scholarly journals New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life

2018 ◽  
Author(s):  
Jürgen F. H. Strassert ◽  
Mahwash Jamy ◽  
Alexander P. Mylnikov ◽  
Denis V. Tikhonenkov ◽  
Fabien Burki
Keyword(s):  
Phylogenetic Signal ◽  
Evolutionary Origin ◽  
Phylogenetic Position ◽  
Aquatic Environments ◽  
Phylogenomic Analysis ◽  
Heterogeneous Mixture ◽  
Phylogenetic Reconstructions ◽  
Phylogenomic Analyses ◽  
Alignment Length ◽  
Broad Scale

AbstractThe broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome datasets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker ‘TSAR’ to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

scholarly journals New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

2019 ◽  
Vol 36 (4) ◽  
pp. 757-765 ◽  
Author(s):  
Jürgen F H Strassert ◽  
Mahwash Jamy ◽  
Alexander P Mylnikov ◽  
Denis V Tikhonenkov ◽  
Fabien Burki
Keyword(s):  
Phylogenetic Signal ◽  
Evolutionary Origin ◽  
Phylogenetic Position ◽  
Aquatic Environments ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Transcriptome Data ◽  
Phylogenetic Reconstructions ◽  
Phylogenomic Analyses ◽  
Alignment Length

AbstractThe resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these “orphan” groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker “TSAR” to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

scholarly journals A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4299 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Sean V. Burke ◽  
William P. Wysocki ◽  
Matthew D. Barrett ◽  
Lynn G. Clark ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Purifying Selection ◽  
Bootstrap Support ◽  
Phylogenomic Analysis ◽  
Branch Points ◽  
Protein Coding ◽  
Selective Forces ◽  
Phylogenomic Analyses

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.

scholarly journals Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Alejandra Serna-Sánchez ◽  
Oscar A. Pérez-Escobar ◽  
Diego Bogarín ◽  
María Fernanda Torres-Jimenez ◽  
Astrid Catalina Alvarez-Yela ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Phylogenetic Placement ◽  
Plastid Genomes ◽  
Phylogenetic Reconstructions ◽  
A Genome ◽  
Tree Models ◽  
Phylogenomic Analyses ◽  
First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

scholarly journals Agromyces humi sp. nov., actinobacterium isolated from farm soil

2020 ◽  
Vol 70 (9) ◽  
pp. 5032-5039 ◽  
Author(s):  
Jae-Chan Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Type Species ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Phyletic Line ◽  
Phylogenomic Analyses ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated ANK073T, was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073T were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20–40 °C (optimum, 30 °C), at pH 6.0–10.0 (optimum, pH 6.5–7.5) and at salinities of 0–4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073T belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5T (98.8 %), Agromyces tardus SJ-23T (98.5 %) and Agromyces iriomotensis IY07-20T (98.4 %). The phylogenetic analysis indicated that strain ANK073T formed a distinct phyletic line in the genus Agromyces and the results of DNA–DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073T could be separated from its closest relatives in the genus Agromyces . The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 :  0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073T is considered to represent a novel species in the genus Agromyces , for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073T (=KACC 18683T=NBRC 111825T).

scholarly journals Importance of the postcranial skeleton in eusuchian phylogeny: Reassessing the systematics of allodaposuchid crocodylians

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251900
Author(s):  
Alejandro Blanco
Keyword(s):  
Current Knowledge ◽  
Phylogenetic Signal ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Postcranial Skeleton ◽  
Skull Morphology ◽  
Taxonomic Descriptions ◽  
The Family ◽  
Phylogenetic Hypotheses ◽  
Internal Relationships

Our current knowledge on the crocodyliform evolution is strongly biased towards the skull morphology, and the postcranial skeleton is usually neglected in many taxonomic descriptions. However, it is logical to expect that it can contribute with its own phylogenetic signal. In this paper, the changes in the tree topology caused by the addition of the postcranial information are analysed for the family Allodaposuchidae, the most representative eusuchians in the latest Cretaceous of Europe. At present, different phylogenetic hypotheses have been proposed for this group without reaching a consensus. The results of this paper evidence a shift in the phylogenetic position when the postcranium is included in the dataset, pointing to a relevant phylogenetic signal in the postcranial elements. Finally, the phylogenetic relationships of allodaposuchids within Eusuchia are reassessed; and the internal relationships within Allodaposuchidae are also reconsidered after an exhaustive revision of the morphological data. New and improved diagnoses for each species are here provided.

scholarly journals Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field

2020 ◽  
Vol 70 (3) ◽  
pp. 1785-1792 ◽  
Author(s):  
Jae-Chan Lee ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Diamino Acid ◽  
Phylogenomic Analyses ◽  
Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5–1.9 µm, and was able to grow at 10–37 °C (optimum, 28–30 °C), at pH 4.5–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2–92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2–83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn–Gly2–d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family Intrasporangiaceae , for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).

scholarly journals Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7484 ◽  
Author(s):  
Amanda E. Haponski ◽  
Diarmaid Ó Foighil
Keyword(s):  
New World ◽  
Genomic Structure ◽  
Initial Study ◽  
Illinois River ◽  
Phylogenomic Analysis ◽  
Tropical Regions ◽  
Population Genomic ◽  
Sequencing Method ◽  
Freshwater Clams ◽  
Phylogenomic Analyses

The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699–30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401–2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineages in our study populations. In contrast, 2/6 C. sandai individuals displayed partial nuclear genomic Structure assignments with multiple invasive clonal lineages. These results provide new insights into the origin and maintenance of clonality in this complex system.

scholarly journals Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica

2020 ◽  
Author(s):  
Yves Bawin ◽  
Tom Ruttink ◽  
Ariane Staelens ◽  
Annelies Haegeman ◽  
Piet Stoffelen ◽  
...  
Keyword(s):  
Coffea Arabica ◽  
Evolutionary Origin ◽  
Phylogenomic Analysis

scholarly journals Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): Combining sequence data and Exploring compositional bias solutions in Next Generation Datasets

2020 ◽  
Author(s):  
Robert S de Moya ◽  
Kazunori Yoshizawa ◽  
Kimberly K O Walden ◽  
Andrew D Sweet ◽  
Christopher H Dietrich ◽  
...  
Keyword(s):  
Sequence Data ◽  
Compositional Bias ◽  
Phylogenomic Analysis ◽  
Data Set ◽  
Genomic Changes ◽  
Insect Order ◽  
Codon Positions ◽  
Phylogenomic Analyses ◽  
Ordinal Level ◽  
Likelihood Mapping

Abstract The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.

scholarly journals Phylogenomic analysis of echinoderm class relationships supports Asterozoa

2014 ◽  
Vol 281 (1786) ◽  
pp. 20140479 ◽  
Author(s):  
Maximilian J. Telford ◽  
Christopher J. Lowe ◽  
Christopher B. Cameron ◽  
Olga Ortega-Martinez ◽  
Jochanan Aronowicz ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Sea Urchins ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Phylogenomic Analysis ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
Complete Dataset ◽  
Type Larva ◽  
Molecular Phylogenetic

While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used ‘phylogenetic signal dissection’ to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.

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