scholarly journals Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

2021 ◽  
Author(s):  
Charles Ross Lindsey ◽  
Frank Rosenzweig ◽  
Matthew D Herron
Keyword(s):  
Cellular Differentiation ◽  
Algal Species ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Character State ◽  
Similar Data ◽  
Volvox Carteri ◽  
Major Transitions ◽  
Volvocine Algae ◽  
History Of

AbstractThe volvocine algae, which include the single-celled speciesChlamydomonas reinhardtiiand the colonial speciesVolvox carteri, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the evolutionary history of this group have often relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. These studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group. We performed RNA-Seq on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes, then subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation independently arose at least four and possibly as many as six times within the group. Altogether, these results show how multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming their importance for the study of major transitions in the history of life.

scholarly journals Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Charles Ross Lindsey ◽  
Frank Rosenzweig ◽  
Matthew D. Herron
Keyword(s):  
Cellular Differentiation ◽  
Algal Species ◽  
Phylogenetic Inference ◽  
Amino Acid Sequences ◽  
Character State ◽  
Similar Data ◽  
Volvox Carteri ◽  
Major Transitions ◽  
Volvocine Algae ◽  
History Of

Abstract Background The volvocine algae, which include the single-celled species Chlamydomonas reinhardtii and the colonial species Volvox carteri, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the history of this group have by and large relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. As a result, volvocine phylogenies lack concordance depending on the number and/or type of genes (i.e., chloroplast vs nuclear) chosen for phylogenetic inference. While multiple studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group, other studies call into question one or more of these conclusions. An accurate assessment of the evolutionary history of the volvocine algae requires inference of a more robust phylogeny. Results We performed RNA sequencing (RNA-seq) on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We then compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes and subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation arose independently at least four, and possibly as many as six times, within the volvocine algae. Conclusions Altogether, our results demonstrate that multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming the importance of this group as a model system for the study of major transitions in the history of life.

The Major Transitions in Evolution

1997 ◽  
Author(s):  
John Maynard Smith ◽  
Eors Szathmary
Keyword(s):  
Full Range ◽  
Evolution Of Cooperation ◽  
Major Transitions ◽  
Insect Societies ◽  
Wide Range ◽  
Major Transition ◽  
Life Itself ◽  
History Of ◽  
Emergence Of Cooperation ◽  
Multicellular Organisms

Over the history of life there have been several major changes in the way genetic information is organized and transmitted from one generation to the next. These transitions include the origin of life itself, the first eukaryotic cells, reproduction by sexual means, the appearance of multicellular plants and animals, the emergence of cooperation and of animal societies, and the unique language ability of humans. This ambitious book provides the first unified discussion of the full range of these transitions. The authors highlight the similarities between different transitions--between the union of replicating molecules to form chromosomes and of cells to form multicellular organisms, for example--and show how understanding one transition sheds light on others. They trace a common theme throughout the history of evolution: after a major transition some entities lose the ability to replicate independently, becoming able to reproduce only as part of a larger whole. The authors investigate this pattern and why selection between entities at a lower level does not disrupt selection at more complex levels. Their explanation encompasses a compelling theory of the evolution of cooperation at all levels of complexity. Engagingly written and filled with numerous illustrations, this book can be read with enjoyment by anyone with an undergraduate training in biology. It is ideal for advanced discussion groups on evolution and includes accessible discussions of a wide range of topics, from molecular biology and linguistics to insect societies.

Four distinct and unusual linker proteins in a mitotically dividing nucleus are derived from a 71-kilodalton polyprotein, lack p34cdc2 sites, and contain protein kinase A sites

1994 ◽  
Vol 14 (1) ◽  
pp. 10-20
Author(s):  
M Wu ◽  
C D Allis ◽  
M T Sweet ◽  
R G Cook ◽  
T H Thatcher ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Protein Kinase A ◽  
Phosphorylation Site ◽  
High Mobility ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Evolutionary Analysis ◽  
Associated Proteins ◽  
Kinase Phosphorylation ◽  
Kinase A

