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16: Taxonomy & Evolution - Biology

16: Taxonomy & Evolution - Biology


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Evolution

It is believed that the Earth is 4.6 billion year old, with the first cells appearing approximately 3.8 billion years ago. Those cells were undoubtably microbes, eventually giving rise to all the life forms that we envision today, as well as the life forms that went extinct before we got here. How did this progression occur?

Early Earth

Conditions on early Earth were most likely extremely hot, anoxic (lacking oxygen), with reduced inorganic chemicals in abundance. While no one knows exactly how cells came about, it is likely that they were initially suited to these harsh conditions.

RNA World

RNA, in its many forms, plays a crucial role in cellular activities. It has been hypothesized that RNA played an even more central role in primitive cells, with self-replicating RNA containing a cell’s information as well as having catalytic activity to synthesize proteins. Eventually this RNA world evolved to one in which proteins took over the catalytic responsibilities and DNA became the common form of information storage.

The “RNA World” and the Modern World.

Metabolic Diversity

Initial cells probably had a relatively primitive electron transference system, perhaps through just one carrier, that still allowed for the development of a proton motive force to conserve energy. As chemolithoautotrophs proliferated, organic material started to accumulate in the environment, providing the conditions needed for the development of chemoorganotrophic organisms. These new cells oxidized organic compounds, with their more negative redox potential and increased number of electrons. This most likely lengthened electron transport chains, resulting in faster growth, and speeding up diversity even more.

Phototrophy & Photosynthesis

At about 3.5 billion year ago some cells evolved phototrophic pigments, allowing for the conversion of light energy into chemical energy. Initially phototrophs utilized anoxygenic phototrophy, using sulfur products as an electron donor when performing CO2 fixation.

Stromatolites are layered rocks that form when minerals are incorporated into thick mats of microbes, growing on water surfaces. Ancient stromatolites contain fossilized microbial mats made up of cyanobacteria-like cells, indicating their presence relatively early in Earth’s history.

Approximately 2.5-3.3 billion year ago the cyanobacterial ancestors developed oxygenic photosynthesis by acquiring two photosystems and the pigment chlorophyll a. This led to the use of water as an electron donor, causing oxygen to accumulate in Earth’s atmosphere. This Great Oxidation Event substantially changed the types of metabolism possible, allowing for the use of oxygen as a final electron acceptor.

Ozone Shield Formation

The development of an ozone shield around the Earth occurred around 2 billion years ago. Ozone (O3) serves to block out much of the ultraviolet (UV) radiation coming from the sun, which can cause significant damage to DNA. As oxygen accumulated in the environment, the O2 was converted to O3 when exposed to UV light, causing an ozone layer to form around Earth. This allowed organisms to start inhabiting the surface of the planet, as opposed to just the ocean depths or soil layers.

Endosymbiosis

Evolution supports the idea of more primitive molecules or organisms being generated first, followed by the more complex components or organisms over time. Endosymbiosis offers an explanation for the development of eukaryotic cells, a more complex cell type with organelles or membrane-bound enclosures.

It is generally accepted that eukaryotic ancestors arose when a cell ingested another cell, a free-living bacterium, but did not digest it. This endosymbiont had capabilities that the proto-eukaryotic cell lacked, such as the ability for phototrophy (i.e. chloroplasts) or oxidative phosphorylation (i.e. mitochondria). Eventually the two became mutually dependent upon one another with the endosymbiont becoming an organelle, with the chloroplast being derived from a cyanobacterial ancestor and the mitochondrion being derived from a gram negative bacillus ancestor.

Endosymbiosis. By Signbrowser (Own work) [CC0], via Wikimedia Commons

Evidence to support this idea includes the fact that mitochondria and chloroplasts: have a single, circular chromosome; undergo binary fission separate from the eukaryotic cell; have 70S sized ribosomes; have a lipid bilayer with a 2:1 ratio of protein to lipid; and, perhaps most importantly, have rRNA sequences that place them phylogenetically with the bacteria.

Phylogeny

Molecular Phylogeny

Phylogeny is a reference to the development of an organism evolutionarily. Molecular techniques allow for the evolutionary assessment of organisms using genomes or ribosomal RNA (rRNA) nucleotide sequences, generally believed to provide the most accurate information about the relatedness of microbes.

Nucleic acid hybridization or DNA-DNA hybridization is a commonly used tool for molecular phylogeny, comparing the similarities between genomes. The genomes of two organisms are heated up or “melted” to separate the complementary strand and then allowed to cool down. Strands that have complementary base sequences will re-anneal, while strands without complementation will remain upaired. Typically one source of DNA is labeled, usually with radioactivity, to allow for identification of each DNA source.

Nucleic acid sequencing, typically using the rRNAs from small ribosomal subunits, allows for direct comparison of sequences. The ribosomal sequence is seen as ideal because the genes encoding it do not change very much over time, nor does it appear to be strongly influenced by horizontal gene transfer. This makes it an excellent “molecular chronometer,” or way to track genetic changes over a long period of time, even between closely related organisms.

Phylogenetic Trees

Phylogenetic trees serve to show a pictorial example of how organisms are believed to be related evolutionarily. The root of the tree is the last common ancestor for the organisms being compared (Last Universal Common Ancestor or LUCA, if we are doing a comparison of all living cells on Earth). Each node (or branchpoint) represents an occurrence where the organisms diverged, based on a genetic change in one organism. The length of each branch indicates the amount of molecular changes over time. The external nodes represent specific taxa or organisms (although they can also represent specific genes). A cladeindicates a group of organisms that all have a particular ancestor in common.

