RedToL
Encyclopedia
RedToL, or Red Algal Tree of Life, is part of the collaborative National Science Foundation
Assembling the Tree of Life activity (AToL), funded through the Division of Environmental Biology, Directorate for Biological Sciences. The overall goal of AToL is to resolve evolutionary relationships for large groups of organisms throughout the history of life, with the research often involving large teams working across institutions and disciplines. Investigators are typically supported for projects in data acquisition, analysis, algorithm development and dissemination in computational
phylogenetics
and phyloinformatics.
The Phylogenetic and Genomic Approaches to Reconstructing the Red Algal Tree of Life focus on the Rhodophyta (red algae
), one of the most ancient eukaryotic phyla
with fossil
evidence for Bangiales stretching back 1.2 billion years. Red algae are not only key members of marine
and freshwater
aquatic
environments but they are sources for important human foods such as dulse
and sushi
wrap, and have a multitude of pharmaceutical and industrial uses (e.g., agarose and carrageenans). Perhaps most important is the role red algae played in the evolution of our planet through secondary endosymbiosis. A red alga was the ancient (>1 billion years ago) donor of the plastid
in chlorophyll c
-containing algae (chromalveolates) that rose to prominence in marine ecosystems after the end of Permian
with groups such as diatoms currently providing ca. 20% of global fixed carbon
.
, 4 plastid
, and 2 mitochondrial encoded gene markers; 2) sequence plastid genomes and generate transcriptome
databases for 16 key taxa that represent the phylogenetic (e.g., class- and order-level) breadth of the red algae, 3) make freely available red algal multi-gene and genome data via release to GenBank
and a project-specific web site. The outreach and student mentoring program is an important component of the RedToL initiative.
The 471 chosen species
from 294 genera
represent the diversity of ca. 6,000 red algal species (i.e., ca. 35% of all red algal genera will be included, which represent all extant orders). The robust phylogenetic framework resulting from this study is the basis for a comprehensive taxonomic revision of the red algae and provides the basis for interpreting key innovations during red algal evolution
. Because the chosen marker genes are shared across different Assembling the Tree of Life (AToL) projects, it will provide a common framework for a future comprehensive eukaryotic tree. Complete plastid genome and transcriptome data from 16 major red algal taxa will provide a genome inventory to facilitate understanding of red algal evolution, as well as provide the basis for phylogenetic analyses using a rich set (i.e., 100s) of vertically inherited genes. The genome data will specifically test the relationships among the major classes and orders of red algae. The RedToL team members come from eight institutions including two foreign collaborators and fifteen advisory board members and represent the most prominent active national and international red algal specialists from different generations who use different methods (from taxonomy
to phylogenomics
) to enhance understanding of red algal biology.
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
Assembling the Tree of Life activity (AToL), funded through the Division of Environmental Biology, Directorate for Biological Sciences. The overall goal of AToL is to resolve evolutionary relationships for large groups of organisms throughout the history of life, with the research often involving large teams working across institutions and disciplines. Investigators are typically supported for projects in data acquisition, analysis, algorithm development and dissemination in computational
Computational
Computational may refer to:* Computer* Computational algebra* Computational Aeroacoustics* Computational and Information Systems Laboratory* Computational and Systems Neuroscience* Computational archaeology* Computational auditory scene analysis...
phylogenetics
Phylogenetics
In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...
and phyloinformatics.
The Phylogenetic and Genomic Approaches to Reconstructing the Red Algal Tree of Life focus on the Rhodophyta (red algae
Red algae
The red algae are one of the oldest groups of eukaryotic algae, and also one of the largest, with about 5,000–6,000 species of mostly multicellular, marine algae, including many notable seaweeds...
), one of the most ancient eukaryotic phyla
Phyla
Phyla, the plural of phylum, may refer to:* Phylum, a biological taxon between Kingdom and Class* Phylum , in linguistics, a large division of possibly related languagesPhyla, as a singular, may refer to:...
with fossil
Fossil
Fossils are the preserved remains or traces of animals , plants, and other organisms from the remote past...
evidence for Bangiales stretching back 1.2 billion years. Red algae are not only key members of marine
Marine (ocean)
Marine is an umbrella term. As an adjective it is usually applicable to things relating to the sea or ocean, such as marine biology, marine ecology and marine geology...