Tetrahymena thermophila micronuclei contain four linker-associated proteins, alpha, beta, gamma, and delta. Synthetic oligonucleotides based on N-terminal protein sequences of beta and gamma were used to clone the micronuclear linker histone (MLH) gene. The MLH gene is single copy and is transcribed into a 2.4-kb message encoding all four linker-associated proteins. The message is translated into a polypeptide (Mic LH) that is processed at the sequence decreases RTK to give proteins whose amino acid sequences differ markedly from each other, from the sequence of macronuclear H1, and from sequences of typical H1s of other organisms. This represents the first example of multiple chromatin proteins derived from a single polyprotein. The delta protein consists largely of two high-mobility-group (HMG) boxes. An evolutionary analysis of HMG boxes indicates that the delta HMG boxes are similar to the HMG boxes of tsHMG, a protein that appears in elongating mouse spermatids when they condense and cease transcription, suggesting that delta could play a similar role in the micronucleus. The micronucleus divides mitotically, while the macronucleus divides amitotically. Surprisingly, macronuclear H1 but not Mic LH contains sequences resembling p34cdc2 kinase phosphorylation sites, while each of the Mic LH-derived proteins contains a typical protein kinase A phosphorylation site in its carboxy terminus.

scholarly journals The origin and early radiation of terrestrial vertebrates

2001 ◽  
Vol 75 (6) ◽  
pp. 1202-1213 ◽  
Author(s):  
Robert L. Carroll
Keyword(s):  
Fossil Record ◽  
Early Carboniferous ◽  
Late Devonian ◽  
Lower Carboniferous ◽  
Major Transitions ◽  
Terrestrial Vertebrates ◽  
History Of ◽  
Paleozoic Tetrapods ◽  
Early Radiation ◽  
Ways Of Life

The origin of tetrapods from sarcopterygian fish in the Late Devonian is one of the best known major transitions in the history of vertebrates. Unfortunately, extensive gaps in the fossil record of the Lower Carboniferous and Triassic make it very difficult to establish the nature of relationships among Paleozoic tetrapods, or their specific affinities with modern amphibians. The major lineages of Paleozoic labyrinthodonts and lepospondyls are not adequately known until after a 20–30 m.y. gap in the Early Carboniferous fossil record, by which time they were highly divergent in anatomy, ways of life, and patterns of development. An even wider temporal and morphological gap separates modern amphibians from any plausible Permo-Carboniferous ancestors. The oldest known caecilian shows numerous synapomorphies with the lepospondyl microsaur Rhynchonkos. Adult anatomy and patterns of development in frogs and salamanders support their origin from different families of dissorophoid labyrinthodonts. The ancestry of amniotes apparently lies among very early anthracosaurs.

scholarly journals Exploring and Reconstructing Ancestral Anatomies using Ontology-Informed Approaches

2019 ◽  
Vol 3 ◽  
Author(s):  
Sergei Tarasov ◽  
Istvan Miko ◽  
Matthew Yoder ◽  
Josef Uyeda
Keyword(s):  
Phylogenetic Trees ◽  
Character State ◽  
Ancestral Reconstruction ◽  
Anatomy Ontology ◽  
Insect Order ◽  
Ancestral Character State ◽  
Body Regions ◽  
Individual Traits ◽  
History Of ◽  
Complex Characters

Ancestral character state reconstruction has been long used to gain insight into the evolution of individual traits in organisms. However, organismal anatomies (= entire phenotypes) are not merely ensembles of individual traits, rather they are complex systems where traits interact with each other due to anatomical dependencies (when one trait depends on the presence of another trait) and developmental constraints. Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of entire organismal anatomies or organismal body regions. Herein, we present a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies, Tarasov and Uyeda 2019) that takes into account anatomical dependencies and uses stochastic maps (i.e., phylogenetic trees with an instance of mapped evolutionary history of characters, Huelsenbeck et al. 2003) along with anatomy ontologies to reconstruct organismal anatomies. Our approach treats the entire phenotype or its component body regions as single complex characters and allows exploring and comparing phenotypic evolution at different levels of anatomical hierarchy. These complex characters are constructed by ontology-informed amalgamation of elementary characters (i.e., those coded in character matrix) using stochastic maps. In our approach, characters are linked with the terms from an anatomy ontology, which allows viewing them not just as an ensemble of character state tokens but as entities that have their own biological meaning provided by the ontology. This ontology-informed framework provides new opportunities for tracking phenotypic radiations and anatomical evolution of organisms, which we explore using a large dataset for the insect order Hymenoptera (sawflies, wasps, ants and bees).

