Accuracy of estimated phylogenetic trees from molecular data

1983 ◽  
Vol 19 (2) ◽  
pp. 153-170 ◽  
Author(s):  
Masatoshi Nei ◽  
Fumio Tajima ◽  
Yoshio Tateno
Keyword(s):  
Phylogenetic Trees ◽  
Molecular Data

scholarly journals Origin of the European avian-like swine influenza viruses

2014 ◽  
Vol 95 (11) ◽  
pp. 2372-2376 ◽  
Author(s):  
Andi Krumbholz ◽  
Jeannette Lange ◽  
Andreas Sauerbrei ◽  
Marco Groth ◽  
Matthias Platzer ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Swine Influenza ◽  
H1n1 Influenza ◽  
Molecular Data ◽  
Influenza Viruses ◽  
Time Resolved ◽  
Genotype Constellation ◽  
Tree Inference

The avian-like swine influenza viruses emerged in 1979 in Belgium and Germany. Thereafter, they spread through many European swine-producing countries, replaced the circulating classical swine H1N1 influenza viruses, and became endemic. Serological and subsequent molecular data indicated an avian source, but details remained obscure due to a lack of relevant avian influenza virus sequence data. Here, the origin of the European avian-like swine influenza viruses was analysed using a collection of 16 European swine H1N1 influenza viruses sampled in 1979–1981 in Germany, the Netherlands, Belgium, Italy and France, as well as several contemporaneous avian influenza viruses of various serotypes. The phylogenetic trees suggested a triple reassortant with a unique genotype constellation. Time-resolved maximum clade credibility trees indicated times to the most recent common ancestors of 34–46 years (before 2008) depending on the RNA segment and the method of tree inference.

New species and findings of Pagastia Oliver (Diptera: Chironomidae: Diamesinae) from Central Asia, with DNA barcoding of known species of the genus

Zootaxa ◽  
2021 ◽  
Vol 4951 (3) ◽  
pp. 559-570
Author(s):  
EUGENYI A.  MAKARCHENKO ◽  
ALEXANDER A. SEMENCHENKO ◽  
DMITRY M. PALATOV
Keyword(s):  
New Species ◽  
Central Asia ◽  
Cytochrome Oxidase ◽  
Phylogenetic Trees ◽  
Morphological Characters ◽  
Molecular Data ◽  
Adult Males ◽  
Cytochrome Oxidase Subunit ◽  
Oxidase Subunit ◽  
Coi Sequences

Chironomids of the genus Pagastia Oliver (Diamesinae, Diamesini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Pagastia (P.) caelestomontana sp. nov. from Kirgizstan and Tajikistan, P. (P.) hanseni sp. nov. from Tajikistan, and record of a finding apparently a new species P. (P.) aff. lanceolata (Tokunaga) from Tajikistan as well as an updated a key to the determination of the adult males of all known species of Pagastia are provided. A phylogenetic framework is reconstructed based on two mitochondrial genes cytochrome oxidase subunit I (COI) sequences of 34 samples belonging to 7 species of the genus Pagastia and cytochrome oxidase subunit II (COII) available for most samples. Phylogenetic trees of some known species of the genus Pagastia were reconstructed using the combined dataset and Bayesian inference (BI) and Maximum Likelihood (ML) methods. The interspecific K2P distances between seven Pagastia species including P. (P.) caelestomontana sp. nov., P. (P.) hanseni sp. nov. and undescribed P. (P.) aff. lanceolata (Tokunaga) are 6.3–13.2 which corresponding to species level. 

Accuracy of estimated phylogenetic trees from molecular data

1982 ◽  
Vol 18 (6) ◽  
pp. 387-404 ◽  
Author(s):  
Yoshio Tateno ◽  
Masatoshi Nei ◽  
Fumio Tajima
Keyword(s):  
Phylogenetic Trees ◽  
Molecular Data

scholarly journals Is there a need for accepting paraphyletic taxa? A case study in the Sardinian endemic Cymbalaria muelleri (Plantaginaceae)