Taxonomy

Taxonomy refers to the organization of organisms, based on their relatedness. Typically it involves some type of classification scheme, the identification of isolates, and the naming or nomenclature of included organisms. Many different classification schemes exist, although many have not been appropriate for comparison of microorganisms.

Classification Systems

A phenetic classification system relies upon the phenotypes or physical appearances of organisms. Phylogenetic classication uses evolutionary relationships of organisms. A genotypic classification compares genes or genomes between organisms. The most popular approach is to use a polyphasic approach, which combines aspects of all three previous systems.

Microbial Species

Currently there is no widely accepted “species definition” for microbes. The definition most commonly used is one that relies upon both genetic and phenotypic information (a polyphasic approach), with a threshold of 70% DNA-DNA hybridization and 97% 16S DNA sequence identity in order for two organisms to be deemed as belonging to the same species.

Key Words

evolution, RNA world, stromatolites, Great Oxidation Event, ozone shield, endosymbiosis, chloroplast, mitochondria, phylogeny, ribosomal RNA/rRNA, molecular phylogeny, nucleic acid hybridization, DNA-DNA hybridization, nucleic acid sequencing, molecular chronometer, phylogenetic tree, Last Universal Common Ancestor/LUCA, node, branch, external node, clade, taxonomy, phonetic classification, phylogenetic classification, genotypic classification, polyphasic classiciation, species definition.

Study Questions

  1. What is the approximate age of earth? What is the age of the oldest microbial fossils?
  2. What are thought to be the conditions of early earth? How would this influence microbial selection?
  3. What is the premise of the “RNA world”?
  4. What are the important steps in the evolution of metabolism? How does each step influence microbial growth/life on earth?
  5. What is the endosymbiotic theory and what evidence do we have for it?
  6. What is phylogeny? What is molecular phylogeny?
  7. What is DNA-DNA hybridization? What is nucleic acid sequencing? How is each performed? What information is gained?
  8. What is a molecular chronometer? Which molecule has been most useful and why?
  9. What is a phylogenetic tree? What is the difference among a node, external node, branch, and a clade? What does the length of a branch indicate? What is LUCA?
  10. What is taxonomy and what is its purpose? What is the difference between classification, nonmenclature, and identification in taxonomy?
  11. What are differences among the following classification systems: phenetic, phylogenetic, genotypic, polyphasic. What characteristics are used for each? Where do they overlap?
  12. How are a microbial species currently defined? What criteria are applied?

The AmP project: Comparing species on the basis of dynamic energy budget parameters

Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Resources, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliation MARETEC – Marine, Environment & Technology Center, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal

Contributed equally to this work with: Gonçalo M. Marques, Starrlight Augustine

Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliation Akvaplan-niva, Fram High North Research Centre for Climate and the Environment, Tromsø, Norway

Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliation Department of Biology, University of Crete, Heraklion, Greece

Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliation LEMAR, IRD, CNRS, UBO, Ifremer, Plouzané, France

Roles Conceptualization, Funding acquisition, Investigation, Methodology, Resources, Supervision, Visualization, Writing – review & editing

Affiliation MARETEC – Marine, Environment & Technology Center, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliation Department of Theoretical Biology, VU University Amsterdam, Amsterdam, The Netherlands


Citation: Thomson SA, Pyle RL, Ahyong ST, Alonso-Zarazaga M, Ammirati J, Araya JF, et al. (2018) Taxonomy based on science is necessary for global conservation. PLoS Biol 16(3): e2005075. https://doi.org/10.1371/journal.pbio.2005075

Received: September 26, 2017 Accepted: February 8, 2018 Published: March 14, 2018

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Funding: The authors received no specific funding for this work.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: CITES, Convention on International Trade in Endangered Species ICB, International Committee on Bionomenclature IUBS, International Union of Biological Sciences IUCN, International Union for Conservation of Nature

Provenance: Not commissioned externally peer reviewed

Taxonomy is a scientific discipline that has provided the universal naming and classification system of biodiversity for centuries and continues effectively to accommodate new knowledge. A recent publication by Garnett and Christidis [1] expressed concerns regarding the difficulty that taxonomic changes represent for conservation efforts and proposed the establishment of a system to govern taxonomic changes. Their proposal to “restrict the freedom of taxonomic action” through governing subcommittees that would “review taxonomic papers for compliance” and their assertion that “the scientific community’s failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss, damages the credibility of science, and is expensive to society” are flawed in many respects. They also assert that the lack of governance of taxonomy damages conservation efforts, harms the credibility of science, and is costly to society. Despite its fairly recent release, Garnett and Christidis' proposition has already been rejected by a number of colleagues [2,3,4,5,6,7,8]. Herein, we contribute to the conversation between taxonomists and conservation biologists aiming to clarify some misunderstandings and issues in the proposition by Garnett and Christidis.

Placing governance over the science of taxonomy blurs the distinction between taxonomy and nomenclature. Garnett and Christidis’s proposal is far-reaching but represents a narrow perspective of taxonomy, as utilized by conservation, and reflects an increasingly broad misunderstanding throughout biology of the scientific basis of taxonomy, formalized nomenclature, and the relationship between them. This trend may have resulted from the attenuation of instruction in taxonomic principles and, in particular, nomenclature at many universities, in part because of a shift in research priorities away from taxonomy.