scholarly journals Independent origins of the Golgi phosphoprotein 3 oncoprotein gene

2021 ◽  
Author(s):  
Juan C. Opazo ◽  
Michael W. Vandewege ◽  
Javier Gutierrez ◽  
Kattina Zavala ◽  
Luis Vargas-Chacoff ◽  
...  
Keyword(s):  
Gene Family ◽  
Transcript Abundance ◽  
Single Copy ◽  
Model Systems ◽  
Deep Roots ◽  
Starting Point ◽  
Amino Acid Divergence ◽  
Evolutionarily Conserved ◽  
History Of ◽  
Divergence Estimates

AbstractGolgi phosphoprotein 3 (GOLPH3) is considered the first oncoprotein of the Golgi apparatus. It was identified as an evolutionarily conserved protein upon its discovery about 20 years ago, but its function remains puzzling in normal and cancer cells. The GOLPH3 gene is part of a group of genes that also includes the GOLPH3L gene. Because cancer has deep roots in multicellular evolution, studying the evolution of the GOLPH3 gene family in non-model species represents an opportunity to identify new model systems that could help better understand the biology behind this group of genes. The main goal of this study is to explore the evolution of the GOLPH3 gene family in birds as a starting point to understand the evolutionary history of this oncoprotein. We identified a repertoire of three GOLPH3 genes in birds. We found duplicated copies of the GOLPH3 gene in all main groups of birds other than paleognaths, and a single copy of the GOLPH3L gene. We suggest there were at least three independent origins for GOLPH3 duplicates. Amino acid divergence estimates show that most of the variation is located in the N-terminal region of the protein. Our transcript abundance estimations show that one paralog is highly and ubiquitously expressed, and the others were variable. Our results are an example of the significance of understanding the evolution of the GOLPH3 gene family, especially for unraveling its structural and functional attributes.

scholarly journals Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

2019 ◽  
Vol 116 (6) ◽  
pp. 2165-2174 ◽  
Author(s):  
Tao Zhao ◽  
M. Eric Schranz
Keyword(s):  
Gene Families ◽  
Single Copy ◽  
Specific Gene ◽  
Phylogenetic Groups ◽  
History Of ◽  
Mammalian Genomes ◽  
Syntenic Conservation ◽  
Genome Assemblies ◽  
Lineage Specific Gene ◽  
Relative Gene

A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across broad phylogenetic groups and divergence times. We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall patterns and major differences between 87 mammalian and 107 angiosperm genomes. These two important groups have both evolved and radiated over the last ∼170 MYR. Secondly, we identified the genomic outliers or “rebel genes” within each clade. We theorize that rebel genes potentially have influenced trait and lineage evolution. Microsynteny networks use genes as nodes and syntenic relationships between genes as edges. Networks were decomposed into clusters using the Infomap algorithm, followed by phylogenomic copy-number profiling of each cluster. The differences in syntenic properties of all annotated gene families, including BUSCO genes, between the two clades are striking: most genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/or have lineage-specific distributions for angiosperms. We propose microsynteny scores as an alternative and complementary metric to BUSCO for assessing genome assemblies. We further found that the rebel genes are different between the two groups: lineage-specific gene transpositions are unusual in mammals, whereas single-copy highly syntenic genes are rare for flowering plants. We illustrate several examples of mammalian transpositions, such as brain-development genes in primates, and syntenic conservation across angiosperms, such as single-copy genes related to photosynthesis. Future experimental work can test if these are indeed rebels with a cause.

scholarly journals The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Xian-Gui Yi ◽  
Xia-Qing Yu ◽  
Jie Chen ◽  
Min Zhang ◽  
Shao-Wei Liu ◽  
...  
Keyword(s):  
Plant Disease Resistance ◽  
De Novo ◽  
Genomic Analysis ◽  
Gene Families ◽  
Single Copy ◽  
Comparative Genomic ◽  
Sequencing Technologies ◽  
History Of ◽  
Flowering Cherry ◽  
Plant Disease Resistance Genes

