scholarly journals The Chloroplast Genomes of the Green Algae Pyramimonas, Monomastix, and Pycnococcus Shed New light on the Evolutionary History of Prasinophytes and the Origin of the Secondary Chloroplasts of Euglenids

2008 ◽  
Vol 26 (3) ◽  
pp. 631-648 ◽  
Author(s):  
Monique Turmel ◽  
Marie-Christine Gagnon ◽  
Charley J. O'Kelly ◽  
Christian Otis ◽  
Claude Lemieux
Keyword(s):  
Green Algae ◽  
Evolutionary History ◽  
Chloroplast Genomes ◽  
History Of

scholarly journals Early photosynthetic eukaryotes inhabited low-salinity habitats

2017 ◽  
Vol 114 (37) ◽  
pp. E7737-E7745 ◽  
Author(s):  
Patricia Sánchez-Baracaldo ◽  
John A. Raven ◽  
Davide Pisani ◽  
Andrew H. Knoll
Keyword(s):  
Green Algae ◽  
Crown Group ◽  
Low Salinity ◽  
Photosynthetic Eukaryotes ◽  
Chloroplast Genomes ◽  
Endosymbiotic Event ◽  
History Of ◽  
Phylogenomic Analyses ◽  
Stochastic Mapping ◽  
Open Question

The early evolutionary history of the chloroplast lineage remains an open question. It is widely accepted that the endosymbiosis that established the chloroplast lineage in eukaryotes can be traced back to a single event, in which a cyanobacterium was incorporated into a protistan host. It is still unclear, however, which Cyanobacteria are most closely related to the chloroplast, when the plastid lineage first evolved, and in what habitats this endosymbiotic event occurred. We present phylogenomic and molecular clock analyses, including data from cyanobacterial and chloroplast genomes using a Bayesian approach, with the aim of estimating the age for the primary endosymbiotic event, the ages of crown groups for photosynthetic eukaryotes, and the independent incorporation of a cyanobacterial endosymbiont by Paulinella. Our analyses include both broad taxon sampling (119 taxa) and 18 fossil calibrations across all Cyanobacteria and photosynthetic eukaryotes. Phylogenomic analyses support the hypothesis that the chloroplast lineage diverged from its closet relative Gloeomargarita, a basal cyanobacterial lineage, ∼2.1 billion y ago (Bya). Our analyses suggest that the Archaeplastida, consisting of glaucophytes, red algae, green algae, and land plants, share a common ancestor that lived ∼1.9 Bya. Whereas crown group Rhodophyta evolved in the Mesoproterozoic Era (1,600–1,000 Mya), crown groups Chlorophyta and Streptophyta began to radiate early in the Neoproterozoic (1,000–542 Mya). Stochastic mapping analyses indicate that the first endosymbiotic event occurred in low-salinity environments. Both red and green algae colonized marine environments early in their histories, with prasinophyte green phytoplankton diversifying 850–650 Mya.

scholarly journals Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos

2020 ◽  
Author(s):  
Cen Guo ◽  
Peng-Fei Ma ◽  
Guo-Qian Yang ◽  
Xia-Ying Ye ◽  
Ying Guo ◽  
...  
Keyword(s):  
Evolutionary History ◽  
East Asian Monsoon ◽  
Nuclear Markers ◽  
Chloroplast Genomes ◽  
Analysis Workflow ◽  
History Of ◽  
Tree Estimation ◽  
Evolutionary Radiations ◽  
Genome Skimming ◽  
Parallel Sampling

Abstract Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology, molecular) or genetic markers (e.g., nuclear, organelle) often yield inconsistent results. The tribe Arundinarieae i.e., the temperate bamboos, is a clade of tetraploid originated 22 million years ago and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome-skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy. We recover five major lineages, two of which are notable (the pachymorph and leptomorph lineages), in that they correspond with distinct rhizome morphologies. By contrast, the phylogeny from chloroplast genomes differed significantly. Based on multiple lines of evidence, the ddRAD tree is favored as the best species tree estimation for temperate bamboos. Using a time-calibrated ddRAD tree we find that Arundinarieae diversified rapidly around the mid-Miocene corresponding with intensification of the East Asian monsoon and the evolution of key innovations including the leptomorph rhizomes. Our results provide a highly resolved phylogeny of Arundinarieae, shed new light on the radiation and reticulate evolutionary history of this tribe, and provide an empirical example for the study of recalcitrant plant radiations.

Applications of next-generation sequencing to unravelling the evolutionary history of algae

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 333-345 ◽  
Author(s):  
Kyeong Mi Kim ◽  
Jun-Hyung Park ◽  
Debashish Bhattacharya ◽  
Hwan Su Yoon
Keyword(s):  
Next Generation Sequencing ◽  
Green Algae ◽  
Evolutionary History ◽  
Next Generation ◽  
Genome Data ◽  
Photosynthetic Eukaryotes ◽  
Effective Manner ◽  
History Of ◽  
Primary Endosymbiosis ◽  
Generation Sequencing

First-generation Sanger DNA sequencing revolutionized science over the past three decades and the current next-generation sequencing (NGS) technology has opened the doors to the next phase in the sequencing revolution. Using NGS, scientists are able to sequence entire genomes and to generate extensive transcriptome data from diverse photosynthetic eukaryotes in a timely and cost-effective manner. Genome data in particular shed light on the complicated evolutionary history of algae that form the basis of the food chain in many environments. In the Eukaryotic Tree of Life, the fact that photosynthetic lineages are positioned in four supergroups has important evolutionary consequences. We now know that the story of eukaryotic photosynthesis unfolds with a primary endosymbiosis between an ancestral heterotrophic protist and a captured cyanobacterium that gave rise to the glaucophytes, red algae and Viridiplantae (green algae and land plants). These primary plastids were then transferred to other eukaryotic groups through secondary endosymbiosis. A red alga was captured by the ancestor(s) of the stramenopiles, alveolates (dinoflagellates, apicomplexa, chromeridae), cryptophytes and haptophytes, whereas green algae were captured independently by the common ancestors of the euglenophytes and chlorarachniophytes. A separate case of primary endosymbiosis is found in the filose amoeba Paulinella chromatophora, which has at least nine heterotrophic sister species. Paulinella genome data provide detailed insights into the early stages of plastid establishment. Therefore, genome data produced by NGS have provided many novel insights into the taxonomy, phylogeny and evolutionary history of photosynthetic eukaryotes.

scholarly journals Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gang Wang ◽  
Xingtan Zhang ◽  
Edward Allen Herre ◽  
Doyle McKey ◽  
Carlos A. Machado ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genomic Data ◽  
Host Switching ◽  
Fig Wasp ◽  
Chloroplast Genomes ◽  
Dominant Feature ◽  
Pollination Mutualism ◽  
History Of ◽  
Coevolutionary History

AbstractFicus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

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