Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

Abstract Background The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood. Results To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

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Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

10.1101/2020.09.22.307728 ◽

2020 ◽

Author(s):

Dario Karmeinski ◽

Karen Meusemann ◽

Jessica A. Goodheart ◽

Michael Schroedl ◽

Alexander Martynov ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Evolutionary History ◽

Transcriptome Assembly ◽

Phylogenetic Signal ◽

Taxon Sampling ◽

Data Sets ◽

Transcriptome Data ◽

Data Set ◽

Sea Slugs ◽

History Of

AbstractBackgroundCladobranch sea slugs represent roughly half of the biodiversity of soft-bodied, marine gastropod molluscs (Nudibranchia) on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as bioindicators and providers of medical drug leads), the evolutionary history of cladobranch sea slugs is not yet fully understood. Here, we amplify the current knowledge on the phylogenetic relationships by extending the cladobranch and outgroup taxon sampling using transcriptome data.ResultsWe generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa. We complemented our taxon sampling with previously published transcriptome data, resulting in a final supermatrix covering 56 species from all but one accepted cladobranch superfamilies. Transcriptome assembly using six different assemblers, selection of those assemblies providing the largest amount of potentially phylogenetically informative sites, and quality-driven compilation of data sets resulted in three different supermatrices: one with a full coverage of genes per species (446 single-copy protein-coding genes) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1,767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximum statistical support for all major splits and phylogenetic relationships on family level. The only discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal.ConclusionsOur data matrices and the inferred trees inferred can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The correct placement of E. pulchra, however, proves challenging, even with large data sets. Moreover, quartet mapping shows that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

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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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Phylogenetic position of Neotropical Bursera-specialist mistletoes: the evolution of deciduousness and succulent leaves in Psittacanthus (Loranthaceae)

Botanical Sciences ◽

10.17129/botsci.1961 ◽

2018 ◽

Vol 96 (3) ◽

pp. 443 ◽

Cited By ~ 2

Author(s):

Andrés Ernesto Ortiz-Rodriguez ◽

Eydi Yanina Guerrero ◽

Juan Francisco Ornelas

Keyword(s):

Phylogenetic Relationships ◽

Evolutionary History ◽

Morphological Evolution ◽

Divergence Time ◽

Molecular Dating ◽

Phylogenetic Position ◽

Long Time ◽

History Of ◽

Nuclear Its ◽

Divergence Timing

Background: The phylogenetic relationships of the Bursera-host specialist Psittacanthus nudus, P. palmeri and P. sonorae (Loranthaceae) remain uncertain. These mistletoe species exhibit morphological and phenological innovations probably related to their dry habitats, so that determining their phylogenetic position is key to the understanding of factors associated with the morphological evolution within Psittacanthus.Questions: (1) Is the evolution of some morphological innovations in the Bursera-host specialists associated with the ecological conditions linked to host diversification? (2) Does time of diversification in both lineages coincide?Study species: Fourteen species of Psittacanthus.Methods: Sequences of nuclear (ITS) and plastid (trnL-trnF) markers are analyzed with Bayesian inference, maximum likelihood and maximum parsimony methods, and molecular dating under a Bayesian approach estimated to elucidate the phylogenetic position and divergence timing of the Bursera-host specialists.Results: The Bursera-host specialists form a strongly supported clade, named here the ‘Bursera group’. The divergence time for the Bursera-host specialists was estimated at 7.89 Ma. Interestingly, phylogenetic relationships between P. nudus and P. palmeri, as currently circumscribed, were not fully resolved, making P. palmeri paraphyletic.Conclusions: Based on these results, the plants collected by type locality of P. nudus in Honduras should be named P. palmeri. The seasonal deciduousness of P. palmeri (including P. nudus) and morphology of P. sonorae (small size, fleshy leaves) are clearly adaptations to dry ecosystems where these species have lived for a long time. In parallel, the evolutionary history of these mistletoes seems to be correlated with the evolutionary history and diversification patterns of Bursera.

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Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

Genome Biology and Evolution ◽

10.1093/gbe/evz155 ◽

2019 ◽

Cited By ~ 4

Author(s):

Sergio A Muñoz-Gómez ◽

Keira Durnin ◽

Laura Eme ◽

Christopher Paight ◽

Christopher E Lane ◽

...