2019 ◽  
Vol 191 (3) ◽  
pp. 325-338 ◽  
Author(s):  
Pau Carnicero ◽  
Peter Schönswetter ◽  
Núria Garcia-Jacas ◽  
Mercè Galbany-Casals
Keyword(s):  
Genome Size ◽  
Phylogenetic Trees ◽  
Fragment Length Polymorphism ◽  
Habitat Preferences ◽  
Molecular Data ◽  
Disjunct Distribution ◽  
Morphological Differences ◽  
A New Species ◽  
The Mediterranean Basin

Abstract Evolution does not always result in dichotomous phylogenetic trees. For instance, in anacladogenetic speciation, where a new species originates by budding, the ancestral taxon is often initially paraphyletic. Here we study Cymbalaria muelleri (Plantaginaceae), a chasmophytic species endemic to Sardinia, a major island in the Mediterranean Basin. Its distribution range is divided into two well-delimited geographical groups with some morphological differences. Using a combination of morphology, molecular data (amplified fragment length polymorphism fingerprinting) and relative genome size, we found that the two geographical groups should be considered two separate taxa, which split through anacladogenesis. Accordingly, we formally describe the new paraphyletic subspecies C. muelleri subsp. villosa as the ancestor, from which C. muelleri subsp. muelleri originated by budding. Morphological analyses support the differentiation of the two subspecies, and there are strong diagnostic characters to differentiate them. In addition to morphology and genetics, slightly divergent habitat preferences and the disjunct distribution of the two subspecies also support the recognition of two taxa. Genome size data obtained for the two subspecies are consistent with the previously established hexaploidy of C. muelleri.

Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 211-223 ◽  
Author(s):  
C. Hsiao ◽  
N. J. Chatterton ◽  
K. H. Asay ◽  
K. B. Jensen
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Parallel Evolution ◽  
Diploid Species ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
The Arctic ◽  
Cytogenetic Evidence

Phylogenetic relationships of 30 diploid species of Triticeae (Poaceae) representing 19 genomes were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The ITS sequence phylogeny indicated that: (i) each genome group of species is monophyletic, concordant with cytogenetic evidence; (ii) Hordeum (I) and Critesion (H) are basal; (iii) Australopyrum (W) is closely related to Agropyron (P); (iv) Peridictyon (G), Heteranthelium (Q), and Dasypyrum (V) are closely related to Pseudoroegneria (S); (v) most of the annuals, Triticum s.l. (A, B, D), Crithopsis (K), Taeniatherum (T), Eremopyrum (F), Henrardia (O), Secale (R), and two perennials, Thinopyrum (J) and Lophopyrum (E), all of Mediterranean origin, are a monophyletic group. However, phylogenetic trees based on morphology group these Mediteranean species with various perennial lineages of the Arctic-temperate region. The molecular data and biogeography of the tribe suggest that the Mediterranean lineage is derived from the Arctic-temperate lineage and that the two lineages have evolved in parallel. Extensive morphological parallelism apparently obscures the true genealogical history of the tribe when only morphology is considered.Key words: Poaceae, Triticeae, rDNA sequence, molecular phylogeny, parallel evolution.

scholarly journals Human origin and migration deciphered from a novel genomic footprints of mitochondrial sequences

2019 ◽  
Author(s):  
Aritra Mahapatra ◽  
Jayanta Mukherjee
Keyword(s):  
Phylogenetic Trees ◽  
Central Africa ◽  
Molecular Data ◽  
Modern Human ◽  
Human Migration ◽  
Genomic Feature ◽  
Genomic Studies ◽  
West And Central Africa ◽  
High Bootstrap ◽  
And Migration

AbstractThe origin of modern human and their migration across the world is one of the most debated topics for the decades. There exist two different hypotheses, recent African origin and multi-regional evolution, based on the genomic studies, haplogroups, archaeological records, cultural behaviors, palaeontology studies, etc. Various studies placed the modern humans in a phylogenetic tree to depict the relationships among them. The debate for determining those regions of Africa which witnessed the first origin of humans still exists. The conflicts between the results obtained from the molecular data and the archaeological and palaeontological reports still exist. We adopt a novel genomic feature derived from the whole mitochondrial sequence, and using a novel distance function the phylogenetic trees are constructed based on the feature which provide a new insight on human migration. We propose a new method to derive the bootstrap replica from the genome sequences by considering the genetic variance to demonstrate the robustness of the obtained trees. The results derived from the genomic feature are more consistent with the archaeological findings based on the time of origin of different communities. We find that west and central African communities are placed at the basal point with a very high bootstrap score. This study roughly estimates the existence of the archaic human at 800-900 kilo years ago and presence of human in Africa at 600-700 kilo years ago. This supports the presence of an ancestor in the west and central Africa much earlier than that of the fossils identified.