Garnett and Christidis assert that an “assumption that species are fixed entities underpins every international agreement on biodiversity conservation.” This assumption demonstrates a fundamental misunderstanding of taxonomy and the evolving view of what species represent. The essential features of science include documenting natural patterns and processes, developing and testing hypotheses, and refining existing ideas and descriptions of nature based on new data and insights. Taxonomy, the science of recognizing and delimiting species, adheres to these fundamental principles. Discoveries of new organisms together with advances in methodology continue unabated, leading to a constant reevaluation of the boundaries between taxonomic entities. Species (and higher taxa) comprise related organisms that may be clustered together differently depending on which sets of criteria are emphasized. Hey et al. [9] acknowledge “the inherent ambiguity of species in nature” but point out that “species-related research and conservation efforts can proceed without suffering from, and without fear of, the ambiguity of species.” Through taxonomic research, our understanding of biodiversity and classifications of living organisms will continue to progress. Any system that restricts such progress runs counter to basic scientific principles, which rely on peer review and subsequent acceptance or rejection by the community, rather than third-party regulation. Thiele and Yeates [10] cautioned that such a system “could lead to authoritarianism and a stifling of innovative taxonomic viewpoints. No other hypothesis-driven field of science would accept such a straitjacket”.

Taxonomy and associated nomenclature are not without problems. Even with a common set of facts, alternative interpretations of how to classify organisms can lead to differing classifications. However, the science of taxonomy is increasingly rigorous, which can improve the foundation for targeted legislative action regarding species [11,12]. Taxonomic instability does not affect all taxonomic groups equally. Garnett and Christidis provide examples from mammals and birds, which collectively represent a small fraction (<1%) of known biodiversity [13]. These groups tend to be the subject of greater levels of taxonomic “fine-tuning”—but less so in bats and rodents, groups in which basic species discoveries frequently take place—leading to disproportionately more lumping, splitting, and nomenclatural issues. In contrast, taxonomists working on most other groups of organisms, with vastly greater diversity, are focused on the basic tasks of discovering, delimiting, and describing species, rather than rearranging classifications of taxa already described. In extreme cases, taxonomic instability results in what has become known as “taxonomic vandalism” [14,15], which usually involves self-published or non–peer-reviewed taxonomic works that unnecessarily disrupt taxonomy without a solid scientific foundation. Academic freedom, needed for scientific progress, may yield undesirable results. However, over some 250 years of taxonomy, the number of authors that would be considered taxonomic vandals is very small, and further improvements to the Codes of nomenclature may reduce the harm they do without impinging on science. Scientists have long worked to achieve a universal species concept and an accompanying set of operational criteria that could serve to define species limits across most, if not all, groups of organisms however, this task remains incomplete for a number of legitimate reasons [16,17,18,19]. Rather than promoting the establishment of a system that would arbitrarily bias community acceptance or rejections of species-level taxonomic hypotheses, many avenues of work seem more likely to improve taxonomy and the sciences that depend on it, including the following: efforts to improve our definitions of what a species is, incorporating more taxonomists into committees of conservation organizations, and providing aid in campaigns aiming to secure funding for education and research in taxonomy, among others.


Charles Darwin

Charles Darwin is arguably the most significant biologist of all-time due to his work on the theory of evolution and the mechanism of natural selection.

Darwin’s publication ‘On the origin of species by means of natural selection’ changed society’s perception on the natural history of Earth. It delivered a solid argument for the theory of evolution and provided a plausible mechanism – natural selection – that could lead to the evolution of new species.

Nearly 150 years have passed since Darwin first published his theory and the quantity of evidence to support his work is staggering. Subsequently, much of the present-day biological research is performed with the theory of evolution as its foundation.

In 1859, Charles Darwin presented a publication titled ‘On the Origin of Species by Means of Natural Selection’. Thirty years of research and thought were collaborated into the publication that changed our understanding of the natural world.

The book presented two arguments backed up with large amounts of evidence from nature. The first point proposed that species were not created in their current forms but evolved from common ancestors. The second proposed the mechanism that pushed the evolution of species – natural selection.

When Darwin presented his paper, creationism was the dominant belief amongst the general public and the scientific community. Naturally, there was great resistance to the theory of evolution as it contradicted the words of the ‘Old Testament’ and flipped the common view of how life had developed.

Darwin wasn’t the first to write about evolution but he was the first to propose the theory with enough evidence and logic for the world to take notice and effectively changed western culture and the study of life, forever. Darwin’s development of the evolutionary theory did not come out of the blue but was a product of the combination of similar geological theories, diligent observation and clear reasoning.

George Cuvier, a pioneer of palaeontology (the study of fossils), observed and documented the change in fossil records from older to younger rock. He also noticed that younger fossils bared a greater resemblance to present-day species than older fossils. However, Cuvier was a fierce opponent of the theory of evolution and explained the changes in time by a theory of catastrophism.


Classification Categories

The second feature of Linnaeus's taxonomy, which simplifies organism ordering, is categorical classification. This means narrowing organism types into categories but this approach has undergone significant changes since its inception. The broadest of these categories within Linnaeus's original system is known as kingdom and he divided all of the world's living organisms into only an animal kingdom and plant kingdom.

Linnaeus further divided organisms by shared physical characteristics into classes, orders, genera, and species. These categories were revised to include kingdom, phylum, class, order, family, genus, and species over time. As more scientific advancements and discoveries were made, domain was added to the taxonomic hierarchy and is now the broadest category. The kingdom system of classification was all but replaced by the current domain system of classification.

