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

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.

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The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0034 ◽

2009 ◽

Vol 364 (1527) ◽

pp. 2197-2207 ◽

Cited By ~ 82

Author(s):

Peter G. Foster ◽

Cymon J. Cox ◽

T. Martin Embley

Keyword(s):

Sequence Data ◽

Phylogenetic Signal ◽

Amino Acid Sequences ◽

Rate Variation ◽

Molecular Sequence Data ◽

Protein Coding ◽

Molecular Sequence ◽

Heterogeneous Models ◽

Matrix Heterogeneity ◽

Rna Genes

The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the ‘eocyte hypothesis’, where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.

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The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes

Plants ◽

10.3390/plants9040456 ◽

2020 ◽

Vol 9 (4) ◽

pp. 456 ◽

Cited By ~ 1

Author(s):

Cornelius M. Kyalo ◽

Zhi-Zhong Li ◽

Elijah M. Mkala ◽

Itambo Malombe ◽

Guang-Wan Hu ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Structural Features ◽

Base Pairs ◽

Protein Coding ◽

Variable Regions ◽

Morphological Heterogeneity ◽

Chloroplast Genomes ◽

Chloroplast Genome Sequence ◽

Phylogenomic Analyses

Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of Str. ionanthus, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (psbM, rps3, atpF-atpH, psbC-psbZ and psaA-ycf3) and five genes with a high number of polymorphic sites (rps16, rpoC2, rpoB, ycf1 and ndhA) which could be investigated further for phylogenetic utility in Str. ionanthus. Phylogenomic analyses here exhibit low polymorphism within Str. ionanthus and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of Str. ionanthus phylogenetic relationships.

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

Systematic Biology ◽

10.1093/sysbio/syaa075 ◽

2020 ◽

Cited By ~ 1

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.

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

Molecular Biology and Evolution ◽

10.1093/molbev/msz012 ◽

2019 ◽

Vol 36 (4) ◽

pp. 757-765 ◽

Cited By ~ 32

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.

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Phylogenomic analysis of the Chilean clade ofLiolaemuslizards (Squamata: Liolaemidae) based on sequence capture data

PeerJ ◽

10.7717/peerj.3941 ◽

2017 ◽

Vol 5 ◽

pp. e3941 ◽

Cited By ~ 7

Author(s):

Alejandra Panzera ◽

Adam D. Leaché ◽

Guillermo D’Elía ◽

Pedro F. Victoriano

Keyword(s):

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Strong Support ◽

Taxon Sampling ◽

Phylogenomic Analysis ◽

Molecular Systematic ◽

Data Set ◽

Protein Coding ◽

Protein Coding Genes ◽

Phylogenomic Analyses

The genusLiolaemusis one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless,Liolaemuslizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenusLiolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic.Liolaemus tenuis tenuisis difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion ofL. t. tenuisfrom analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships betweenL. fuscus,L. monticola,L. nigroviridisandL. nitidus, andL. plateiandL. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade ofLiolaemusthat will help future work aimed at resolving theLiolaemusphylogeny.

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Hybrid origin of Populus tomentosa Carr. identified through genome sequencing and phylogenomic analysis

10.1101/2020.04.07.030692 ◽

2020 ◽

Author(s):

Xinmin An ◽

Kai Gao ◽

Zhong Chen ◽

Juan Li ◽

Xiong Yang ◽

...

Keyword(s):

Populus Tomentosa ◽

Central China ◽

Hybrid Origin ◽

Phylogenomic Analysis ◽

Structural Variations ◽

Protein Coding ◽

Populus Tomentosa Carr ◽

Dynamic Genome ◽

Ecological Importance ◽

Phylogenomic Analyses

AbstractPopulus tomentosa is widely distributed and cultivated in the Northern and Central China, where it is of great economic and ecological importance. However, the origin of P. tomentosa remains controversial. Here, we used a PacBio+Hi-C+Illumina strategy to sequence and assemble its 740.2 Mb (2n) genome. The assembly accounts for greater than 92.1% of the 800-megabase genome, comprises 38 chromosomes, and contains 59,124 annotated protein-coding genes. Phylogenomic analyses elucidated dynamic genome evolution events among its closely related white poplars, and revealed that tomentosa is comprised of two subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female, and Populus alba var. pyramidalis as the male, around 3.93 Mya. We also detected structural variations and allele-indels across genome. Our study presents a high quality and well assembled genome, unveils the origin of the widely distributed and planted P. tomentosa, and provides a powerful resource for comparative plant biology, breeding, and biotechnology.

