The origin and evolution of model organisms

Key Points

  • The number of model organisms has grown in concert with the increasing number of genome-sequencing projects.

  • As a result, the 'tree of life', which was previously based on a ribosomal RNA gene sequence, has been replaced by one that is based on genome-wide sequence data.

  • Eukaryotes are no longer considered to be close relatives of Archaebacteria, but rather genomic hybrids of Archaebacteria and Eubacteria.

  • Large numbers of genes were transferred from prokaryotes to the eukaryote nucleus during symbiotic events.

  • Owing to recent analyses of genomic sequences, phylogenetic support for the presence of hyperthermophiles — species that live at high temperatures — at the base of the tree of life has been weakened.

  • Molecular-clock analyses have supported a more recent origin of Cyanobacteria than indicated by the fossil record. The date is now estimated to be closer to the time at which oxygen levels began to rise in the Earth's atmosphere, as indicated by geological evidence.

  • Some cytological and genomic evidence support the existence of a premitochondrial period in the history of eukaryotes, although this topic has been debated.

  • Whether the ancestors of some amitochondriate eukaryotes once had mitochondria also remains controversial.

  • The basal position of liverworts among land plants has been uprooted, although an alternative phylogeny has not yet been established.

  • Molecular-clock analyses indicate that the main groups of fungi diverged hundreds of millions of years earlier than indicated by the fossil record.

  • The relationships between humans, nematodes and fruitflies continue to be debated, despite the knowledge of their complete genomes.

Abstract

The phylogeny and timescale of life are becoming better understood as the analysis of genomic data from model organisms continues to grow. As a result, discoveries are being made about the early history of life and the origin and development of complex multicellular life. This emerging comparative framework and the emphasis on historical patterns is helping to bridge barriers among organism-based research communities.

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Figure 1: Changing views of the tree and timescale of life.
Figure 2: A phylogeny of prokaryotes.
Figure 3: A phylogeny of protists.
Figure 4: A phylogeny of plants.
Figure 5: A phylogeny of fungi.
Figure 6: A phylogeny of animals.

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Acknowledgements

I thank J. Blair, D. Geiser, S. Kumar, and D. Pisani for comments. I apologize to colleagues whose work could not be cited due to space constraints. Research in the author's laboratory is supported by the National Aeronautics and Space Administration (Astrobiology Institute) and National Science Foundation.

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FURTHER INFORMATION

AlgaeBase

All species foundation

Amphibian taxonomy

Amphibiaweb

Angiosperm phylogeny

Animal diversity web

Animal genome size database

Bird families

Birds of the world

Blair Hedges laboratory

Deep hypha (phylogeny of Fungi)

Dictyostelium database (DictyBase)

DOE microbial genomics gateway

Fishbase

FlyBase (Drosophila)

Fossil record 2

Generic model organism database

Genome web

Human genome databases

Index to organism names

International geologic timescale

Land plants online

List of bacterial names

Mammal species of the world

Model organism resources

NASA Astrobiology Institute

NASA evolutionary genomics web site

NCBI genome databases

NCBI taxonomy browser

NIH model organism database report

NIH model organism initiatives

Phylogeny of life

Phylogeny programs

Sanger genome databases

The EMBL reptile database

The global plant checklist

The international plant names index

TIGR genome databases

Tree of life web project

Treebase

World taxonomist database

Wormbase (Caenorhabditis elegans)

Glossary

HORIZONTAL TRANSFER

The transfer of genetic material between the genomes of two organisms, which are usually different species.

NEIGHBOUR JOINING

A method that selects the tree that has the shortest overall length (sum of all branch lengths).

MAXIMUM LIKELIHOOD

A method that selects the tree that has the highest probability of explaining the sequence data, under a specific model of substitution (changes in the nucleotide or amino-acid sequence).

BAYESIAN METHOD

A method that selects the tree that has the greatest posterior probability (probability that the tree is correct), under a specific model of substitution.

MAXIMUM PARSIMONY

A method that selects the tree that requires the fewest number of substitutions.

