Reticulate Evolution Everywhere

Part of the Interdisciplinary Evolution Research book series (IDER, volume 3)

Abstract

Reticulation is a recurring evolutionary pattern found in phylogenetic reconstructions of life. The pattern results from how species interact and evolve by mechanisms and processes including symbiosis; symbiogenesis; lateral gene transfer (that occurs via bacterial conjugation, transformation, transduction, Gene Transfer Agents, or the movements of transposons, retrotransposons, and other mobile genetic elements); hybridization or divergence with gene flow; and infectious heredity (induced either directly by bacteria, bacteriophages, viruses, prions, protozoa and fungi, or via vectors that transmit these pathogens). Research on reticulate evolution today takes on inter- and transdisciplinary proportions and is able to unite distinct research fields ranging from microbiology and molecular genetics to evolutionary biology and the biomedical sciences. This chapter summarizes the main principles of the diverse reticulate evolutionary mechanisms and situates them into the chapters that make up this volume.

Keywords

Reticulate evolution Symbiosis Symbiogenesis Lateral Gene Transfer Infectious agents Microbiome Viriome Virolution Hybridization Divergence with gene flow Evolutionary patterns Extended Synthesis 

Notes

Acknowlegements

This work was written with the support of the Portuguese Fund for Scientific Research (grant ID SFRH/BPD/89195/2012 and project number UID/FIL/00678/2013) and the John Templeton Foundation (grant ID 36288).

Glossary

Aerobe organisms

Organisms that require gaseous oxygen to metabolize. Compare to anaerobes

Algae

(Aquatic) eukaryotic organisms that photosynthesize

Anaerobe organisms

Organisms that are poisoned by gaseous oxygen and that live in oxygen-low or oxygen-free environments. Compare to aerobes

Archaea

First domain of life, previously designated as Archaeabacteria in the kingdom of Monera

Axoneme

Shaft of undulipodia

Bacteria

Second domain of life, previously designated as Eubacteria in the kingdom of Monera

Bacteriophage

Virus that infects bacteria

Centrioli

Cylindrical cell organelle, found in pairs (together called the centrosome) in many eukaryotic organisms, built up from microtubules (tubulin protein structures) structured according to a [9(3) + 0] pattern. They help build the mitotic spindle that separates the chromosomes during division. Compare to undulipodia and cilia

Chloroplasts

Organelles found in plant cells that have evolved by symbiogenesis from photosynthesizing cyanobacteria, currently enabling cells to photosynthesize

Cilium/Cilia

Type of undulipodium that visually appears as hairs on the cell and functions as sensory organelles, often enabling motility. Their basal body has a [9(3) + 0] microtubular structure, and their shaft a [9(2) + 2] one. Compare to undulipodia and centrioli

Coevolution

Process whereby distinct species reciprocally influence each other’s future course of evolution

Computational evolution

Field in computer science and artificial intelligence that develops computational models to investigate evolutionary problems

Cyanobacteria

Chlorophyll pigment-containing and photosynthetic bacteria, previously known as blue-green algae, but algae are eukaryotes, while cyanobacteria are prokaryotes

Cytoplasm

Cell liquid

Domains of life/3-domain classification

According to Carl Woese, and based upon comparative molecular phylogenetics (in particular comparisons of sections of ribosomal RNA), life is classifiable into 3 major domains: Archaea, Bacteria and Eukaryota. This undoes the previous 5-kingdom classification

Eukaryota

The third domain of life, consisting of protists, fungi, plants, and animals. Eukaryotes can be unicellular or multicellular organisms. Their distinctive feature is that their cells have nucleated genomes where the genes are packaged into separate chromosomes. Besides a nucleus, the cells of these organisms often also contain organelles, organ-like structures such as mitochondria and chloroplasts, peroxisomes, and Golgi that associate with specific metabolic functions

Flagellum/Flagella

Bacterial motile extensions made up of flagellin protein

Fitness

Reproductive success, measured by the number of offspring

Five-kingdom classification of life

According to Whitaker and Margulis, and based upon the 3 symbiogenetic mergings proposed by the serial endosymbiotic theory, life can be classified into 5 kingdoms: prokaryotic  Monera (that contain the Archaebacteria, and Eubacteria) and the eukaryotic Protoctist (alternatively known as Protists, Rothschild 1989), Fungi, Plant, and Animal kingdoms

