Order, Please! Uncertainty in the Ordinal-Level Classification of Chlorophyceae

Background. Chlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several incertae sedis taxa. Methods. We sequenced 18 chloroplast genomes across Chlorophyceae to compile a data set of 58 protein-coding genes of a total of 68 chlorophycean taxa. We analyzed the concatenated nucleotide and amino acid datasets in the Bayesian and Maximum Likelihood frameworks, supplemented by analyses to examine potential discordant signal among genes. We also examined gene presence and absence data across Chlorophyceae. Results. Concatenated analyses yielded at least two well-supported phylogenies: nucleotide data supported the traditional classification with the inclusion of the enigmatic Treubarinia into Sphaeropleales sensu lato. However, amino acid data yielded equally strong support for Sphaeropleaceae as sister to Volvocales, with the rest of the taxa traditionally classified in Sphaeropleales in a separate clade, and Treubarinia as sister to all of the above. Single-gene and other supplementary analyses indicated that the data have low phylogenetic signal at these critical nodes. Major clades were supported by genomic structural features such as gene losses and trans-spliced intron insertions in the plastome. Discussion. While the sequence and gene order data support the deep split between the SV and OCC lineages, multiple phylogenetic hypotheses are possible for Sphaeropleales s.l. Given this uncertainty as well as the higher-taxonomic disorder seen in other algal groups, dwelling on well-defined, strongly supported Linnaean orders is not currently practical in Chlorophyceae and a less formal clade system may be more useful in the foreseeable future. For example, we identify two strongly and unequivocally supported clades: Treubarinia and Scenedesminia, as well as other smaller groups that could serve a practical purpose as named clades. This system does not preclude future establishment of new orders, or emendment of the current ordinal classification if new data support such conclusions

Order, Please! Uncertainty in the Ordinal-Level Classification of Chlorophyceae

Background. Chlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several incertae sedis taxa. Methods. We sequenced 18 chloroplast genomes across Chlorophyceae to compile a data set of 58 protein-coding genes of a total of 68 chlorophycean taxa. We analyzed the concatenated nucleotide and amino acid datasets in the Bayesian and Maximum Likelihood frameworks, supplemented by analyses to examine potential discordant signal among genes. We also examined gene presence and absence data across Chlorophyceae. Results. Concatenated analyses yielded at least two well-supported phylogenies: nucleotide data supported the traditional classification with the inclusion of the enigmatic Treubarinia into Sphaeropleales sensu lato. However, amino acid data yielded equally strong support for Sphaeropleaceae as sister to Volvocales, with the rest of the taxa traditionally classified in Sphaeropleales in a separate clade, and Treubarinia as sister to all of the above. Single-gene and other supplementary analyses indicated that the data have low phylogenetic signal at these critical nodes. Major clades were supported by genomic structural features such as gene losses and trans-spliced intron insertions in the plastome. Discussion. While the sequence and gene order data support the deep split between the SV and OCC lineages, multiple phylogenetic hypotheses are possible for Sphaeropleales s.l. Given this uncertainty as well as the higher-taxonomic disorder seen in other algal groups, dwelling on well-defined, strongly supported Linnaean orders is not currently practical in Chlorophyceae and a less formal clade system may be more useful in the foreseeable future. For example, we identify two strongly and unequivocally supported clades: Treubarinia and Scenedesminia, as well as other smaller groups that could serve a practical purpose as named clades. This system does not preclude future establishment of new orders, or emendment of the current ordinal classification if new data support such conclusions

Assessing Combinability of Phylogenomic Data Using Bayes Factors

With the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes to infer phylogeny of any study system. While sampling a large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the incorporation of accurate marginal likelihood estimation methods into popular Bayesian software programs, it is natural to consider using the Bayes Factor (BF) to compare different partition models in which genes within any given partition subset share both tree topology and edge lengths. We explore using marginal likelihood to assess data subset combinability when data subsets have varying levels of phylogenetic discordance due to deep coalescence events among genes (simulated within a species tree), and compare the results with our recently described phylogenetic informational dissonance index (D) estimated for each data set. BF effectively detects phylogenetic incongruence and provides a way to assess the statistical significance of D values. We use BFs to assess data combinability using an empirical data set comprising 56 plastid genes from the green algal order Volvocales. We also discuss the potential need for calibrating BFs and demonstrate that BFs used in this study are correctly calibrated

