Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids

Bacteria and Eukarya have cell membranes withsn-glycerol-3-phosphate (G3P), whereas archaeal membranes containsn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis. Together with the distribution of these protein-encoding genes among archaeal and bacterial groups, our phylogenetic analyses suggested that GlpA/GlpD in the Commonote (the last universal common ancestor of all extant life with a cellular form,Commonote commonote) acquired EgsA (G1PDH) from the archaeal common ancestor (Commonote archaea) and acquired GpsA and GlpK from a bacterial common ancestor (Commonote bacteria). In our scenario based on this study, the Commonote probably possessed a G3P-lipid membrane synthesized enzymatically, after which the archaeal lineage acquired G1PDH followed by the replacement of a G3P-lipid membrane with a G1P-lipid membrane.

Download Full-text

SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system

Nature Communications ◽

10.1038/s41467-021-23099-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Nika Pende ◽

Adrià Sogues ◽

Daniela Megrian ◽

Anna Sartori-Rupp ◽

Patrick England ◽

...

Keyword(s):

Cell Division ◽

Common Ancestor ◽

Phylogenetic Analyses ◽

Super Resolution ◽

Binding Mode ◽

Last Universal Common Ancestor ◽

Division Plane ◽

Multiple Factors ◽

Universal Common Ancestor ◽

Super Resolution Microscopy

AbstractMost archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.

Download Full-text

Lifeforms as criterion for species delimitation: Are Aristida adscensionis and A. coerulescens (Aristidoideae, Poaceae) two species?

Phytotaxa ◽

10.11646/phytotaxa.393.1.6 ◽

2019 ◽

Vol 393 (1) ◽

pp. 67 ◽

Cited By ~ 1

Author(s):

MIKE THIV ◽

J. ALFREDO REYES-BETANCORT ◽

ORI FRAGMAN-SAPIR

Keyword(s):

Morphometric Analysis ◽

Species Delimitation ◽

Phylogenetic Trees ◽

Morphological Analysis ◽

Phylogenetic Analyses ◽

Life Forms ◽

Clear Separation ◽

Taxonomic Treatment ◽

Molecular Phylogenetic ◽

The Mediterranean

The distinction of the perennial Aristida coerulescens from the annual A. adscensionis and its taxonomic treatment has been subject of long discussions. We here include accessions from the Mediterranean and Macaronesia for molecular phylogenetic analyses and conducted a morphometric analysis. A lineage of A. adscensionis, A. coerulescens and A. effusa is well supported in phylogenetic trees. Moreover, a group of Mediterranean, Macaronesia and Arabian A. coerulescens and A. adscensionis is revealed where both taxa are intermingled. A morphological analysis of traditionally used spikelet characters did not indicate a clear separation of both taxa. We therefore conclude that A. coerulescens should best be treated as synonym of A. adscensionis. The differential character of annual and perennial life forms seems to be plastic in this taxon indicating rapid shifts between these two strategies.

Download Full-text

Do genomic datasets resolve the correct relationship among the placental, marsupial and monotreme lineages?

Australian Journal of Zoology ◽

10.1071/zo09049 ◽

2009 ◽

Vol 57 (4) ◽

pp. 167 ◽

Cited By ~ 4

Author(s):

Gavin Huttley

Keyword(s):

Common Ancestor ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

Protein Coding ◽

Substitution Models ◽

True Tree ◽

Molecular Phylogenetic ◽

Tree Topologies ◽

Mammal Evolution ◽

Genome Projects

Did the mammal radiation arise through initial divergence of prototherians from a common ancestor of metatherians and eutherians, the Theria hypothesis, or of eutherians from a common ancestor of metatherians and prototherians, the Marsupionta hypothesis? Molecular phylogenetic analyses of point substitutions applied to this problem have been contradictory – mtDNA-encoded sequences supported Marsupionta, nuclear-encoded sequences and RY (purine–pyrimidine)-recoded mtDNA supported Theria. The consistency property of maximum likelihood guarantees convergence on the true tree only with longer alignments. Results from analyses of genome datasets should therefore be impervious to choice of outgroup. We assessed whether important hypotheses concerning mammal evolution, including Theria/Marsupionta and the branching order of rodents, carnivorans and primates, are resolved by phylogenetic analyses using ~2.3 megabases of protein-coding sequence from genome projects. In each case, only two tree topologies were being compared and thus inconsistency in resolved topologies can only derive from flawed models of sequence divergence. The results from all substitution models strongly supported Theria. For the eutherian lineages, all models were sensitive to the outgroup. We argue that phylogenetic inference from point substitutions will remain unreliable until substitution models that better match biological mechanisms of sequence divergence have been developed.