Domain System

Organisms are now grouped primarily according to differences in ribosomal ​RNA structures, not physical properties. The domain system of classification was developed by Carl Woese and places organisms under the following three domains:

  • Archaea:This domain includes prokaryotic organisms (which lack a nucleus) that differ from bacteria in membrane composition and RNA. They are extremophiles capable of living in some of the most inhospitable conditions on earth, such as hydrothermal vents.
  • Bacteria: This domain includes prokaryotic organisms with unique cell wall compositions and RNA types. As part of the human microbiota, bacteria are vital to life. However, some bacteria are pathogenic and cause disease.
  • Eukarya: This domain includes eukaryotes or organisms with a true nucleus. Eukaryotic organisms include plants, animals, protists, and fungi.

Under the domain system, organisms are grouped into six kingdoms which include Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista, Fungi, Plantae, and Animalia. The process of classifying organisms by categories was conceived by Linnaeus and has been adapted since.

Taxonomy Example

The table below includes a list of organisms and their classification within this taxonomy system using the eight major categories. Notice how closely dogs and wolves are related. They are similar in every aspect except species name.

Intermediate Categories

Taxonomic categories can be even more precisely divided into intermediate categories such as subphyla, suborders, superfamilies, and superclasses. A table of this taxonomy scheme appears below. Each main category of classification has its own subcategory and supercategory.


History of Botany – A Timeline

During the Pre-17 th Century

4 th Century B.C.E: Both Aristotle and Theophrastus got involved in identifying plants and describing them. Because of his contributions, Theophrastus was hailed as the “Father of botany” because of his two surviving works on plant studies. Although Aristotle also wrote about plants, he received more recognition for his studies of animals.

In A.D. 60: Dioscorides wrote De Materia Medica. This work described a thousand medicines, majority of which came from plants. For 1500 years, it remained the guidebook on medicines in the Western world until the invention of the compound microscope.

Quote:Medicine sometimes grants health, sometimes destroys it, showing which plants are helpful, which do harm.

During the 17 th Century

Early 17 th century: For a brief period, the search for knowledge in the field of Botany temporarily became stagnant. However, the revival of learning during the European Renaissance renewed interest in plants

The number of scientific publications increased.

1640: Johannes van Helmont measured the uptake of water in a tree. Brittanica.com explains (refer to Major Experiments section) “In what is perhaps his best-known experiment, van Helmont placed a 5-pound (about 2.2-kg) willow in an earthen pot containing 200 pounds (about 90 kg) of dried soil, and over a five-year period he added nothing to the pot but rainwater or distilled water. After five years, he found that the tree weighed 169 pounds (about 77 kg), while the soil had lost only 2 ounces (57 grams). He concluded that “164 pounds of wood, barks, and roots arose out of water only,” and he had not even included the weight of the leaves that fell off every autumn.

1665: Robert Hooke invented the microscope. Because of this, Robert Hooke had the chance to take a close look of a cell looks like. His description of these cells was published in Micrographia. However, the cells seen by Hooke showed no signs of the nucleus and other organelles found in most living cells (Rhoads 2007).

1674: Anton van Leeuwenhoek saw a live cell under a microscope. Before his discovery, the existence of single-celled organisms were unknown and initially were met with skepticism.

1686: John Ray published his book, Historia Plantarum. This became an important step towards modern taxonomy (Arber 2010).

1694: Rudolf Camerarius established plant sexuality in his book entitled De Sexu Plantarum Epistola. There, he stated that: “No ovules of plants could ever develop into seeds from the female style and ovary without first being prepared by the pollen from the stamens, the male sexual organs of the plant“.

During the 18 th Century

1727: Stephen Hales successfully established plant physiology as a science. He published his experiments dealing with the nutrition and respiration of plants in his publication entitled Vegetable Staticks. He developed techniques to measure area, mass, volume, temperature, pressure, and even gravity in plants.

1758: Carolus Linnaeus (Carl von Linne), the “Father of Taxonomy“, introduced the science of taxonomy which deals with the identification, nomenclature, description and classification of organisms (species). His classification is based on the fact that species was the smallest unit and each species (taxon) is under a higher category (Farabee 2001).

1760s: Botany became even more widespread among educated women who painted plants, attended classes on plant classification, and collected herbarium specimens. However, the focus of their study was on the healing properties of plants rather than plant reproduction. Women began publishing on botanical topics and children’s books on botany appeared (Mason 2016).

The prize resulting from the period of exploration was accumulated in gardens and herbaria. And the task of systematically cataloging them was left to the taxonomists.

Later part of the eighteenth century: Joseph Priestley laid the foundation for the chemical analysis of plant metabolism. Joseph Priestley published his works as Experiments and Observations on Different Kinds of Air in 1774. The published paper demonstrated that green plants absorb “fixed air” (carbon dioxide) from the atmosphere, give off “gas” or “dephlogisticated air”, which is now known as oxygen, and that this gas is essential to animal life (Rook 1964).

During the 19 th Century

Early part of the nineteenth century: Progress in the study of plant fossils was made.

1818: Chlorophyll was discovered.

1840: Advances were made in the study of plant diseases because of the potato blight that killed potato crops in Ireland. This led to the further study of plant diseases (Richman 2016).

1847: The process of photosynthesis was first elucidated by Mayer. However, the exact and detailed mechanism remained a mystery until the 1862.

1859: Charles Darwin proposed his theory of evolution and adaptation, or more commonly referred to as “survival of the fittest” (kenyon.edu 2016).