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

10.1101/403329 ◽

2018 ◽

Cited By ~ 1

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.

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Mitochondrial Evidence on the Phylogenetic Position of Caecilians (Amphibia: Gymnophiona)

Genetics ◽

10.1093/genetics/155.2.765 ◽

2000 ◽

Vol 155 (2) ◽

pp. 765-775

Author(s):

Rafael Zardoya ◽

Axel Meyer

Keyword(s):

Tandem Repeats ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Maximum Parsimony Analysis ◽

Bootstrap Support ◽

Phylogenetic Position ◽

Trna Genes ◽

Data Sets ◽

Data Set ◽

Protein Coding

Abstract The complete nucleotide sequence (17,005 bp) of the mitochondrial genome of the caecilian Typhlonectes natans (Gymnophiona, Amphibia) was determined. This molecule is characterized by two distinctive genomic features: there are seven large 109-bp tandem repeats in the control region, and the sequence for the putative origin of replication of the L strand can potentially fold into two alternative secondary structures (one including part of the tRNACys). The new sequence data were used to assess the phylogenetic position of caecilians and to gain insights into the origin of living amphibians (frogs, salamanders, and caecilians). Phylogenetic analyses of two data sets—one combining protein-coding genes and the other combining tRNA genes—strongly supported a caecilian + frog clade and, hence, monophyly of modern amphibians. These two data sets could not further resolve relationships among the coelacanth, lungfishes, and tetrapods, but strongly supported diapsid affinities of turtles. Phylogenetic relationships among a larger set of species of frogs, salamanders, and caecilians were estimated with a mitochondrial rRNA data set. Maximum parsimony analysis of this latter data set also recovered monophyly of living amphibians and favored a frog + salamander (Batrachia) relationship. However, bootstrap support was only moderate at these nodes. This is likely due to an extensive among-site rate heterogeneity in the rRNA data set and the narrow window of time in which the three main groups of living amphibians were originated.

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Severe Plastid Genome Size Reduction in a Mycoheterotrophic Orchid, Danxiaorchis singchiana, Reveals Heavy Gene Loss and Gene Relocations

Plants ◽

10.3390/plants9040521 ◽

2020 ◽

Vol 9 (4) ◽

pp. 521

Author(s):

Shiou Yih Lee ◽

Kaikai Meng ◽

Haowei Wang ◽

Renchao Zhou ◽

Wenbo Liao ◽

...

Keyword(s):

Purifying Selection ◽

Housekeeping Genes ◽

Single Copy ◽

Intact Protein ◽

Bootstrap Support ◽

Protein Coding ◽

Gene Block ◽

Protein Coding Genes ◽

Strong Bootstrap Support ◽

Cremastra Appendiculata

Danxiaorchis singchiana (Orchidaceae) is a leafless mycoheterotrophic orchid in the subfamily Epidendroideae. We sequenced the complete plastome of D. singchiana. The plastome has a reduced size of 87,931 bp, which includes a pair of inverted repeat (IR) regions of 13,762 bp each that are separated by a large single copy (LSC) region of 42,575 bp and a small single copy (SSC) region of 17,831 bp. When compared to its sister taxa, Cremastra appendiculata and Corallorhiza striata var. involuta, D. singchiana showed an inverted gene block in the LSC and SSC regions. A total of 61 genes were predicted, including 21 tRNA, 4 rRNA, and 36 protein-coding genes. While most of the housekeeping genes were still intact and seem to be protein-coding, only four photosynthesis-related genes appeared presumably intact. The majority of the presumably intact protein-coding genes seem to have undergone purifying selection (dN/dS < 1), and only the psaC gene was positively selected (dN/dS > 1) when compared to that in Cr. appendiculata. Phylogenetic analysis of 26 complete plastome sequences from 24 species of the tribe Epidendreae had revealed that D. singchiana diverged after Cr. appendiculata and is sister to the genus Corallorhiza with strong bootstrap support (100%).

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Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

Systematic Biology ◽

10.1093/sysbio/syz044 ◽

2019 ◽

Vol 69 (3) ◽

pp. 431-444 ◽

Cited By ~ 5

Author(s):

Emily J Roycroft ◽

Adnan Moussalli ◽

Kevin C Rowe

Keyword(s):

Sequence Data ◽

Incomplete Lineage Sorting ◽

Phylogenetic Signal ◽

Strong Support ◽

Bootstrap Support ◽

Data Sets ◽

Lineage Sorting ◽

Nucleotide Sequence Data ◽

Branch Support ◽

Partitioning Strategy

Abstract The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support ($>$ 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.

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