Download Full-text

Did viruses evolve as a distinct supergroup from common ancestors of cells?

10.1101/049171 ◽

2016 ◽

Cited By ~ 1

Author(s):

Ajith Harish ◽

Aare Abroi ◽

Julian Gough ◽

Charles Kurland

Keyword(s):

Common Ancestor ◽

Phylogenetic Analyses ◽

Marker Gene ◽

Host Cells ◽

Data Driven ◽

Evolutionary Origins ◽

Phylogenetic Methods ◽

Universal Common Ancestor ◽

Phylogenomic Analyses ◽

Genome Scale

AbstractThe evolutionary origins of viruses according to marker gene phylogenies, as well as their relationships to the ancestors of host cells remains unclear. In a recent article Nasir and Caetano-Anollés reported that their genome-scale phylogenetic analyses identify an ancient origin of the “viral supergroup” (Nasir et al (2015) A phylogenomic data-driven exploration of viral origins and evolution. Science Advances, 1(8):e1500527). It suggests that viruses and host cells evolved independently from a universal common ancestor. Examination of their data and phylogenetic methods indicates that systematic errors likely affected the results. Reanalysis of the data with additional tests shows that small-genome attraction artifacts distort their phylogenomic analyses. These new results indicate that their suggestion of a distinct ancestry of the viral supergroup is not well supported by the evidence.

Download Full-text

High species diversity of the soft coral family Xeniidae (Octocorallia, Alcyonacea) in the temperate region of Japan revealed by morphological and molecular analyses

ZooKeys ◽

10.3897/zookeys.862.31979 ◽

2019 ◽

Vol 862 ◽

pp. 1-22 ◽

Cited By ~ 1

Author(s):

Tatsuki Koido ◽

Yukimitsu Imahara ◽

Hironobu Fukami

Keyword(s):

Species Diversity ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Soft Coral ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Temperate Region ◽

High Species Diversity ◽

Molecular Phylogenetic ◽

Traditional Taxonomy

The soft coral family Xeniidae, commonly found in tropical and subtropical regions, consists of 20 genera and 162 species. To date, few studies on this family have been conducted in Japan, especially at higher latitudes. Although molecular phylogenetic analyses have recently been used to distinguish soft coral species, it is difficult to identify species and genera in this family due to the limited taxonomic indices and high morphological variation. In this study, we found a large Xeniidae community off the coast of Oshima Island (31°31.35'N, 131°24.27'E) at Miyazaki, Kyushu Island, located in the temperate region of Japan. The species composition and molecular phylogenetic relationships were investigated to uncover the species diversity of Xeniidae in this community. A total of 182 xeniid specimens were collected and identified to the species level, after which the samples were molecularly analyzed using a mitochondrial marker (ND2) and a nuclear marker (ITS) to infer the phylogenetic relationships. A total of 14 xeniid species were identified, including five undescribed species from five genera (Anthelia, Heteroxenia, Sympodium, Xenia, and Yamazatum). Miyazaki was identified as having the highest xeniid species diversity in Japan. The molecular phylogenetic trees inferred from each marker recovered very similar topologies: four genera (Anthelia, Heteroxenia, Sympodium, and Yamazatum) were monophyletic, whereas one (Xenia) was polyphyletic. Thus, except for Xenia, the morphological characteristics used for traditional taxonomy well reflected the phylogeny of the Xeniidae at the genus level. On the other hand, our results show that further taxonomic revisions of Xenia are needed.

Download Full-text

A new species of whip spider, Weygoldtia hainanensis sp. nov., from Hainan, China (Arachnida: Amblypygi: Charinidae)

Zootaxa ◽

10.11646/zootaxa.5082.1.6 ◽

2021 ◽

Vol 5082 (1) ◽

pp. 65-76

Author(s):

XIAO-YU ZHU ◽

SHI-YANG WU ◽

YI-JIAO LIU ◽

CHRIS R. REARDON ◽

CRISTIAN ROMÁN-PALACIOS ◽

...

