from alluvium in Mimer river valley of the Svalbard archipelago

Phytotaxa ◽  
2020 ◽  
Vol 442 (2) ◽  
pp. 61-79 ◽  
Author(s):  
DENIS DAVYDOV ◽  
SERGEI SHALYGIN ◽  
ANNA VILNET
Keyword(s):  
Phylogenetic Analyses ◽  
Natural Populations ◽  
Its Region ◽  
Total Evidence ◽  
Rrna Gene ◽  
New Taxon ◽  
Cyanobacterial Strain ◽  
Svalbard Archipelago ◽  
Molecular Approaches ◽  
The 16S Rrna Gene

A cyanobacterial strain isolated from the Svalbard archipelago was studied using morphological, ecological, and molecular approaches. The morphology of natural populations fit well the description of the Leptolyngbya s.l. however, in culture, they formed specific nodules that prevented affiliation to this genus. Further phylogenetic analyses including the 16S rRNA gene and 16S-23S ITS region revealed that the strain corresponds to the genus Nodosilinea. Based on this total evidence approach, we provide here a description of the new taxon Nodosilinea svalbardensis sp. nov.

scholarly journals Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

2016 ◽  
Vol 12 (5) ◽  
pp. 20151003 ◽  
Author(s):  
Thomas Guillerme ◽  
Natalie Cooper
Keyword(s):  
Data Collection ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Living Species ◽  
Anatomical Characters ◽  
The Impact

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.

scholarly journals Phylogeny, evolution, and classification of the ant genus Lasius, the tribe Lasiini, and the subfamily Formicinae (Hymenoptera: Formicidae)

2021 ◽  
Author(s):  
Brendon E Boudinot ◽  
Marek L Borowiec ◽  
Matthew M Prebus
Keyword(s):  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Social Parasitism ◽  
Molecular Data ◽  
Species Group ◽  
Total Evidence ◽  
Death Process ◽  
Ancestral State ◽  
Fossil Species

Within the Formicidae, the higher classification of nearly all subfamilies has been recently revised due to the findings of molecular phylogenetics. Here, we integrate morphology and molecular data to holistically address the evolution and classification of the ant genus Lasius, its tribe Lasiini, and their subfamily Formicinae. We accomplish this through a critical re-examination of morphology of extant and fossil taxa, molecular phylogenetic analyses, total-evidence dating under fossilized birth-death process, phylogeography, and ancestral state estimation. We use these results to provide revised taxonomic definitions for the Lasiini and select genera, and we provide a key to the genera of the Lasiini with emphasis on the Lasius genus group. We find that the crown Lasiini originated around the end of the Cretaceous on the Eurasian continent and is divisible into four morphologically distinct clades: Cladomyrma, the Lasius genus group, the Prenolepis genus group, and a previously undetected lineage we name XXXgen. n. The crown of the Lasius genus group is considerably younger than that of the Prenolepis genus group, indicating that extinction has played a major role in the evolution of the former clade. Lasius itself is divided into two well-supported monophyletic groups which are approximately equally speciose. We present evidence that temporary social parasitism and fungiculture arose in Lasius two times independently. Additionally, we recover the paraphyly of three Lasius subgenera and propose replacing all subgenera with an informal species group classification: Lasius = Acanthomyopssyn. rev., = Austrolasiussyn. n., = Cautolasiussyn. n., = Chthonolasius vsyn. n., = Dendrolasiussyn. n. Total-evidence analysis reveals that the Baltic-region amber fossil species Lasius pumilus and Pseudolasius boreus are misplaced to genus; we therefore designate XXXgen. n. for the former and XXXgen. n. for the latter. Further, we transfer XXX and Glaphyromyrmex out of the tribe, considering the former to be incertae sedis in the subfamily, and the latter a member of the Formicini (tribal transfer). Two final taxonomic actions are deemed necessary: synonymy of Lasius escamole Reza, 1925 with Liometopum apiculatum Mayr, 1870 syn. n. (subfamilial transfer), and transfer of Paratrechina kohli to Anoplolepis (tribal transfer, forming A. kohli (Forel, 1916) n. comb.).

scholarly journals Molecular phylogeny of porcelain crabs (Porcellanidae:Petrolisthesand allies) from the south eastern Pacific: the generaAllopetrolisthesandLiopetrolisthesare not natural entities

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1805 ◽  
Author(s):  
J. Antonio Baeza
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Eastern Pacific ◽  
Total Evidence ◽  
The South ◽  
South Eastern ◽  
Single Marker ◽  
Porcelain Crabs

Porcelain crabs from the closely related generaPetrolisthes,Liopetrolisthes, andAllopetrolisthesare known for their diversity of lifestyles, habitats, and coloration. The evolutionary relationships among the species belonging to these three genera is not fully resolved. A molecular phylogeny of the group may help to resolve the long-standing taxonomic question about the validity of the generaAllopetrolisthesandLiopetrolisthes. Using both ‘total evidence’ and single-marker analyses based on a 362-bp alignment of the 16S rRNA mitochondrial DNA and a 328-bp alignment of the Histone 3 nuclear DNA, the phylogenetic relationships among 11 species fromPetrolisthes(6 species),Liopetrolisthes(2 species), andAllopetrolisthes(3 species), all native to the south eastern Pacific, were examined. The analyses supported three pairs of sister species:L. mitra+L. patagonicus,P. tuberculatus+P. tuberculosus, andA. angulosus+A. punctatus. No complete segregation of species, according to genera, was evident from tree topologies. Bayesian-factor analyses revealed strong support for the unconstrained tree instead of an alternative tree in which monophyly of the three genera was forced. Thus, the present molecular phylogeny does not support the separation of the species within this complex into the generaPetrolisthes,Liopetrolisthes, andAllopetrolisthes. Taking into account the above and other recent molecular phylogenetic analyses focused on other representatives from the family Porcellanidae, it is tentatively proposed to eliminate the generaLiopetrolisthesandAllopetrolisthes, and to transfer their members to the genusPetrolisthes.

