scholarly journals Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

2018 ◽  
Author(s):  
Enrico Cappellini ◽  
Frido Welker ◽  
Luca Pandolfi ◽  
Jazmin Ramos Madrigal ◽  
Anna K. Fotakis ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Dental Enamel ◽  
Sister Group ◽  
Direct Access ◽  
Early Pleistocene ◽  
Middle Pleistocene ◽  
Time Range ◽  
Molecular Evidence ◽  
Type I ◽  
Taxonomic Assignment

ABSTRACTAncient DNA (aDNA) sequencing has enabled unprecedented reconstruction of speciation, migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible aDNA post-mortem degradation2 has so far limited aDNA recovery within the ˜0.5 million years (Ma) time range3. Tandem mass spectrometry (MS)-based collagen type I (COL1) sequencing provides direct access to older biomolecular information4, though with limited phylogenetic use. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae5-7 using ˜1.77 million years (Ma) old dental enamel proteome sequences of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)8. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that this genus includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference, and also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

scholarly journals Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations

2018 ◽  
Author(s):  
Johanna L.A. Paijmans ◽  
Axel Barlow ◽  
Daniel W. Förster ◽  
Kirstin Henneberger ◽  
Matthias Meyer ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Dna Sequences ◽  
Sister Group ◽  
Historical Biogeography ◽  
Early Pleistocene ◽  
Middle Pleistocene ◽  
Recent Common Ancestor ◽  
Panthera Pardus ◽  
Phylogenetic Placement ◽  
Out Of Africa

AbstractBackgroundResolving the historical biogeography of the leopard(Panthera pardus)is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?ResultsIn this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (∼710 Ka), with the European ancient samples as sister to all Asian lineages (∼483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (∼122 Ka), and we find one Javan sample nested within these.ConclusionsThe phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.

Phylogenetic relationships in Hypomyces and allied genera, with emphasis on species growing on wood-decaying homobasidiomycetes

2000 ◽  
Vol 77 (12) ◽  
pp. 1756-1768 ◽  
Author(s):  
Kadri Põldmaa ◽  
Ellen Larsson ◽  
Urmas Kõljalg
Keyword(s):  
Maximum Likelihood ◽  
Sexual Reproduction ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sister Group ◽  
28S Rdna ◽  
The Other ◽  
Molecular Evidence

To infer phylogenetic relationships among species of Hypomyces (Fr.) Tul and allied genera, partial sequences of the 28S rDNA were obtained for 21 strains representing 19 species. On the basis of these data and 38 sequences obtained from GenBank, phylogenetic analyses were performed using the programs PAUP and Pee-Wee. Hypomyces appears to be paraphyletic, with species having wet-conidial phialidic anamorphs more closely related to other genera. Hypomyces chrysostomus Berk & Broome is a sister group to the clade that includes species of Aphysiostroma Barrasa et al., Arachnocrea Moravec, and Hypocrea Fr. Based on morphological and molecular evidence, a new genus, Sporophagomyces, is described for Hypomyces chrysostomus and two allied species. Hypomyces broomeanus Tul. forms one clade with species of Sphaerostilbella Sacc. and is transferred to this genus. The recognition of Arachnocrea is justified. The integration of Cladobotryum Nees species that are not known to undergo sexual reproduction with Hypomyces species that possess Cladobotryum anamorphs receives strong support, but the whole complex of these species appears to be paraphyletic. However, constraint trees, which require monophyly of all these ana- and pleo-morphic species, do not appear significantly less likely than the other trees obtained under maximum likelihood or parsimony criteria. For the remaining species of Hypomyces, four distinct lineages are distinguished.

Morphological characteristics and phylogenetic analyses reveal Antrodia yunnanensis sp. nov. (Polyporales, Basidiomycota) from China

Phytotaxa ◽  
2020 ◽  
Vol 460 (1) ◽  
pp. 1-11
Author(s):  
MEI-LING HAN ◽  
QI AN ◽  
WEN-XIAN FU ◽  
XUAN CHENG ◽  
TIAN BU ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Sister Group ◽  
Southwestern China ◽  
Molecular Evidence ◽  
Pore Surface ◽  
Hyphal System ◽  
Thin Walled

A new polypore, Antrodia yunnanensis, collected from southwestern China, is described and illustrated based on morphological characteristics and molecular evidence. It is characterized by annual, resupinate basidiocarps with greyish blue to dark greyish blue pore surface upon drying, round to angular pores measuring 2–3 per mm, a dimitic hyphal system with clamped generative hyphae, subicular hyphae bearing fine crystals, and cylindrical, thin-walled, smooth basidiospores measuring 7–9.9 × 2.5–3.1 µm. Molecular phylogeny inferred from ITS and nLSU sequence data showed that samples of A. yunnanensis formed a distinctive lineage in Antrodia sensu lato, and it nested a sister group with A. tropica.

