{{unsourced, date=July 2022
RedToL, or Red Algal Tree of Life, is part of the collaborative
National Science Foundation
The National Science Foundation (NSF) is an independent agency of the United States government that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National I ...
Assembling the Tree of Life activity (AToL), funded through the Division of
Environmental Biology
Environmental science is an interdisciplinary academic field that integrates physics, biology, and geography (including ecology, chemistry, plant science, zoology, mineralogy, oceanography, limnology, soil science, geology and physical geograp ...
, Directorate for
Biological Sciences
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary ...
. The overall goal of AToL is to resolve
evolutionary
Evolution is change in the heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, expressions of genes, which are passed on from parent to ...
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
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic
and phyloinformatics.
The Phylogenetic and Genomic Approaches to Reconstructing the Red Algal Tree of Life focus on the
Rhodophyta
Red algae, or Rhodophyta (, ; ), are one of the oldest groups of eukaryotic algae. The Rhodophyta also comprises one of the largest phyla of algae, containing over 7,000 currently recognized species with taxonomic revisions ongoing. The majority ...
(
red algae
Red algae, or Rhodophyta (, ; ), are one of the oldest groups of eukaryotic algae. The Rhodophyta also comprises one of the largest phyla of algae, containing over 7,000 currently recognized species with taxonomic revisions ongoing. The majority ...
), one of the most ancient
eukaryotic
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
fossil
A fossil (from Classical Latin , ) is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved ...
evidence for Bangiales stretching back 1.2 billion years. Red algae are not only key members of
marine
Marine is an adjective meaning of or pertaining to the sea or ocean.
Marine or marines may refer to:
Ocean
* Maritime (disambiguation)
* Marine art
* Marine biology
* Marine debris
* Marine habitats
* Marine life
* Marine pollution
Military
* ...
and
freshwater
Fresh water or freshwater is any naturally occurring liquid or frozen water containing low concentrations of dissolved salts and other total dissolved solids. Although the term specifically excludes seawater and brackish water, it does include ...
aquatic environments but they are sources for important human foods such as
dulse
''Palmaria palmata'', also called dulse, dillisk or dilsk (from Irish/Scottish Gaelic '/'), red dulse, sea lettuce flakes, or creathnach, is a red alga ( Rhodophyta) previously referred to as ''Rhodymenia palmata''. It grows on the northern coas ...
and
sushi
is a Japanese cuisine, Japanese dish of prepared , usually with some sugar and salt, accompanied by a variety of , such as seafood, often raw, and vegetables. Styles of sushi and its presentation vary widely, but the one key ingredient is " ...
wrap, and have a multitude of pharmaceutical and industrial uses (e.g.,
agarose
Agarose is a heteropolysaccharide, generally extracted from certain red seaweed. It is a linear polymer made up of the repeating unit of agarobiose, which is a disaccharide made up of D-galactose and 3,6-anhydro-L-galactopyranose. Agarose is o ...
and carrageenans). Perhaps most important is the role red algae played in
symbiogenesis
Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory,) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possi ...
. A red alga was the ancient (>1 billion years ago) donor of the
plastid
The plastid (Greek: πλαστός; plastós: formed, molded – plural plastids) is a membrane-bound organelle found in the Cell (biology), cells of plants, algae, and some other eukaryotic organisms. They are considered to be intracellular endosy ...
in
chlorophyll c
Chlorophyll ''c'' is a form of chlorophyll found in certain marine algae, including the photosynthetic Chromista (e.g. diatoms and brown algae) and dinoflagellates.
It has a blue-green color and is an accessory pigment, particularly significant i ...
-containing algae (
heterokonta
Heterokonts are a group of protists (formally referred to as Heterokonta, Heterokontae or Heterokontophyta). The group is a major line of eukaryotes. Most are algae, ranging from the giant multicellular kelp to the unicellular diatoms, which a ...
or stramenopiles) that rose to prominence in marine ecosystems after the end of
Permian
The Permian ( ) is a geologic period and stratigraphic system which spans 47 million years from the end of the Carboniferous Period million years ago (Mya), to the beginning of the Triassic Period 251.9 Mya. It is the last period of the Paleoz ...
with groups such as
diatoms
A diatom (New Latin, Neo-Latin ''diatoma''), "a cutting through, a severance", from el, διάτομος, diátomos, "cut in half, divided equally" from el, διατέμνω, diatémno, "to cut in twain". is any member of a large group com ...
currently providing ca. 20% of global fixed
carbon
Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent
In chemistry, the valence (US spelling) or valency (British spelling) of an element is the measure of its combining capacity with o ...
.
Aims
The aims of RedToL are: 1) reconstruct a robust
phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
of 471 red algal species using a
concatenated
In formal language theory and computer programming, string concatenation is the operation of joining character strings end-to-end. For example, the concatenation of "snow" and "ball" is "snowball". In certain formalisations of concatenat ...
dataset of 2
nuclear
Nuclear may refer to:
Physics
Relating to the nucleus of the atom:
* Nuclear engineering
*Nuclear physics
*Nuclear power
*Nuclear reactor
*Nuclear weapon
*Nuclear medicine
*Radiation therapy
*Nuclear warfare
Mathematics
*Nuclear space
*Nuclear ...
, 4
plastid
The plastid (Greek: πλαστός; plastós: formed, molded – plural plastids) is a membrane-bound organelle found in the Cell (biology), cells of plants, algae, and some other eukaryotic organisms. They are considered to be intracellular endosy ...
, and 2
mitochondrial
A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is use ...
encoded gene markers; 2) sequence plastid
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
s and generate
transcriptome
The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The t ...
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
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part ...
and a project-specific web site. The outreach and student mentoring program is an important component of the RedToL initiative.
The 471 chosen
species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
from 294
genera
Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomenclat ...
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
Taxonomy is the practice and science of categorization or classification.
A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
revision of the red algae and provides the basis for interpreting key innovations during red algal
evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
. 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
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
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., hundreds) 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 is the practice and science of categorization or classification.
A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
to
phylogenomics
Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger field ...