A new record of the rare alga Pachycladella P. C. Silva (Chlorophyceae) in New England

Volume: 56Start Page: 19End Page: 2

Monograph of the Genus Bracteacoccus (Sphaeropleales, Chlorophyceae), with Systematic Clarification of Taxonomically Related Genera

Green algae are ubiquitous, abundant, and ecologically important worldwide, and therefore an accurate understanding of their biodiversity and evolutionary relationships is of great interest to biologists. This systematic study focused on a group of morphologically simple unicellular algae from the order Sphaeropleales (Chlorophyceae, Chlorophyta), specifically four genetically divergent genera that share a similar vegetative morphology: Bracteacoccus, Chromochloris, Dictyococcus, and Pseudomuriella . This study employed phylogenetic analyses of nuclear ribosomal loci (18S, 5.8S and ITS2) as well as two plastid protein-coding genes ( rbcL and tufA) and one mitochondrial protein-coding gene (cox1) to distinguish among the morphologically similar genera and species within them using the phylogenetic species concept. Contrary to the expectation formulated historically in the literature, the genus Dictyococcus was found to be distantly related to Bracteacoccus and this finding was supported by light microscope observations that revealed that Dictyococcus can be identified by its chloroplast morphology. On the other hand, Pseudomuriella and the hereby resurrected genus Chromochloris were found to be close relatives of Bracteacoccus and morphologically indistinguishable from it and one another using standard microscopic means, providing an example of cryptic genera. Species-level diversity within Bracteacoccus and Pseudomuriella was assessed, and by adding a number of newly isolated strains the current knowledge about the diversity and geographic distribution of these genera was greatly increased. Furthermore, the utility of four putative barcode markers was investigated for recognizing the newly revealed diversity within the previously monotypic genus Pseudomuriella. Based on the phylogenetic findings, new species were also described within Bracteacoccus and an exhaustive revision of the genus is presented in form of a monograph.

Monograph of the Genus Bracteacoccus (Sphaeropleales, Chlorophyceae), with Systematic Clarification of Taxonomically Related Genera

Green algae are ubiquitous, abundant, and ecologically important worldwide, and therefore an accurate understanding of their biodiversity and evolutionary relationships is of great interest to biologists. This systematic study focused on a group of morphologically simple unicellular algae from the order Sphaeropleales (Chlorophyceae, Chlorophyta), specifically four genetically divergent genera that share a similar vegetative morphology: Bracteacoccus, Chromochloris, Dictyococcus, and Pseudomuriella . This study employed phylogenetic analyses of nuclear ribosomal loci (18S, 5.8S and ITS2) as well as two plastid protein-coding genes ( rbcL and tufA) and one mitochondrial protein-coding gene (cox1) to distinguish among the morphologically similar genera and species within them using the phylogenetic species concept. Contrary to the expectation formulated historically in the literature, the genus Dictyococcus was found to be distantly related to Bracteacoccus and this finding was supported by light microscope observations that revealed that Dictyococcus can be identified by its chloroplast morphology. On the other hand, Pseudomuriella and the hereby resurrected genus Chromochloris were found to be close relatives of Bracteacoccus and morphologically indistinguishable from it and one another using standard microscopic means, providing an example of cryptic genera. Species-level diversity within Bracteacoccus and Pseudomuriella was assessed, and by adding a number of newly isolated strains the current knowledge about the diversity and geographic distribution of these genera was greatly increased. Furthermore, the utility of four putative barcode markers was investigated for recognizing the newly revealed diversity within the previously monotypic genus Pseudomuriella. Based on the phylogenetic findings, new species were also described within Bracteacoccus and an exhaustive revision of the genus is presented in form of a monograph

Monograph of the Genus Bracteacoccus (Sphaeropleales, Chlorophyceae), with Systematic Clarification of Taxonomically Related Genera