scholarly journals Total-Evidence Framework Reveals Complex Morphological Evolution in Nightbirds (Strisores)

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 143 ◽  
Author(s):  
Albert Chen ◽  
Noor D. White ◽  
Roger B.J. Benson ◽  
Michael J. Braun ◽  
Daniel J. Field
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Sequence Data ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Anatomical Data ◽  
Evidence Framework

Strisores is a clade of neoavian birds that include diurnal aerial specialists such as swifts and hummingbirds, as well as several predominantly nocturnal lineages such as nightjars and potoos. Despite the use of genome-scale molecular datasets, the phylogenetic interrelationships among major strisorean groups remain controversial. Given the availability of next-generation sequence data for Strisores and the clade’s rich fossil record, we reassessed the phylogeny of Strisores by incorporating a large-scale sequence dataset with anatomical data from living and fossil strisoreans within a Bayesian total-evidence framework. Combined analyses of molecular and morphological data resulted in a phylogenetic topology for Strisores that is congruent with the findings of two recent molecular phylogenomic studies, supporting nightjars (Caprimulgidae) as the extant sister group of the remainder of Strisores. This total-evidence framework allowed us to identify morphological synapomorphies for strisorean clades previously recovered using molecular-only datasets. However, a combined analysis of molecular and morphological data highlighted strong signal conflict between sequence and anatomical data in Strisores. Furthermore, simultaneous analysis of molecular and morphological data recovered differing placements for some fossil taxa compared with analyses of morphological data under a molecular scaffold, highlighting the importance of analytical decisions when conducting morphological phylogenetic analyses of taxa with molecular phylogenetic data. We suggest that multiple strisorean lineages have experienced convergent evolution across the skeleton, obfuscating the phylogenetic position of certain fossils, and that many distinctive specializations of strisorean subclades were acquired early in their evolutionary history. Despite this apparent complexity in the evolutionary history of Strisores, our results provide fossil support for aerial foraging as the ancestral ecological strategy of Strisores, as implied by recent phylogenetic topologies derived from molecular data.

Evaluating Results

2021 ◽  
pp. 186-216
Author(s):  
Andrew V. Z. Brower ◽  
Randall T. Schuh
Keyword(s):  
Sensitivity Analysis ◽  
Phylogenetic Analyses ◽  
Total Evidence ◽  
Consistency Index ◽  
Successive Approximations ◽  
Randomization Tests ◽  
Discrete Character ◽  
Branch Support

This chapter explores the tools used to evaluate the quality and plausibility of results of phylogenetic analyses. The term “fit” has been widely used in the phylogenetic literature to indicate the degree to which data conform to (or are explained by) a cladogram. The most commonly used measure of fit applied to discrete character data is the consistency index, or ci. Meanwhile, measures of synapomorphy are less frequently reported than the consistency index. The chapter then considers the resolution of branches; multiple equally parsimonious cladograms; successive approximations weighing; and data decisiveness. It also differentiates between total evidence and consensus, before describing supertrees. Finally, the chapter looks at approaches for evaluating support or stability of phylogenetic results, including branch support, jackknifing, bootstrapping, randomization tests, and sensitivity analysis.

scholarly journals A total-evidence approach resolves phylogenetic placement of ‘Cafius’ gigas, a unique recently extinct rove beetle from Lord Howe Island

2020 ◽  
Author(s):  
Arn Rytter Jensen ◽  
Josh Jenkins Shaw ◽  
Dagmara Żyła ◽  
Alexey Solodovnikov
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Total Evidence ◽  
New Combination ◽  
Phylogenetic Placement ◽  
Lord Howe Island ◽  
Rove Beetle ◽  
Morphological And Molecular Data

Abstract Cafius gigas Lea, 1929 (Coleoptera: Staphylinidae) was a large rove beetle endemic to Lord Howe Island (LHI) resembling Cafius and the LHI flightless endemic Hesperus dolichoderes (Lea, 1925). Like several other LHI endemics, C. gigas became extinct due to human-introduced rats. It is a legacy species valuable for understanding the LHI biota in terms of evolutionary biology and historical biogeography. Whether C. gigas was a member of Cafius Curtis, 1829, restricted to oceanic shores and prone to trans-oceanic dispersal, or related to H. dolichoderes, would have different implications. We subjected C. gigas to a total-evidence phylogenetic analyses of morphological and molecular data using model-based and parsimony methods. As a result, it is transferred to Hesperus Fauvel, 1874 with the new combination Hesperus gigas (Lea, 1929) comb. nov. Our analysis indicates that the montane leaf litter inhabitant H. gigas evolved neither in situ nor from a seashore Cafius-ancestor, or from an ancestor shared by two other LHI endemic congeners, Hesperus pacificus Olliff, 1887 and H. dolichoderes. It also suggests that all three Hesperus species that currently occur on LHI could have evolved on various seamounts at various times before reaching LHI.

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