Perspectives on the Phylogenetic Tree Quiz

PDF page 837: Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonally. That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science. This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species. The concept of genes being transferred between unrelated species was not considered as a possibility until relatively recently. Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. HGT has been shown to be an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships. The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence.

PDF page 854: b. the transmission of genetic material from one

PDF page 836: The concepts of phylogenetic modeling are constantly changing. It is one of the most dynamic fields of study in all of biology. Over the last several decades, new research has challenged scientists’ ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community. Many phylogenetic trees have been shown as models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 (Figure 20.12a), which served as a pattern for subsequent studies for more than a century. The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak (Figure 20.12b). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the validity of the standard tree model in the scientific community.

PDF page 837: Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process. Some researchers believe such estimates are premature: the actual importance of HGT to evolutionary processes must be viewed as a work in progress. As the phenomenon is investigated more thoroughly, it may be revealed to be more common. Many scientists believe that HGT and mutation appear to be (especially in prokaryotes) a significant source of genetic variation, which is the raw material for the process of natural selection. These transfers may occur between any two species that share an intimate relationship (Table 20.1).

PDF page 837: Mechanism Mode of Transmission Example Prokaryotes transformation DNA uptake many prokaryotes transduction bacteriophage (virus) bacteria conjugation pilus many prokaryotes

PDF page 837: Mechanism Mode of Transmission Example Prokaryotes transformation DNA uptake many prokaryotes transduction bacteriophage (virus) bacteria conjugation pilus many prokaryotes

PDF page 838: More recently, a fourth mechanism of gene transfer between prokaryotes has been discovered. Small, virus-like particles called gene transfer agents (GTAs) transfer random genomic segments from one species of prokaryote to another. GTAs have been shown to be responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. The first GTA was characterized in 1974 using purple, non-sulfur bacteria. These GTAs, which are thought to be bacteriophages that lost the ability to reproduce on their own, carry random pieces of DNA from one organism to another. The ability of GTAs to act with high frequency has been demonstrated in controlled studies using marine bacteria. Gene

PDF page 845: analogy (also, homoplasy) characteristic that is similar between organisms by convergent evolution, not due to the same evolutionary path basal taxon branch on a phylogenetic tree that has not diverged significantly from the root ancestor binomial nomenclature system of two-part scientific names for an organism, which includes genus and species names branch point node on a phylogenetic tree where a single lineage splits into distinct new ones cladistics system used to organize homologous traits to describe phylogenies cladograms visual representations of evolutionary relationships between organisms class division of phylum in the taxonomic classification system eukaryote-first hypothesis proposal that prokaryotes evolved from eukaryotes family division of order in the taxonomic classification system gene transfer agent (GTA) bacteriophage-like particle that transfers random genomic segments from one species of prokaryote to another genome fusion fusion of two prokaryotic genomes, presumably by endosymbiosis genus division of family in the taxonomic classification system; the first part of the binomial scientific name horizontal gene transfer (HGT) (also, lateral gene transfer) transfer of genes between unrelated species kingdom division of domain in the taxonomic classification system maximum parsimony applying the simplest, most obvious way with the least number of steps mitochondria-first hypothesis proposal that prokaryotes acquired a mitochondrion first, followed by nuclear development molecular systematics technique using molecular evidence to identify phylogenetic relationships monophyletic group (also, clade) organisms that share a single ancestor nucleus-first hypothesis proposal that prokaryotes acquired a nucleus first, and then the mitochondrion order division of class in the taxonomic classification system parsimony the simplest, most straightforward way of constructing phylogenetic and evolutionary relationships between organisms

PDF page 839: to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been further shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color (Figure 20.13).

PDF page 839: to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been further shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color (Figure 20.13).

PDF page 838: HGT in Prokaryotes The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed. The majority of evolutionary models, such as in the Endosymbiont Theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species. The fact that genes are transferred among common bacteria is well known to microbiology students. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer has been thought to occur by three different mechanisms:

PDF page 840: Barbara McClintock (1902–1992) discovered transposons while working on maize genetics.

PDF page 841: The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first (Figure 20.16a), followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis proposes that mitochondria were first established in a prokaryotic host (Figure 20.16b), which subsequently acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity (Figure 20.16c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.

PDF page 845: analogy (also, homoplasy) characteristic that is similar between organisms by convergent evolution, not due to the same evolutionary path basal taxon branch on a phylogenetic tree that has not diverged significantly from the root ancestor binomial nomenclature system of two-part scientific names for an organism, which includes genus and species names branch point node on a phylogenetic tree where a single lineage splits into distinct new ones cladistics system used to organize homologous traits to describe phylogenies cladograms visual representations of evolutionary relationships between organisms class division of phylum in the taxonomic classification system eukaryote-first hypothesis proposal that prokaryotes evolved from eukaryotes family division of order in the taxonomic classification system gene transfer agent (GTA) bacteriophage-like particle that transfers random genomic segments from one species of prokaryote to another genome fusion fusion of two prokaryotic genomes, presumably by endosymbiosis genus division of family in the taxonomic classification system; the first part of the binomial scientific name horizontal gene transfer (HGT) (also, lateral gene transfer) transfer of genes between unrelated species kingdom division of domain in the taxonomic classification system maximum parsimony applying the simplest, most obvious way with the least number of steps mitochondria-first hypothesis proposal that prokaryotes acquired a mitochondrion first, followed by nuclear development molecular systematics technique using molecular evidence to identify phylogenetic relationships monophyletic group (also, clade) organisms that share a single ancestor nucleus-first hypothesis proposal that prokaryotes acquired a nucleus first, and then the mitochondrion order division of class in the taxonomic classification system parsimony the simplest, most straightforward way of constructing phylogenetic and evolutionary relationships between organisms

PDF page 840: Scientists believe the ultimate in HGT occurs through genome fusion between different species of prokaryotes when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside the cytoplasm of another species, which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which is accepted by a majority of biologists as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in the development of the nucleus is more controversial. Nuclear and mitochondrial DNA are thought to be of different (separate) evolutionary origin, with the mitochondrial DNA being derived from the circular genomes of bacteria that were engulfed by ancient prokaryotic cells. Mitochondrial DNA can be regarded as the smallest chromosome. Interestingly enough, mitochondrial DNA is inherited only from the mother. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the flagellum of the sperm fails to enter the egg. Within the past decade, the process of genome fusion by endosymbiosis has been proposed by James Lake of the UCLA/ NASA Astrobiology Institute to be responsible for the evolution of the first eukaryotic cells (Figure 20.15a). Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), his laboratory proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species, one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea, whereas others resemble those from Bacteria. An endosymbiotic fusion event, such as Lake has proposed, would clearly explain this observation. On the other hand, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis. More recent work by Lake (Figure 20.15b) proposes that gram-negative bacteria, which are unique within their domain