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.

DISTATIS: A Promising Framework to Integrate Distance Matrices in Molecular Phylogenetics.

2021 ◽  
Vol 21 ◽  
Author(s):  
Guillermin Agüero-Chapin ◽  
Yuliana Jiménez ◽  
Aminael Sánchez-Rodríguez ◽  
Reinaldo Molina-Ruiz ◽  
Oscar Vivanco ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Molecular Phylogenetics ◽  
Molecular Data ◽  
Morphological Data ◽  
Reproduction Mode ◽  
Alignment Free ◽  
Morphological Criteria ◽  
Distance Matrices ◽  
Ascospore Morphology

Background: Molecular phylogenetic algorithms frequently disagree with the approaches considering reproductive compatibility and morphological criteria for species delimitation. The question stems if the resulting species boundaries from molecular, reproductive and/or morphological data are definitively not reconcilable; or if the existing phylogenetic methods are not sensitive enough to agree morphological and genetic variation in species delimitation. Objectives : We propose to DISTATIS as an integrative framework to combine alignment-based (AB) and alignment-free (AF) distance matrices from ITS2 sequences/structures to shed light whether Gelasinospora and Neurospora are sister but independent genera? Methodology: We aimed at addressing this standing issue by harmonizing genus-specific classification based on their ascospore morphology and ITS2 molecular data. To validate our proposal, three phylogenetic approaches: i) traditional alignment-based, ii) alignment-free and iii) novel distance integrative (DI)-based were comparatively evaluated on a set of Gelasinospora and Neurospora species. All considered species have been extensively characterized at both the morphological and reproductive levels and there are known incongruences between their ascospore morphology and molecular data that hampers genus-specific delimitation. Results: Traditional AB phylogenetic analyses fail at resolving the Gelasinospora and Neurospora genera into independent monophyletic clades following ascospore morphology criteria. In contrast, AF and DI approaches produced phylogenetic trees that could properly delimit the expected monophyletic clades. Conclusions: The DI approach outperformed the AF one in the sense that it could also divide the Neurospora species according to their reproduction mode.

Pycnoclavella stolonialis n. sp. (Tunicata: Ascidiacea), with phylogenetic and distributional remarks on the genus in Europe

Zootaxa ◽  
2010 ◽  
Vol 2407 (1) ◽  
pp. 51 ◽  
Author(s):  
R. PÉREZ-PORTELA ◽  
C. E. GOODWIN ◽  
B. E. PICTON ◽  
X. TURON
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Molecular Data ◽  
Coi Gene ◽  
Irish Sea ◽  
Colony Structure ◽  
Colonial Ascidian ◽  
Sea Squirt ◽  
The Irish Sea

Morphological and molecular data based on the COI gene were used to describe a new species of the colonial ascidian genus Pycnoclavella. The new species, P. stolonialis, is widespread sublittorally in the Irish Sea and also occurs on the western Irish coast, Wales and eastern England and may be locally common. It has been commonly known as the ‘pin head’ sea squirt since first recorded from Northern Ireland in 1984 but has not yet been formally described. P. stolonialis is the only described species of Pycnoclavella combining the presence of stolons, peribranchial incubation mode and a larva lacking an otolith. In addition, it features ca. 10% sequence divergence with the closest species of the genus in our phylogenetic trees. P. stolonialis showed intermediate characters between two groups of Pycnoclavella; the stanleyi and the aurilucens groups. Larval morphology and molecular data supported the inclusion of P. stolonialis within the aurilucens group, but the stolonial colony structure is characteristic of the stanleyi group. This implies that colony structure may not be a good character for separating these two groups. New information on distribution is given for P. atlantica, P. aurilucens and P. communis.

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