scholarly journals Phylogenetic Analysis of Polyketide Synthase I Domains from Soil Metagenomic Libraries Allows Selection of Promising Clones

2004 ◽  
Vol 70 (9) ◽  
pp. 5522-5527 ◽  
Author(s):  
Aurélien Ginolhac ◽  
Cyrille Jarrin ◽  
Benjamin Gillet ◽  
Patrick Robe ◽  
Petar Pujic ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Selection Process ◽  
Phylogenetic Analyses ◽  
Metagenomic Library ◽  
Protein Sequences ◽  
Direct Access ◽  
Type I ◽  
Ketosynthase Domain ◽  
New Compounds ◽  
Uncultivated Bacteria

ABSTRACT The metagenomic approach provides direct access to diverse unexplored genomes, especially from uncultivated bacteria in a given environment. This diversity can conceal many new biosynthetic pathways. Type I polyketide synthases (PKSI) are modular enzymes involved in the biosynthesis of many natural products of industrial interest. Among the PKSI domains, the ketosynthase domain (KS) was used to screen a large soil metagenomic library containing more than 100,000 clones to detect those containing PKS genes. Over 60,000 clones were screened, and 139 clones containing KS domains were detected. A 700-bp fragment of the KS domain was sequenced for 40 of 139 randomly chosen clones. None of the 40 protein sequences were identical to those found in public databases, and nucleic sequences were not redundant. Phylogenetic analyses were performed on the protein sequences of three metagenomic clones to select the clones which one can predict to produce new compounds. Two PKS-positive clones do not belong to any of the 23 published PKSI included in the analysis, encouraging further analyses on these two clones identified by the selection process.

Molecular phylogeny of the Annelida

2000 ◽  
Vol 78 (11) ◽  
pp. 1873-1884 ◽  
Author(s):  
Damhnait McHugh
Keyword(s):  
Molecular Analysis ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Nuclear Gene ◽  
Sister Group ◽  
The Body ◽  
Sister Group Relationship ◽  
Molecular Evidence ◽  
Gene Sequences ◽  
Sister Relationship

Traditionally, the Annelida has been classified as a group comprising the Polychaeta and the Clitellata. Recent phylogenetic analyses have led to profound changes in the view that the Annelida, as traditionally formulated, is a natural, monophyletic group. Both molecular and morphological analyses support placement of the Siboglinidae (formerly the Pogonophora) as a derived group within the Annelida; there is also evidence, based on molecular analysis of the nuclear gene elongation factor-1α, that the unsegmented echiurids are derived annelids. While monophyly of the Clitellata is well-supported by both molecular and morphological analyses, there is no molecular evidence to support monophyly of the polychaete annelids; the Clitellata fall within a paraphyletic polychaete grade. Relationships among groups of polychaete annelids have not yet been resolved by molecular analysis. Within the Clitellata, paraphyly of the Oligochaeta was indicated in a phylogenetic analysis of cytochrome c oxidase I, which supported a sister relationship between the leeches, including an acanthobdellid and a branchiobdellid, and two of the four oligochaetes in the analysis. There is some evidence from analysis of 18S rRNA sequences for a sister-group relationship between the clitellates and the taxon Aeolosoma. There is no agreement regarding the body form of the basal annelid, and while molecular analyses provide strong support for the Eutrochozoa, the identity of sister-group to the Annelida among the Eutrochozoa remains enigmatic. It is recommended that future investigations include additional conserved gene sequences and expanded taxon sampling. It is likely that the most productive approach to resolving annelid phylogeny, and thus increasing our understanding of annelid evolution, will come from combined analyses of several gene sequences.

scholarly journals Mitochondrial Genomes of the Genus Claassenia (Plecoptera: Perlidae) and Phylogenetic Assignment to Subfamily Perlinae

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1986
Author(s):  
Yanan Xiang ◽  
Mengyuan Zhao ◽  
Qingbo Huo ◽  
Yuzhou Du
Keyword(s):  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Molecular Evidence ◽  
Stem Loop ◽  
Protein Coding ◽  
Transitional Group ◽  
Noncoding Control Region ◽  
General Standard

Mitochondrial genomes of three stoneflies, e.g., Claassenia magna Wu, 1948, Claassenia sp. 2 and Claassenia xucheni Chen, 2019 were sequenced in this study with 15,774, 15,777 and 15,746 bp in length, respectively. Each mitogenome contained 37 genes including 22 tRNAs, two ribosomal RNAs, 13 protein-coding genes (PCGs), and a noncoding control region (CR). In general, standard ATN start and TAN termination codons were evident in the PCGs. Although the dihydrouridine arm was absent in trnSer, the remaining 21 tRNAs displayed the characteristic cloverleaf secondary structure. Stem-loop structures were identified in the CRs of all three mitogenomes, but tandem repeats were only apparent in Claassenia xucheni. The mitogenomes of three Claassenia species were analyzed and compared with mitogenomes in 21 other stoneflies from the Perlidae and three Euholognatha species (Rhopalopsole bulbifera, Capnia zijinshana and Amphinemura longispina) as outgroups. Phylogenetic analyses using maximum likelihood and Bayesian inference. Phylogenetic analysis supported that Claassenia was recovered as the sister group of other Perlinae and Claassenia+Perlinae emerged from the paraphyletic Acroneuriinae. The final results supported that Claassenia was classified into subfamily Perlinae and proposed Claassenia represent a transitional group of the subfamilies Acroneuriinae and Perlinae. This study provided new molecular evidence for exploring the debatable taxonomic position of the genus Claassenia in Perlidae.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