Charles Darwin and Alfred Russel Wallace collaborated. Darwin soon published his renowned and highly recognized book On the Origin of Species by Means of Natural Selection.

Around the same time, Gregor Mendel, was performing experiments on the inheritance among pea plants.

Gregor Mendel became the “Father of Genetics”.

1862: The exact mechanism of photosynthesis was discovered when it was observed that starch was formed in green cells only in the presence of light.

1865: The results of Mendel’s experiments in 1865 showed that both parents should pass distinct physical factors which code information to their offspring at conception. The offspring then inherits one unit for each trait from each of his parents (Richman 2016)

Twentieth Century up to the Present

Early 20 th Century: The process of nitrogen fixation, nitrification, and ammonification was discovered.

1903: The two types of chlorophyll—a and b were discovered. Learn more here.

1936: Through his experiment, Alexander Oparin demonstrated the mechanism of the synthesis of organic matter from inorganic molecules. Refer to a controversial observation of his findings at later years.

1940s: Ecology became a separate discipline. Technology has helped specialists in botany to see and understand the three-dimensional nature of cells, and genetic engineering of plants. This had greatly improved agricultural crops and products (Arber 2010).

Up until the present, the study of plants continues as botanists try to both understand the structure, behavior, and cellular activities of plants. This endeavor is in order to develop better crops, find new medicines, and explore ways of maintaining an ecological balance on Earth to continue to sustain both plant and animal life (Mason 2016).


Receptor usage of SARS-CoV and SARSr-CoV

ACE2 binding is a critical determinant for the host range of SARS-CoV 72,73 . Electron microscopic studies have shown that the SARS-CoV S protein forms a clover shaped trimer, with three S1 heads and a trimeric S2 stalk 74,75 . The RBD is located on the tip of each S1 head. The RBD binds to the outer surface of ACE2, away from its zinc-chelating enzymatic site 77,141 (Fig. 6a). Different SARS-CoV strains isolated from several hosts vary in their binding affinities for human ACE2 and consequently in their infectivity of human cells 76,78 (Fig. 6b). The epidemic strain hTor02 was isolated from humans during the late phase of the outbreak in 2002–2003. It has a high affinity for human ACE2 and high infectivity in human cells, and consequently, it was transmitted efficiently between humans 62 . Strains cSz02 and cHb05 were isolated from palm civets in 2002–2003 and 2005, respectively. Both have low affinity for human ACE2 and low infectivity in human cells but have high affinity for civet ACE2 and high infectivity in civet cells 12,79 . Strain hcGd03 was isolated from both humans and palm civets in 2003–2004 and has moderate affinity for human ACE2 and moderate infectivity in human cells it infected humans but did not transmit between humans 80 . Strain hHae08 was isolated from human cell culture and has high affinity for human ACE2 and high infectivity in human cells 81 . Understanding the molecular basis for human receptor usage by different SARS-CoV strains is crucial for understanding the cross-species transmission of SARS-CoV and for epidemiological monitoring of potential future outbreaks.

a | Severe acute respiratory syndrome coronavirus (SARS-CoV) uses its receptor-binding domain (RBD) (as shown in the structure of strain hTor02, containing core structure (cyan) and receptor-binding motif (RBM magenta)) to bind human angiotensin-converting enzyme 2 (ACE2 green Protein Data Bank ID: 2AJF). ACE2 is a peptidase with zinc (blue) in its active centre. b | Several residues in the host and viral receptor, as well as two salt bridges that stabilize the structure (dotted lines) and form two binding hot spots, are crucial for binding of the severe acute respiratory syndrome (SARS) epidemic strain hTor02. Hydrophobic residues surrounding the two salt bridges are present in the structure but are not shown in the figure. c | By contrast, the SARS-related coronavirus (SARSr-CoV) strain bWIV1, which was isolated from bats and can infect both civet and human cells, differs in residues 442, 472 and 487. The mutation from threonine to asparagine in residue 487 introduces a polar side chain and is predicted to interfere with binding at hot spot 353. The model shown here was built on the basis of the structure of hTor02 RBD complexed with human ACE2 (Protein Data Bank ID: 2AJF), in which residues 442, 472 and 487 were mutated from those in strain hTor02 to those in strain bWIV1. d | The bat SARSr-CoV strain bRsSHC014 can also infect human and civet cells it carries an alanine in position 487, and the short side chain of this residue does not support the structure of hot spot 353. The model was built on the basis of the structure of cOptimize RBD complexed with human ACE2 (Protein Data Bank ID: 3SCJ), in which residues 442, 480 and 487 were mutated from those in strain cOptimize to those in strain bWIV1. e | The Middle East respiratory syndrome coronavirus (MERS-CoV) RBD (core structure in cyan and RBM in magenta) binds human dipeptidyl peptidase 4 (DPP4 green Protein Data Bank ID: 4KR0). Structure figures were made using PyMOL 115 . Modelled mutations in panels c and d were performed using Coot 140 . Panels a–d are adapted from ref. 83 : this research was originally published in The Journal of Biological Chemistry. Wu, K. L., Peng, G. Q., Wilken, M., Geraghty, R. J. & Li, F. Mechanisms of host receptor adaptation by severe acute respiratory syndrome coronavirus. J. Biol. Chem. 2012 287:8904–8911. © American Society for Biochemistry and Molecular Biology.