Keyword(s):

Life Style ◽

Metabolic Pathways ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Biosynthetic Pathways ◽

History Of ◽

Sea Squirts ◽

Shed Light ◽

Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

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Phylogenetic position and evolutionary history of the turtle and whale barnacles (Cirripedia: Balanomorpha: Coronuloidea)

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2012.12.018 ◽

2013 ◽

Vol 67 (1) ◽

pp. 9-14 ◽

Cited By ~ 16

Author(s):

Ryota Hayashi ◽

Benny K.K. Chan ◽

Noa Simon-Blecher ◽

Hiromi Watanabe ◽

Tamar Guy-Haim ◽

...

Keyword(s):

Evolutionary History ◽

Phylogenetic Position ◽

History Of

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Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l. derived from mitochondrial DNA

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2003.07.015 ◽

2004 ◽

Vol 31 (1) ◽

pp. 39-49 ◽

Cited By ~ 82

Author(s):

Shane Lavery ◽

T.Y Chan ◽

Y.K Tam ◽

K.H Chu

Keyword(s):

Mitochondrial Dna ◽

Phylogenetic Relationships ◽

Evolutionary History ◽

History Of

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A fossil record of land plant origins from charophyte algae

Science ◽

10.1126/science.abj2927 ◽

2021 ◽

Vol 373 (6556) ◽

pp. 792-796 ◽

Cited By ~ 1

Author(s):

Paul K. Strother ◽

Clinton Foster

Keyword(s):

Fossil Record ◽

Evolutionary History ◽

Phylogenetic Signal ◽

Land Plant ◽

Fossil Plants ◽

Fossil Plant ◽

Molecular Phylogenetic ◽

History Of ◽

Time Gap ◽

Evolutionary Continuity

Molecular time trees indicating that embryophytes originated around 500 million years ago (Ma) during the Cambrian are at odds with the record of fossil plants, which first appear in the mid-Silurian almost 80 million years later. This time gap has been attributed to a missing fossil plant record, but that attribution belies the case for fossil spores. Here, we describe a Tremadocian (Early Ordovician, about 480 Ma) assemblage with elements of both Cambrian and younger embryophyte spores that provides a new level of evolutionary continuity between embryophytes and their algal ancestors. This finding suggests that the molecular phylogenetic signal retains a latent evolutionary history of the acquisition of the embryophytic developmental genome, a history that perhaps began during Ediacaran-Cambrian time but was not completed until the mid-Silurian (about 430 Ma).

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Three new Cenomanian conifers from El Chango (Chiapas, Mexico) offer a snapshot of the geographic mosaic of the Mesozoic conifer decline

10.1101/2021.09.01.458614 ◽

2021 ◽

Author(s):

Ixchel Gonzalez-Ramirez ◽

Sergio RS Cevallos-Ferriz ◽

Carl Rothfels

Keyword(s):

Evolutionary History ◽

Mixed Forest ◽

Freshwater Ecosystems ◽

Total Evidence ◽

Morphological Data ◽

Phylogenetic Position ◽

Dominant Group ◽

Geographic Mosaic ◽

History Of ◽

Rare Opportunity

Premise of study: El Chango is a recently discovered quarry that contains extremely well preserved fossils. The Cenomanian age of the locality corresponds to a time when the global flora was transitioning from gymnosperm- to angiosperm-dominated, yet conifers predominate in this locality. These fossils thus provide a rare opportunity to understand the replacement of conifers by angiosperms as the dominant group of plants. Methods: We collected material from El Chango in annual expeditions (2010 to 2014). We selected the three most abundant and best preserved conifer morphotypes and conducted a total-evidence (i.e., including molecular and morphological data) phylogenetic analysis of a sample of 72 extant conifer species plus the three fossils. We use these results to inform our taxonomic decisions. Results: We obtained four equally most-parsimonious trees (consistency index = 44.1%, retention index = 78.8%). Despite ambiguous relationships among some extant taxa, the three fossil conifers had the same phylogenetic position in all four most parsimonious trees; we describe these species as new: Sequoiadendron helicalancifolium sp. nov. (Cupressaceae), and Microcachrys rhomboidea sp. nov. and Dacrydium bifoliosus sp. nov (Podocarpaceae). The ecosystem is interpreted as a coastal humid mixed forest. Conclusions: Our findings contribute to the understanding of Cenomanian equatorialregions, and support the hypothesis of a geographically and ecologically structured rise of angiosperms, with conifers remaining dominant in brackish-water and angiosperms becoming dominant in freshwater-ecosystems. These fossils fill in gaps in the evolutionary history of lineages like Microcachrys, which we demonstrate occurred in the Northern hemisphere before becoming restricted to its current range (Tasmania).

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