Actin type I introns offer potential for increasing phylogenetic resolution in Asterochloris (Chlorophyta: Trebouxiophyceae)

2006 ◽  
Vol 38 (5) ◽  
pp. 435-440 ◽  
Author(s):  
Matthew P. NELSEN ◽  
Andrea GARGAS
Keyword(s):  
Population Genetics ◽  
Phylogenetic Analyses ◽  
Species Concepts ◽  
Its Rdna ◽  
Type I ◽  
Phylogenetic Resolution

Primers are presented to amplify an intron-containing portion of the actin type I locus from Asterochloris algae. The amount of variation and phylogenetic resolution provided by the ITS rDNA are compared with that from the actin locus. The number of variable and parsimony-informative sites within the actin locus was drastically higher than that of the ITS. Phylogenetic analyses of the ITS resulted in poorly resolved trees with low support values. In contrast, phylogenetic analyses of the actin locus yielded trees with better support and resolution. It is concluded that the actin type I introns will be useful for studies investigating species concepts and population genetics.

Affinities of the Boletus chromapes group to Royoungia and the description of two new genera, Harrya and Australopilus

2012 ◽  
Vol 25 (6) ◽  
pp. 418 ◽  
Author(s):  
Roy E. Halling ◽  
Mitchell Nuhn ◽  
Todd Osmundson ◽  
Nigel Fechner ◽  
James M. Trappe ◽  
...  
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Sister Group ◽  
Molecular Data ◽  
Translation Elongation ◽  
Spore Deposit ◽  
Large Subunit Rdna ◽  
Translation Elongation Factor 1Α

Harrya is described as a new genus of Boletaceae to accommodate Boletus chromapes, a pink-capped bolete with a finely scabrous stipe adorned with pink scabers, a chrome yellow base and a reddish-brown spore deposit. Phylogenetic analyses of large-subunit rDNA and translation elongation factor 1α confirmed Harrya as a unique generic lineage with two species, one of which is newly described (H. atriceps). Some Chinese taxa were recently placed in a separate genus, Zangia, supported by both morphology and molecular data. Multiple accessions from Queensland, Australia, support the synonymy of at least three species in a separate Australian clade in the new genus, Australopilus. The truffle-like Royoungia is also supported as a separate lineage in this clade of boletes. Even though it lacks stipe characters, it possesses the deep, bright yellow to orange pigments in the peridium. Additional collections from Zambia and Thailand represent independent lineages of uncertain phylogenetic placement in the Chromapes complex, but sampling is insufficient for formal description of new species. Specimens from Java referable to Tylopilus pernanus appear to be a sister group of the Harrya lineage.

Aeolian influx and related environmental conditions on Gran Canaria during the early Pleistocene

2018 ◽  
Vol 91 (1) ◽  
pp. 35-50 ◽  
Author(s):  
Inmaculada Menéndez ◽  
José Mangas ◽  
Esperança Tauler ◽  
Vidal Barrón ◽  
José Torrent ◽  
...  
Keyword(s):  
Late Quaternary ◽  
Textural Analysis ◽  
Climatic Conditions ◽  
Saharan Dust ◽  
Early Pleistocene ◽  
Middle Pleistocene ◽  
Quartz Content ◽  
Gran Canaria ◽  
Climatic Oscillations ◽  
Climatic Variations

AbstractThe island of Gran Canaria is regularly affected by dust falls due to its proximity to the Saharan desert. Climatic oscillations may affect the Saharan dust input to the island. Geochemical, mineralogical, and textural analysis was performed on a well-developed and representative early Pleistocene paleosol to examine Saharan dust contribution to Gran Canaria. Significant and variable Saharan dust content was identified in addition to weathering products such as iron oxides and clay minerals. Variations in quartz and iron oxide concentrations in the paleosol likely reflect different Saharan dust input in more/less-contrasted rhexistasic/biostatic climatic conditions. Linking the quartz content in Canarian soils, the Ingenio paleosol, and two Canarian loess-like deposits to different ages from the Quaternary, we hypothesized that the dust input should be lower (about 33–38%) throughout the early to middle Pleistocene than during the late Quaternary. The Saharan dust input to the Gran Canaria profile in the Pleistocene persisted in spite of climatic variations.

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