Green algae are ubiquitous, abundant, and ecologically important worldwide, and therefore an accurate understanding of their biodiversity and evolutionary relationships is of great interest to biologists. This systematic study focused on a group of morphologically simple unicellular algae from the order Sphaeropleales (Chlorophyceae, Chlorophyta), specifically four genetically divergent genera that share a similar vegetative morphology: Bracteacoccus, Chromochloris, Dictyococcus, and Pseudomuriella . This study employed phylogenetic analyses of nuclear ribosomal loci (18S, 5.8S and ITS2) as well as two plastid protein-coding genes ( rbcL and tufA) and one mitochondrial protein-coding gene (cox1) to distinguish among the morphologically similar genera and species within them using the phylogenetic species concept. Contrary to the expectation formulated historically in the literature, the genus Dictyococcus was found to be distantly related to Bracteacoccus and this finding was supported by light microscope observations that revealed that Dictyococcus can be identified by its chloroplast morphology. On the other hand, Pseudomuriella and the hereby resurrected genus Chromochloris were found to be close relatives of Bracteacoccus and morphologically indistinguishable from it and one another using standard microscopic means, providing an example of cryptic genera. Species-level diversity within Bracteacoccus and Pseudomuriella was assessed, and by adding a number of newly isolated strains the current knowledge about the diversity and geographic distribution of these genera was greatly increased. Furthermore, the utility of four putative barcode markers was investigated for recognizing the newly revealed diversity within the previously monotypic genus Pseudomuriella. Based on the phylogenetic findings, new species were also described within Bracteacoccus and an exhaustive revision of the genus is presented in form of a monograph.

Data from: Hiding in plain sight: Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhiza

Premise of the study: Discovery and morphological characterization of a novel epiphytic aquatic green alga increases our understanding of Chaetopeltidales, a poorly known order in Chlorophyceae. Chloroplast genomic data from this taxon reveals an unusual architecture previously unknown in green algae. Methods: Using light and electron microscopy, we characterized the morphology and ultrastructure of a novel taxon of green algae. Bayesian phylogenetic analyses of nuclear and plastid genes were used to test the hypothesized membership of this taxon in order Chaetopeltidales. With next-generation sequence data, we assembled the plastid genome of this novel taxon and compared its gene content and architecture to that of related species to further investigate plastid genome traits. Key results: The morphology and ultrastructure of this alga are consistent with placement in Chaetopeltidales (Chlorophyceae), but a distinct trait combination supports recognition of this alga as a new genus and species—Koshicola spirodelophila gen. et sp. nov. Its placement in the phylogeny as a descendant of a deep division in the Chaetopeltidales is supported by analysis of molecular data sets. The chloroplast genome is among the largest reported in green algae and the genes are distributed on three large (rather than a single) chromosome, in contrast to other studied green algae. Conclusions: The discovery of Koshicola spirodelophila gen. et sp. nov. highlights the importance of investigating even commonplace habitats to explore new microalgal diversity. This work expands our understanding of the morphological and chloroplast genomic features of green algae, and in particular those of the poorly studied Chaetopeltidales

Johansenicoccus eremophilus gen. et sp. nov., a novel evolutionary lineage in Chlorophyceae with unusual genomic features

Background – Green algae are a diverse group of photosynthetic eukaryotes, yet are still vastly understudied compared to land plants. For many years, green algae were characterized based on their morphology and life cycles. More recently, phylogenetic and genomic analyses have been added to the phycological toolkit for a better understanding of algal biodiversity and evolutionary history. Material and methods – A desert strain of green algae was isolated from Joshua Tree National Park (JTNP) in southern California as part of a larger biodiversity survey. The alga’s nuclear rRNA genes as well as the chloroplast genome were sequenced, annotated, and analysed in addition to a morphological assessment. Results – Morphologically this strain is especially similar to Pseudomuriella and Rotundella, and its lipid profile resembles that of other soil algae, but phylogenomic analyses demonstrate that it is a distinct evolutionary lineage in Chlorophyceae. The alga exhibits several unusual genomic features, the most remarkable being its highly derived yet apparently functional nuclear rRNA genes, 18S and 28S. Both genes are GC-rich and bear many compensatory base changes to maintain a similar secondary structure to that of other green algae. The chloroplast genome has a distinct gene order and repeat arrangement from other published green algal plastomes, but contains the expected genes and also provides phylogenetically informative data. Conclusion – We conclude that the strain be placed into a new species and genus in the class Chlorophyceae, and propose the name Johansenicoccus eremophilus for this new taxon. Johansenicoccus eremophilus exemplifies science’s insufficient understanding of the range of genomic variations among inconspicuous soil algae

DNA sequence alignments and Python scripts for performing analyses

Nucleotide alignments of individual chloroplast genes. Python scripts for removal of masked sites. Deploy scripts for producing concatenated data set from individual genes