BOOTSTRAP METHOD

As applied to molecular phylogenies. Nucleotide or amino-acid sites are sampled randomly, with replacement, and a new tree is constructed. This is repeated many times and the frequency of appearance of a particular node among the bootstrap trees is viewed as a support (confidence) value for deciding on the significance of that node.

RELATIVE RATE TESTS

Statistical tests that determine, at a given level of stringency, whether two or more branches in a tree have evolved at the same rate of sequence change.

CYANOBACTERIA

A phylum of Eubacteria, formerly known as the “blue-green algae”. These prokaryotes are the only organisms known to be capable of oxygenic photosynthesis.

SPIROCHAETES

A phylum of Eubacteria that has a spiral or corkscrew-like appearance and axial filaments (similar to flagella). These prokaryotes are responsible for human diseases, such as Lyme disease and syphilis.

MONOPHYLETIC

Includes all the descendants of a single common ancestor.

ELONGATION FACTOR 1

An enzyme that functions in the process of protein translation.

PARAPHYLETIC

Includes some, but not all, of the descendants of a single common ancestor.

ADAPTIVE RADIATION

The rapid diversification of a group of species into various habitats over a relatively short period of geological time. However, the term is often used as a synonym for any large monophyletic group of taxa.

GLAUCOCYSTOPHYTES

A small group of freshwater algae, also called 'glaucophytes'. Species in this group have plastids with a peptidoglycan cell wall (peptidoglycan is the main component of bacterial cell walls).

BRYOPHYTES

A term that refers traditionally to non-vascular land plants, nearly all of which are quite small (1–2 cm high). Bryophytes include hornworts, liverworts and mosses; however, the term might also be used in a more restricted sense to refer to the mosses alone (Division: Bryophyta).

HORNWORTS

A group of small, non-vascular plants (Division: Anthocerotophyta) that are distinguished by their tall horn-like sporophyte (diploid generation) that grows on the more flattened gametophyte (haploid generation). They usually have a single, large chloroplast in each cell.

LIVERWORTS

A group of small, mat-like, non-vascular plants (Division: Marchantiophyta) that occur in diverse habitats but most commonly on the forest floor. Some species have lobe-shaped leaves that resemble a liver.

MONOCOTS

(Monocotyledonous plants). Flowering plants with one cotyledon (or seed leaf).

EUDICOTS

The largest clade of angiosperms, characterized by two cotyledons (seed leaves) and three symmetrically placed pollen apertures or aperture arrangements that are derived from this.

ANGIOSPERMS

Flowering vascular plants that form seeds inside an ovary.

GYMNOSPERMS

Non-flowering vascular plants with naked seeds that are not enclosed in an ovary (for example, pine).

PRECAMBRIAN

An informal geological time period that spans from the time the Earth was born, 4,500 million years ago (Mya), until 545 Mya.

LOCAL-CLOCK METHOD

A method for estimating divergence time by accounting for differences in the rate of substitution among lineages (branches) in a tree.

CAMBRIAN EXPLOSION

The sudden appearance, 520 million years ago, of many major groups (phyla) of animals, as witnessed in the fossil record.

ASCOMYCOTA

The largest phylum of fungi; also called ascomycetes or 'sac fungi'. They produce sexual spores in specialized sac-like cells called asci.

PYRENOMYCETES

The largest subgroup of ascomycotan fungi, which are characterized by flask-shaped fruiting bodies.

ARTIODACTYLS

Hoofed animals with an even number of digits. They belong to the mammalian Order Artiodactyla and include animals such as cattle, deer and pigs.

TAXON SAMPLING

A term that indicates that the branching pattern of a tree might be influenced by the number or type of taxa (for example, species) included.

PSEUDOCOELOM

Literally 'false cavity'; the body cavity of an animal, such as a nematode, that is not fully lined with mesodermal cells.

COELOM

The body cavity of an animal, such as a vertebrate or insect, which is completely lined with mesodermal cells.

CENOZOIC

The geological time period (era) that spans from 65 million years ago to the present day.

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Hedges, S. The origin and evolution of model organisms. Nat Rev Genet 3, 838–849 (2002). https://doi.org/10.1038/nrg929

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