and freshwater
Freshwater
Fresh water is naturally occurring water on the Earth's surface in ice sheets, ice caps, glaciers, bogs, ponds, lakes, rivers and streams, and underground as groundwater in aquifers and underground streams. Fresh water is generally characterized by having low concentrations of dissolved salts and...
aquatic
Aquatic ecosystem
An aquatic ecosystem is an ecosystem in a body of water. Communities of organisms that are dependent on each other and on their environment live in aquatic ecosystems. The two main types of aquatic ecosystems are marine ecosystems and freshwater ecosystems....
environments but they are sources for important human foods such as dulse
Dulse
Palmaria palmata Kuntze, also called dulse, dillisk, dilsk, red dulse, sea lettuce flakes or creathnach, is a red alga previously referred to as Rhodymenia palmata Greville. It grows on the northern coasts of the Atlantic and Pacific oceans. It is a well-known snack food...
and sushi
Sushi
is a Japanese food consisting of cooked vinegared rice combined with other ingredients . Neta and forms of sushi presentation vary, but the ingredient which all sushi have in common is shari...
wrap, and have a multitude of pharmaceutical and industrial uses (e.g., agarose and carrageenans). Perhaps most important is the role red algae played in the evolution of our planet through secondary endosymbiosis. A red alga was the ancient (>1 billion years ago) donor of the plastid
Plastid
Plastids are major organelles found in the cells of plants and algae. Plastids are the site of manufacture and storage of important chemical compounds used by the cell...
in chlorophyll c
Chlorophyll c
Chlorophyll c can refer to:* Chlorophyll c1* Chlorophyll c2* Chlorophyll c3...
-containing algae (chromalveolates) that rose to prominence in marine ecosystems after the end of Permian
Permian
The PermianThe term "Permian" was introduced into geology in 1841 by Sir Sir R. I. Murchison, president of the Geological Society of London, who identified typical strata in extensive Russian explorations undertaken with Edouard de Verneuil; Murchison asserted in 1841 that he named his "Permian...
with groups such as diatoms currently providing ca. 20% of global fixed carbon
Carbon
Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...
.
Aims
The aims of RedToL are: 1) reconstruct a robust phylogeny of 471 red algal species using a concatenated dataset of 2 nuclearCell nucleus
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...
, 4 plastid
Plastid
Plastids are major organelles found in the cells of plants and algae. Plastids are the site of manufacture and storage of important chemical compounds used by the cell...
, and 2 mitochondrial encoded gene markers; 2) sequence plastid genomes and generate transcriptome
Transcriptome
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.-Scope:...
databases for 16 key taxa that represent the phylogenetic (e.g., class- and order-level) breadth of the red algae, 3) make freely available red algal multi-gene and genome data via release to GenBank
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
and a project-specific web site. The outreach and student mentoring program is an important component of the RedToL initiative.
The 471 chosen species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
from 294 genera
Genera
Genera is a commercial operating system and development environment for Lisp machines developed by Symbolics. It is essentially a fork of an earlier operating system originating on the MIT AI Lab's Lisp machines which Symbolics had used in common with LMI and Texas Instruments...
represent the diversity of ca. 6,000 red algal species (i.e., ca. 35% of all red algal genera will be included, which represent all extant orders). The robust phylogenetic framework resulting from this study is the basis for a comprehensive taxonomic revision of the red algae and provides the basis for interpreting key innovations during red algal evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
. Because the chosen marker genes are shared across different Assembling the Tree of Life (AToL) projects, it will provide a common framework for a future comprehensive eukaryotic tree. Complete plastid genome and transcriptome data from 16 major red algal taxa will provide a genome inventory to facilitate understanding of red algal evolution, as well as provide the basis for phylogenetic analyses using a rich set (i.e., 100s) of vertically inherited genes. The genome data will specifically test the relationships among the major classes and orders of red algae. The RedToL team members come from eight institutions including two foreign collaborators and fifteen advisory board members and represent the most prominent active national and international red algal specialists from different generations who use different methods (from taxonomy
Taxonomy
Taxonomy is the science of identifying and naming species, and arranging them into a classification. The field of taxonomy, sometimes referred to as "biological taxonomy", revolves around the description and use of taxonomic units, known as taxa...
to phylogenomics
Phylogenomics
Phylogenomics can be regarded as the intersection between the fields of evolution and genomics. The term has been used in multiple ways to refer to some type of analysis involving genome data and evolutionary reconstructions. It is an expansion of earlier phylogenetics...
) to enhance understanding of red algal biology.