SARS-CoV mutations that affect human and civet receptor binding

Crystal structures of the SARS-CoV RBD complexed with human ACE2 revealed that the SARS-CoV RBD contains a core structure and a receptor-binding motif (RBM) 82,141 (Fig. 6a). Two virus-binding hot spots have been identified at the interface of the RBD and human ACE2, centring on ACE2 residues Lys31 (hot spot 31) and Lys353 (hot spot 353) 83,84 (Fig. 6b). They both consist of a salt bridge (between Lys31 and Glu35 for hot spot 31 and between Lys353 and Asp38 for hot spot 353) both salt bridges are buried in hydrophobic pockets and contribute a substantial amount of energy to RBD–ACE2 binding as well as filling voids at the RBD–ACE2 interface. Naturally selected RBM mutations all interact with the hot spots (Fig. 6b Table 1) and affect RBD–ACE2 binding.

Mutations in RBM residue 479 had an important role in the civet-to-human transmission of SARS-CoV 42,76,78,85 . Residue 479 is an asparagine in strains hTor02, hcGd03 and hHae08 but is a lysine in strain cSz02 and an arginine in strain cHb05 (Table 1). Asn479 is located near hot spot 31, without interfering with the structure of hot spot 31 (ref. 85 ) (Fig. 6b, c). However, a change to Lys479 leads to steric and electrostatic interference with hot spot 31, reducing the binding affinity between the SARS-CoV RBD and human ACE2. By contrast, Arg479 reaches the vicinity of hot spot 353 and forms a salt bridge with ACE2 residue Asp38 (ref. 83 ) (Fig. 6d). Hence, strains hTor02, hcGd03 and hHae08 (all of which contain Asn479) and strain cHb05 (which contains Arg479) recognize human ACE2 and infect human cells efficiently, whereas strain cSz02 (which contains Lys479) recognizes human ACE2 inefficiently and infects human cells inefficiently. The above structural analyses are supported by biochemical, functional and epidemiological data 42,76,78,83,84,85 . Because of residue differences between human ACE2 and civet ACE2, both Asn479 and Lys479 fit well into the interface between the RBD and civet ACE2, although Arg479 fits even better 83,85 consequently, strains hTor02, cSz02, hcGd03 and cHb05 (which contain either Asn479, Lys479 or Arg479) recognize civet ACE2 and infect civet cells efficiently 79 . In sum, Asn479 and Arg479 are viral adaptations to human ACE2, whereas Lys479 is incompatible with human ACE2 Arg479 is a viral adaptation to civet ACE2, whereas Asn479 and Lys479 are also compatible with civet ACE2.

Mutations in RBM residue 487 had an important role in the human-to-human transmission of SARS-CoV. Residue 487 is a threonine in strain hTor02 but is a serine in the other strains isolated from humans and civets. The methyl group of Thr487 interacts with hot spot 353 in human ACE2 by providing stacking support for the formation of the salt bridge between Lys353 and Asp38 consequently, strain hTor02 recognizes human ACE2 efficiently and was transmitted between humans during the 2002–2003 SARS epidemic. By contrast, Ser487 cannot provide support to hot spot 353, and hence the other strains isolated from humans and civets recognize human ACE2 inefficiently. Consequently, neither cSz02 nor hcGd03 was transmitted between humans. The above structural analyses are supported by biochemical, functional and epidemiological data 42,76,78,83,84,85 . Because of residue differences between human ACE2 and civet ACE2, Ser487 fits well into the RBD–civet ACE2 interface although still not as well as Thr487 (refs 83,85 ) consequently, strains sSZ02, hcGd03 and cHb05 (which contain Ser487) recognize civet ACE2 and infect civet cells efficiently 79 . In sum, Thr487 is a viral adaptation to both human and civet ACE2, and Ser487 is much more compatible with civet ACE2 than with human ACE2 (Fig. 6b).

RBM residues 442, 472 and 480 also contribute to receptor recognition and host range of SARS-CoV although not as much as residues 479 and 487. Detailed structural, biochemical and functional analyses showed that Phe442, Phe472 and Asp480 are viral adaptations to human ACE2, whereas Tyr442, Leu472 or Pro472, and Gly480 are viral adaptations to civet ACE2 (refs 72,83 ). To corroborate the importance of these residues for SARS-CoV binding to either human or civet ACE2, two SARS-CoV S proteins, hOptimize and cOptimize, were rationally designed: the former contains all of the human ACE2-adapted residues (Phe442, Phe472, Asn479, Asp480 and Thr487), whereas the latter contains the civet ACE2-adapted residues (Tyr442, Pro472, Arg479, Gly480 and Thr487). These two S proteins demonstrate exceptionally high affinity for human ACE2 and civet ACE2, confirming that the human ACE2-adapted and civet ACE2-adapted RBM residues help determine SARS-CoV host range 72,83 . In addition to receptor binding, proteolytic cleavage of S and potentially other mutations that affect virion and trimer stability may also be important for virus transmissibility in different hosts, and these factors need to be studied further.