Keyword(s):

New Species ◽

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Coi Gene ◽

Gene Region ◽

East China ◽

Type Specimens ◽

Molecular Phylogenetic ◽

Normal University ◽

A New Species

To date, only one species of whip spider has been recorded in China. Here, we describe a new species, Weygoldtia hainanensis sp. nov., from Hainan, China. The new species is morphologically similar to W. davidovi (Fage, 1946) and W. consonensis Miranda et al. 2021, but can be distinguished with a combination of the following characters: 26 segments in tibia I, 6-7 teeth on chelicerae, distitibia IV trichobothria sc and sf series each with 10-11 trichobothria. To validate our morphological inferences and support the erection of W. hainanensis sp. nov. as a new species, we sequenced the COI gene region for two individuals and performed molecular phylogenetic analyses. The inferred phylogenetic trees placed the new species within Weygoldtia and highlighted the evolutionary distinction between W. hainanensis sp. nov. and currently described whip spiders. The type specimens are deposited in the Museum of Biology, East China Normal University (ECNU).

Download Full-text

The molecular evolution of Dabie bandavirus (Phenuiviridae: Bandavirus: Dabie bandavirus), the agent of severe fever with thrombocytopenia syndrome

Voprosy Virusologii ◽

10.36233/0507-4088-68 ◽

2022 ◽

Vol 66 (6) ◽

pp. 409-416

Author(s):

T. E. Sizikova ◽

V. N. Lebedev ◽

S. V. Borisevich

Keyword(s):

Molecular Evolution ◽

Phylogenetic Trees ◽

Common Ancestor ◽

Phylogenetic Analyses ◽

Virus Transmission ◽

Infectious Agent ◽

Global Public Health ◽

The Common ◽

Epidemiological Characteristics ◽

Severe Fever

Since the Dabie bandavirus (DBV; former SFTS virus, SFTSV) was identified, the epidemics of severe fever with thrombocytopenic syndrome (SFTS) caused by this virus have occurred in several countries in East Asia. The rapid increase in incidence indicates that this infectious agent has a pandemic potential and poses an imminent global public health threat.The analysis of molecular evolution of SFTS agent that includes its variants isolated in China, Japan and South Korea was performed in this review. The evolution rate of DBV and the estimated dates of existence of the common ancestor were ascertained, and the possibility of reassortation was demonstrated.The evolutionary rates of DBV genome segments were estimated to be 2.28 × 10-4 nucleotides/site/year for S-segment, 2.42 × 10-4 for M-segment, and 1.19 × 10-4 for L-segment. The positions of positive selection were detected in the viral genome.Phylogenetic analyses showed that virus may be divided into two clades, containing six different genotypes. The structures of phylogenetic trees for S-, M- and L-segments showed that all genotypes originate from the common ancestor.Data of sequence analysis suggest that DBV use several mechanisms to maintain the high level of its genetic diversity. Understanding the phylogenetic factors that determine the virus transmission is important for assessing the epidemiological characteristics of the disease and predicting its possible outbreaks.

Download Full-text

Molecular phylogeny of the family Vorticellidae (Ciliophora, Peritrichia) using combined datasets with a special emphasis on the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.020255-0 ◽

2011 ◽

Vol 61 (4) ◽

pp. 1001-1010 ◽

Cited By ~ 13

Author(s):

Ping Sun ◽

John C. Clamp ◽

Dapeng Xu ◽

Yasushi Kusuoka ◽

Manabu Hori

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Small Subunit ◽

Rrna Gene ◽

Evolutionary Divergence ◽

Ssu Rrna ◽

Generic Level ◽

Ssu Rrna Gene ◽

The Family ◽

Molecular Phylogenetic

Little is known about the phylogeny of the family Vorticellidae at the generic level because few comprehensive analyses of molecular phylogenetic relationships between members of this group have, so far, been done. As a result, the phylogenetic positions of some genera that were based originally on morphological analyses remain controversial. In the present study, we performed phylogenetic analyses of vorticellids based on the sequence of the small-subunit (SSU) rRNA gene, including one species of the genus Apocarchesium, for which no sequence has previously been reported. Phylogenetic trees were reconstructed with SSU rRNA gene sequences by using four different methods (Bayesian analysis, maximum-likelihood, neighbour-joining and maximum-parsimony) and had a consistent branching pattern. Members of the genera Vorticella (except V. microstoma) and Carchesium formed a clearly defined, well supported clade that was divergent from the clade comprising members of the genera Pseudovorticella and Epicarchesium, suggesting that the differences in the silverline system (transverse vs reticulate) among vorticellids may be the result of genuine evolutionary divergence. Members of the newly established genus Apocarchesium clustered within the family Vorticellidae basal to the clade containing members of the genera Pseudovorticella and Epicarchesium and were distinct from members of the genus Carchesium, supporting the validity of Apocarchesium as a novel genus. Additional phylogenetic analyses of 21 strains representing seven genera from the families Vorticellidae and Zoothamniidae were performed with single datasets (ITS1–5.8S–ITS2, ITS2 alone) and combined datasets (SSU rRNA+ITS1–5.8S–ITS2, SSU rRNA+ITS2) to explore further the phylogenetic relationship between the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium, using characteristics not included in previous analyses. The phylogenetic trees reconstructed with combined datasets were more robust and therefore more reliable than those based on single datasets and supported the results of trees based on SSU rRNA sequences.