Fungi

An eukaryotic kingdom of life that evolved after archaea, bacteria, and protists, and distinct from animals and plants. They contain microorganisms such as yeast and molds, but also larger organisms such as mushrooms

Germ theory of disease

Theories first introduced by scholars such as Pasteur and Koch that indentify microorganisms as causal agents of disease

Holobiont

Term first introduced by Margulis and Fester (1991) to designate an organism and its symbiotically associating partners

Horizontal transmission

Any type of exchange between distinct individuals that happens during their lifetime and outside of the germ line (in a non-Mendelian fashion)

Host

The larger partner in a symbiotic association

Jumping genes

Genes that can switch position in the genome they are part of, as well as travel to adjacent intracellular genomes (neighboring organelles for example), thereby causing deletions, insertions, and duplications in turn responsible for mutations, malfunctions, or the introduction of novel traits. Today known as transposons

Kinetosomes

Basal body of undulipodia

Microbiome

The complete ecological community of microorganisms that inhabit a species. Compare to viriome

Microtubules

Polymers (strings) of tubulin proteins

Mitochondria

Eukaryotic cell organelles that evolved from aerobe proteobacteria by symbiogenesis, functionally resembling power factories because they produce and store energy

Modern Synthesis

The standard evolutionary paradigm that unites (aspects of) Darwinian selection theory with Mendelian hereditary laws, Boveri–Sutton’s chromosome theory; Weismann’s vertical hereditary descent theory; and de Vries’ and others’ mutation theory to explain the evolution of life. Alternatively known as neo-Darwinism

Monera

Taxonomic unit previously known as the first Kingdom of life, subdivided into Archae- and Eubacteria

Nucleoid

Prokaryotic genome, not bounded by a membrane, not packaged into separate chromosomes. Compare to nucleus

Nucleus

Membrane-bounded cell organelle that contains DNA packaged into separate chromosomes, only present in eukaryotes

Pathogens

Disease-causing agents such as bacteria, bacteriophages, viruses, prions, fungi, and other protozoan microorganisms

Phagocytosis

The act of “eating” whereby a cell engulfs a solid particle that either becomes an organelle or vesicle

Phylogenetics

The systematic study of the evolutionary relationship amongst species, phyla, and higher taxa

Plasmid

Extrachromosomal, often circular DNA, often the seat of antibiotic resistance genes and crucial for bacterial conjugation

Prions

Infectious pathogenic proteins

Prokaryotes

All organisms that neither have a membrane-bounded nucleus nor organelles inside their cell. Instead, their genome floats freely inside the cytoplasm in a structure called the nucleoid

Speciation

The origin of new species out of old ones, induced by evolutionary mechanisms including, among others, symbiogenesis, lateral gene transfer, hybridization, drift, virolution and natural selection; biotic factors including geographical barriers or species-mate recognition factors; and abiotic factors such as climate change

Spirochetes

A phylum of gram-negative, anaerobe, double-membraned, corkscrew-shaped, mobile bacteria

Symbiont

The smaller partner in a symbiotic association

Thermoplasma

A genus of Archaea (prokaryotes), consisting of anaerobe and fermenting microorganisms

Undulipodium/undulipodia

Motile extension of eukaryotic cells, visually resembling a tail. Undulipodia are typified by their [9(2) + 2] microtubullar pattern in their shaft (called the axoneme) and a [9(3) + 0] pattern in their basal body (called the kinetosome). They are similar and presumed evolutionary homologous to eukaryotic centrioli and cilia, and distinct from bacterial flagella. Compare to cilia and centrioli

Vector

Any organism that functions as a medium for the distribution of pathogens or microorganisms

Viriome

All viruses infectious for, and viral parts present in, a certain species. Compare tomicrobiome

Virus

Infectious genetic agent

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.AppEEL—Applied Evolutionary Epistemology LabUniversity of LisbonLisbonPortugal

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