SARSr-CoV mutations that affect receptor binding

To date, numerous SARSr-CoV strains have been identified from bats 15,16,18,19,20 . These bat SARSr-CoVs are the likely progenitors of SARS-CoV that infected humans and civets, and hence understanding their interactions with human or civet ACE2 is critical for tracing the origins of SARS-CoV and for preventing and controlling future SARS-CoV outbreaks in humans. The RBD sequences of these bat SARSr-CoVs fall into three major groups the representative strains from each group are bHKU3 (isolated in 2005), bWIV1 (isolated in 2013) and bRsSHC014 (isolated in 2013) (Table 1). Strains bWIV1 and bRsSHC014, but not strain bHKU3, use both human and civet ACE2 and hence can infect both human and civet cells 16,18,19,20,86,87 . Strain bHKU3 has a truncated RBM (Table 1), which distorts the structure of the RBM and abolishes its binding to human and civet ACE2. Neither strain bWIV1 nor strain bRsSHC014 contains truncations in its RBM, and hence, their RBMs likely retain the same structure as SARS-CoV RBMs. Here, we analysed the potential interactions between these two strains (bWIV1 and bRsSHC014) and human ACE2 by building homology structural models of their RBDs complexed with human ACE2, focusing on residues 479 and 487 (Fig. 6c, d). Strain bWIV1 contains Asn479 and Asn487 in its RBM. Whereas Asn479 is a viral adaptation to human ACE2, the polar side chain of Asn487 may have unfavourable interactions with the aliphatic portion of residue Lys353 in human ACE2, which is part of hot spot 353 (Fig. 6c). Strain bRsSHC014 contains Arg479 and Ala487 in its RBM. Whereas Arg479 is a viral adaptation to human ACE2, the small side chain of Ala487 does not provide support to the structure of hot spot 353 (Fig. 6d). Therefore, although both bWIV1 and bRsSHC014 can infect human airway cells, they bind human ACE2 less well than hTor02 and produce less severe symptoms than the epidemic strain of SARS-CoV in vivo 88,89 . Similarly, both bWIV1 and bRsSHC014 can infect civet cells, but they bind civet ACE2 less well than cSz02. Thus, it is predicted that both strains will be attenuated compared with early-phase or late-phase human SARS epidemic viruses. Future evolution of bat SARSr-CoV strains bWIV1 and bRsSHC014 in crucial RBM residues may allow them to cross the species barriers between bats, civets and humans, posing potential health threats.


The Evolution of Antifungal Peptides in Drosophila

An essential component of the immune system of animals is the production of antimicrobial peptides (AMPs). In vertebrates and termites the protein sequence of some AMPs evolves rapidly under positive selection, suggesting that they may be coevolving with pathogens. However, antibacterial peptides in Drosophila tend to be highly conserved. We have inferred the selection pressures acting on Drosophila antifungal peptides (drosomycins) from both the divergence of drosomycin genes within and between five species of Drosophila and polymorphism data from Drosophila simulans and D. melanogaster. In common with Drosophila antibacterial peptides, there is no evidence of adaptive protein evolution in any of the drosomycin genes, suggesting that they do not coevolve with pathogens. It is possible that this reflects a lack of specific fungal and bacterial parasites in Drosophila populations. The polymorphism data from both species differed from neutrality at one locus, but this was not associated with changes in the protein sequence. The synonymous site diversity was greater in D. simulans than in D. melanogaster, but the diversity both upstream of the genes and at nonsynonymous sites was similar. This can be explained if both upstream and nonsynonymous mutations are slightly deleterious and are removed more effectively from D. simulans due to its larger effective population size.

GENES involved in host-parasite interactions are often subject to strong balancing or directional selection. For example, parasite antigens commonly evolve rapidly, and natural selection can maintain many different alleles in a population (E scalante et al. 1998). Similarly, vertebrate MHC genes are highly polymorphic and have elevated levels of nonsynonymous substitutions (H ughes and N ei 1988). However, most of our understanding of the molecular evolution of immune systems comes from studies of the acquired immune response of vertebrates. Acquired immune responses detect and eliminate many different parasites by generating a huge repertoire of receptor molecules with different specificities by somatic rearrangement. This type of immune system is a relatively recent evolutionary innovation of vertebrates invertebrates instead rely on an innate immune response for defense against pathogens. The innate immune response also remains an essential component of the vertebrate immune response.

The innate immune response relies on a limited number of germline-encoded receptor and effecter molecules. Despite this, it is still highly effective in defending against a diverse array of pathogens. This is thought to be because parasites are recognized using highly conserved molecular patterns and eliminated using responses that are effective across a broad range of parasite taxa (M edzhitov and J aneway 1997). Presumably these parasite molecules are highly conserved because they are under strong functional constraints, unlike protein antigens that commonly evolve very quickly. Under this scenario, there may be less opportunity for rapid host-parasite coevolution between pathogens and the innate immune system than between pathogens and the acquired immune system.

There is, however, indirect evidence of coevolution between parasites and invertebrate hosts (which possess only innate immune systems). For example, parasites are often adapted to their local host population, as is predicted by most theoretical models of host-parasite coevolution (E bert 1994 M orand et al. 1996 L ively and D ybdahl 2000). However, it is currently unclear whether these patterns result from coevolution between parasites and components of the innate immune system. Alternatively, coevolution could occur between parasites and other host molecules involved in host-parasite interactions (e.g., cell surface molecules exploited by pathogens to enter cells).

If the innate immune system does coevolve with pathogens, then we would expect immune system genes to show patterns of rapid adaptive evolution or elevated polymorphism. This is the case in Drosophila simulans, where a survey of immune system genes showed evidence of stronger directional selection than was the case for nonimmunity genes (S chlenke and B egun 2003). This could be the result of coevolution, but there is currently no evidence of reciprocal changes in parasite genes. Alternatively, directional selection may result from ecological factors that change the type of opportunistic infections acquired by flies or alter the costs of mounting an immune response.