Abstract Cerasus serrulata is a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly of C. serrulata by the use of Nanopore and Hi-C sequencing technologies. The assembled C. serrulata genome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated that C. serrulata and C. avium have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of C. serrulata are distributed on all chromosomes of C. avium, implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed that C. serrulata has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present C. serrulata species diverged from Prunus yedoensis ~17.34 million years ago (Mya), while the divergence of C. serrulata and C. avium was estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified in C. serrulata, accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies in C. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching C. serrulata within the PRGdb. This research provides high-quality genomic information about C. serrulata as well as insights into the evolutionary history of Cerasus species.

scholarly journals A transcriptome-based phylogenetic study of hard ticks (Ixodidae)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
N. Pierre Charrier ◽  
Axelle Hermouet ◽  
Caroline Hervet ◽  
Albert Agoulon ◽  
Stephen C. Barker ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Nuclear Genome ◽  
Single Copy ◽  
Phylogenetic Study ◽  
Data Sets ◽  
Hard Tick ◽  
Rna Seq ◽  
Hard Ticks ◽  
History Of ◽  
Mitochondrial Sequences

Abstract Hard ticks are widely distributed across temperate regions, show strong variation in host associations, and are potential vectors of a diversity of medically important zoonoses, such as Lyme disease. To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for nine different Ixodes species. We combined this new data with 18 data sets obtained from public databases, both for Ixodes and non-Ixodes hard tick species, using soft ticks as an outgroup. We assembled transcriptomes (for 27 species in total), predicted coding sequences and identified single copy orthologues (SCO). Using Maximum-likelihood and Bayesian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome. We also obtained a mitochondrial DNA-based phylogeny using published genome sequences and mitochondrial sequences derived from the new transcriptomes. Our results confirm previous studies showing that the Ixodes genus is monophyletic and clarify the relationships among Ixodes sub-genera. This work provides a baseline for studying the evolutionary history of ticks: we indeed found an unexpected acceleration of substitutions for mitochondrial sequences of Prostriata, and for nuclear and mitochondrial genes of two species of Rhipicephalus, which we relate with patterns of genome architecture and changes of life-cycle, respectively.

Convergence to the tiniest detail: vocal sac structure in torrent-dwelling frogs

2019 ◽  
Author(s):  
Agustín J Elias-Costa ◽  
Julián Faivovich
Keyword(s):  
Background Noise ◽  
Evolutionary History ◽  
Visual Display ◽  
Character State ◽  
Visual Displays ◽  
State Reconstruction ◽  
Ancestral Character State ◽  
History Of ◽  
Ancestral Character State Reconstruction ◽  
Detection And Recognition

Abstract Cascades and fast-flowing streams impose severe restrictions on acoustic communication, with loud broadband background noise hampering signal detection and recognition. In this context, diverse behavioural features, such as ultrasound production and visual displays, have arisen in the evolutionary history of torrent-dwelling amphibians. The importance of the vocal sac in multimodal communication is being increasingly recognized, and recently a new vocal sac visual display has been discovered: unilateral inflation of paired vocal sacs. In the diurnal stream-breeding Hylodidae from the Atlantic forest, where it was first described, this behaviour is likely to be enabled by a unique anatomical configuration of the vocal sacs. To assess whether other taxa share this exceptional structure, we surveyed torrent-dwelling species with paired vocal sacs across the anuran tree of life and examined the vocal sac anatomy of exemplar species across 18 families. We found striking anatomical convergence among hylodids and species of the distantly related basal ranid genera Staurois, Huia, Meristogenys and Amolops. Ancestral character state reconstruction identified three new synapomorphies for Ranidae. Furthermore, we surveyed the vocal sac configuration of other anuran species that perform visual displays and report observations on what appears to be unilateral inflation of paired vocal sacs, in Staurois guttatus – an extremely rare behaviour in anurans.

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