Download Full-text

Molecular phylogenetic study of the tribe Tropidieae (Orchidaceae, Epidendroideae) with taxonomic and evolutionary implications

PhytoKeys ◽

10.3897/phytokeys.140.46842 ◽

2020 ◽

Vol 140 ◽

pp. 11-22

Author(s):

Izai A. B. Sabino Kikuchi ◽

Paul J. A. Keβler ◽

André Schuiteman ◽

Jin Murata ◽

Tetsuo Ohi-Toma ◽

...

Keyword(s):

Ribosomal Dna ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Nuclear Ribosomal Dna ◽

Phylogenetic Study ◽

Molecular Phylogenetic Study ◽

Molecular Phylogenetic ◽

High Support ◽

Photosynthetic Ability

The orchid tribe Tropidieae comprises three genera, Tropidia, Corymborkis and Kalimantanorchis. There are three fully mycoheterotrophic species within Tropidieae: Tropidia saprophytica, T. connata and Kalimantanorchis nagamasui. A previous phylogenetic study of K. nagamasui, based only on plastid matK data, placed K. nagamasui outside the clade of Tropidia and Corymborkis without support. In this study, we performed phylogenetic analyses using a nuclear ribosomal DNA spacer (ITS1-5.8S-ITS2), a low-copy nuclear coding gene (Xdh) and a mitochondrial intron (nad1b-c intron) to study the phylogenetic relationships within Tropidieae. We included six photosynthetic and all three fully mycoheterotrophic Tropidieae species. The resulting phylogenetic trees placed these fully mycoheterotrophic species inside the Tropidia clade with high support. In our trees, these three species do not form a monophyletic group together, because the photosynthetic T. graminea is nested amongst them. Our results also suggest that the loss of photosynthetic ability occurred at least twice in Tropidia.

Download Full-text

A New Analysis of Archaea–Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution

Molecular Biology and Evolution ◽

10.1093/molbev/msaa089 ◽

2020 ◽

Vol 37 (8) ◽

pp. 2332-2340 ◽

Cited By ~ 6

Author(s):

Sarah J Berkemer ◽

Shawn E McGlynn

Keyword(s):

Phylogenetic Trees ◽

Molecular Phylogenetics ◽

Common Ancestor ◽

Rapid Evolution ◽

Biological Evolution ◽

Protein Family ◽

Phylogenetic Distance ◽

Protein Families ◽

Last Universal Common Ancestor ◽

Universal Common Ancestor

Abstract Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al. (Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. 2016. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 1(9):16116.) identified a number of protein families in the last universal common ancestor of archaea and bacteria (LUCA) which were not found in previous works. Here, we report new research that suggests the clustering approaches used in this previous study undersampled protein families, resulting in incomplete phylogenetic trees which do not reflect protein family evolution. Phylogenetic analysis of protein families which include more sequence homologs rejects a simple LUCA hypothesis based on phylogenetic separation of the bacterial and archaeal domains for a majority of the previously identified LUCA proteins (∼82%). To supplement limitations of phylogenetic inference derived from incompletely populated orthologous groups and to test the hypothesis of a period of rapid evolution preceding the separation of the domains, we compared phylogenetic distances both within and between domains, for thousands of orthologous groups. We find a substantial diversity of interdomain versus intradomain branch lengths, even among protein families which exhibit a single domain separating branch and are thought to be associated with the LUCA. Additionally, phylogenetic trees with long interdomain branches relative to intradomain branches are enriched in information categories of protein families in comparison to those associated with metabolic functions. These results provide a new view of protein family evolution and temper claims about the phenotype and habitat of the LUCA.

Download Full-text