Clues as to how innate immune systems adapt to novel parasites or parasite genotypes can be gained by comparing the lists of genes under directional and purifying selection. For example, peptidoglycan recognition proteins, which include receptors that bind to bacteria leading to the expression of antimicrobial peptides (AMPs), tend to be highly conserved (J iggins and H urst 2003). In contrast, thioester-containing proteins and scavenger receptors, some members of which bind to pathogens and are involved in their subsequent phagocytosis or encapsulation, can be under strong directional selection (L azzaro 2005 L ittle and C obbe 2005).

In this study we have focused on the evolution of AMPs, which are an important component of the innate immune response. Most AMPs are thought to exploit the fact that the outer surface of bacterial membranes contains negatively charged phospholipid headgroups that are absent from animal and plant cells (Z asloff 2002). Because AMPs have an amphipathic structure (separate hydrophobic and hydrophilic domains) they can first carpet and then integrate into the outer layer of the membrane. This then allows them either to disrupt the integrity of the cell membrane (e.g., by lysing the membrane or forming pores) or to enter the cell to disrupt some intracellular target (Z asloff 2002).

In vertebrates, AMPs appear to be a hotspot of rapid adaptive evolution. The most dramatic case is found in frogs, each species of which produces 10� AMPs in their dermal gland secretions. These AMPs differ among closely related species in their size, sequence, and antimicrobial specificity, and this rapid diversification has been driven by diversifying selection (D uda et al. 2002). In various groups of mammals, both α- and β-defensins have diversified under positive selection, and this has led to changes in their antimicrobial specificity (H ughes and Y eager 1997 M orrison et al. 2003 S emple et al. 2003 A ntcheva et al. 2004 L ynn et al. 2004). These patterns strongly suggest that these AMPs are subject to continually changing selection pressures, presumably due a changing pathogen environment. The changing selection pressures may be the result of parasites coevolving with the AMP molecules.

Studies of insect AMPs have produced more varied results. In termites, the antifungal peptide termicin evolves rapidly under positive selection (B ulmer and C rozier 2004). However, several studies of six different families of antibacterial peptides in Drosophila have consistently failed to produce evidence for rapid adaptive evolution of the amino acid sequence (C lark and W ang 1997 R amos -O nsins and A guade 1998 L azzaro and C lark 2003). Although these studies have detected some evidence of positive selection, it is clear that the rate of adaptive protein evolution is dramatically less than that in vertebrates and termites [an exception, andropin, is discussed later (D ate -I to et al. 2002)].

We wanted to test whether this pattern of evolution was general across Drosophila AMPs. Therefore, we have investigated the evolution of the drosomycins, a family of AMPs that are active against fungi rather than against bacteria and that show no homology to previously studied antibacterial peptides. Drosomycin (Drs) strongly inhibits the growth of filamentous fungi, but has no effect on the growth of a range of bacteria (F ehlbaum et al. 1994). This makes it the only purely antifungal peptide characterized in Drosophila. At low concentrations, drosomycin causes the cell cytoplasm to be extruded along the hyphae, suggesting that it lyses cell membranes (F ehlbaum et al. 1994). However, drosomycin's exact mechanism of action is unknown. There are also six drosomycin-like genes in the D. melanogaster genome, all found within a 56-kb region of the left arm of chromosome 3 ( Figure 1 ). Unlike drosomycin itself, the antifungal activity of these genes has not been tested experimentally, although it is known that one of them (Dro5) is upregulated following fungal infection (D e G regorio et al. 2001).


Multiskilled genes

Another reason why apparent adaptations can be side effects of selection for other traits is that genes can have different roles at different times of development or in different parts of the body. So selection for one variant can have all sorts of seemingly unrelated effects. Male homosexuality might be linked to gene variants that increase fertility in females, for instance.

A non-adaptive or detrimental gene variant can also spread rapidly through a population if it is on the same DNA strand as a highly beneficial variant. This is one reason why sex matters&colon when bits of DNA are swapped between chromosomes during sexual reproduction, good and bad variants can be split up.

Other features of plants and animals, such as the wings of ostriches, may once have been adaptations but are no longer needed for their original purpose. Such “vestigial traits” can persist because they are neutral, because they have taken on another function or because there hasn’t been enough evolution to eliminate them even though they have become disadvantageous. Take the appendix. There are plenty of claims that it has this or that function but the evidence is clear&colon you are more likely to survive without an appendix than with one.

So why hasn’t it disappeared? Because evolution is a numbers game. The worldwide human population was tiny until a few thousand years ago, and people have few children with long periods between each generation. That means fewer chances for evolution to throw up mutations that would reduce the size of the appendix or eliminate it altogether – and fewer chances for those mutations to spread through populations by natural selection. Another possibility is that we are stuck in an evolutionary Catch-22 where, as the appendix shrinks, appendicitis becomes more likely, favouring its retention.

Wisdom teeth are another vestigial remnant. A smaller, weaker jaw allowed our ancestors to grow larger brains, but left less room for molars. Yet many of us still grow teeth for which there is no room, with potentially fatal consequences. One possible reason why wisdom teeth persist is that they usually appear after people reach reproductive age, meaning selection against them is weak.

For all these reasons and more, we need to be sceptical of headline-grabbing claims about evolutionary explanations for different behaviours. Evolutionary psychology in particular is notorious for attempting to explain every aspect of behaviour, from gardening to rape, as an adaptation that arose when our ancestors lived on the African savannah.

Needless to say, without solid evidence, claims about how, for instance, TV dinners “evolved” should be taken with a large pinch of salt.


Watch the video: Evolution u0026 Classification of Life. Single Celled Bacteria to Humans (January 2023).