Phylogenies by Owen Borville September 24, 2024
In biology, proponents of the theory of evolution describe the concept of phylogeny as the evolutionary history and relationship of an organism or group of organisms. There is a creationist version, however the creationist version of phylogenies do not branch into different kinds.
In other words, all species within a kind stay in the kind group. Evolutionists link species between kinds to show a linkage over supposed long periods of time in the millions of years. Creationist phylogenies look more like forks, while ev0lutionist phylogenies look more like trees or tree branches.
A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Again, the evolutionist versions of phylogenetic trees look like trees or tree branches, while the creationist versions look more like forks.
Phylogenetic trees with a single lineage at the base representing a common ancestor are called rooted. Unrooted trees do not show a common ancestor, but show common relationships among species. In a rooted tree, the branching indicates evolutionary relationships, and the branch point, where a split occurs, represents a single lineage evolving into a distinct new one.
Lineage that evolved early from the root that remains unbranched a basal taxon. Two lineages stemming from the same branch point sister taxa. A branch with more than two lineages is a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships.
Systematics is the field that scientists use to organize and classify organisms based on evolutionary relationships. Data from fossils, from studying the body part structures, or molecules that an organism uses, and DNA analysis are used to construct phylogenetic trees.
However, there are still many assumptions made that have not been verified about the evolutionary relationships between species where a common ancestor cannot be identified, in addition to the time frame between each relationship. Therefore, phylogenetic trees can be more hypothetical than confirmed.
Classification levels in biology are determined by the field of taxonomy, which is is the science of classifying organisms to construct internationally shared classification systems with each organism placed into increasingly more inclusive groupings.
The taxonomic classification system used in biology was developed by Carl Linnaeus, a Swedish scientist, using a hierarchical model where groups in the classification become more specific, until one branch ends as a single species.
In the Linnaean system, classification begins with domains, such as Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species.
Kingdoms include: Animalia, Plantae, Fungi, Protista, Archaea/Archaebacteria, and Bacteria or Eubacteria. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, or binomial nomenclature. Therefore, the scientific name of the dog, for example, is Canis lupus. The name at each level is also a taxon.
Homologous structures are features of organisms that overlap in morphology and genetically, such as the bones in bird and bat wings. Homologous structures share similar embryonic origin. An analogy or homoplasy is when features on two different organisms appear similar, such as wings of insects compared to wings of bats and birds.
Molecular systematics is a field of biology that studies the evolutionary relationships in taxonomy and biogeography between organisms by analyzing their DNA and RNA. Molecular systematics is also known as computational systematics, molecular genetics, or molecular evolution that help confirm classification taxonomy and identify errors.
Building Phylogenetic Trees Phylogenetic trees are built by sorting homologous and analogous traits. The homologous traits are organized by using cladistics, or hypothesizing relationships among organisms according to common traits. These organisms are sorted into clades, or organisms that descend from a common ancestor (and a single point on the phylogenetic tree). A single clade is a monophyletic group that has a common ancestor and all of its descendants.
Shared Characteristics Pattern of Classification of Organisms Cycle: 1 A change in an organism's genetic makeup leads to a new trait which becomes prevalent in the group. 2 Many organisms descend from this point and have this trait. 3 New variations continue to arise: some are adaptive and persist, leading to new traits. 4 With new traits, a new branch point is determined.
A shared ancestral character is when a characteristic is found in the ancestor of a group because all of the organisms in the taxon or clade have that trait. A shared derived character, however, is a trait derived at some point but is not included in all of the ancestors in the tree.
Maximum parsimony is the concept that phylogenetic trees likely occurred in the simplest or most obvious way. This concept is used to construct phylogenetic trees.
Charles Darwin sketched the first phylogenetic tree in 1837. However, evidence from modern DNA sequencing has caused skepticism about the validity about the standard classic phylogenetic tree model and limitations of this model have been discovered.
Horizontal gene transfer (HGT), or lateral gene transfer, is the transfer of genes between unrelated species. HGT is a concept that was not considered until recently, but HGT exists and makes phylogenetic trees more complicated. HGT is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parents to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes.
Many scientists believe that HGT and mutations are a significant source of genetic variation, which causes natural selection. HGT can occur between any two species that share an intimate relationship.
HGT in Prokaryotes is believed to be caused by these mechanisms: 1 transformation, where bacteria takes up naked DNA; 2 transduction, where a virus transfers the genes; 3 conjugation, where a hollow tube, or pilus transfers genes between organisms; 4 gene transfer agents (GTA), where small, virus-like particles transfer random genomic segments from one prokaryote species to another.
HGT in Eukaryotes was once thought to not exist, but was discovered later. HGT in eukaryotes is less evident and more difficult to observe. HGT has been observed in plants that cannot cross-pollinate like other plants. Scientists have claimed to observe HGT in aphids, as they have been observed to change color when ingesting fungi containing carotenoids that change their color from green to red-orange.
Genome fusion is a type of horizontal gene transfer (HGT) that occurs when two symbiotic organisms become endosymbiotic, and one species is taken inside another's cytoplasm, or one species lives inside another species, resulting in a genome that contains genes from both organisms. This process is considered to be the ultimate in HGT. Evolutionists believe that genome fusion is the mechanism of evolution of the first eukaryotic cells.
The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first, 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, which then acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell.
The eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity.
Some scientists propose discarding phylogenetic tree model because of HGT. Other scientists have proposed a phylogenetic model that resembles a web or a network in order to showcase the many species sharing genes by HGT mechanisms. Other scientists use phylogenetic trees and include horizontal gene transfer relationships on the chart.
The ring of life model is a phylogenetic model used by some scientists that proposes that all three domains of life (Archaea, Bacteria, and Eukarya) evolved from a single pool of primitive prokaryotes shown in the center of the ring. This model challenges the traditional tree of life model and is based on the idea that the evolution of life includes both Darwinian survival of the fittest and symbiotic cooperation.
All of these phylogenetic models of life (tree, web, ring) are methods used by proponents of evolution theory to explain the evolution of life and these models continue to be under development.
In biology, proponents of the theory of evolution describe the concept of phylogeny as the evolutionary history and relationship of an organism or group of organisms. There is a creationist version, however the creationist version of phylogenies do not branch into different kinds.
In other words, all species within a kind stay in the kind group. Evolutionists link species between kinds to show a linkage over supposed long periods of time in the millions of years. Creationist phylogenies look more like forks, while ev0lutionist phylogenies look more like trees or tree branches.
A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Again, the evolutionist versions of phylogenetic trees look like trees or tree branches, while the creationist versions look more like forks.
Phylogenetic trees with a single lineage at the base representing a common ancestor are called rooted. Unrooted trees do not show a common ancestor, but show common relationships among species. In a rooted tree, the branching indicates evolutionary relationships, and the branch point, where a split occurs, represents a single lineage evolving into a distinct new one.
Lineage that evolved early from the root that remains unbranched a basal taxon. Two lineages stemming from the same branch point sister taxa. A branch with more than two lineages is a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships.
Systematics is the field that scientists use to organize and classify organisms based on evolutionary relationships. Data from fossils, from studying the body part structures, or molecules that an organism uses, and DNA analysis are used to construct phylogenetic trees.
However, there are still many assumptions made that have not been verified about the evolutionary relationships between species where a common ancestor cannot be identified, in addition to the time frame between each relationship. Therefore, phylogenetic trees can be more hypothetical than confirmed.
Classification levels in biology are determined by the field of taxonomy, which is is the science of classifying organisms to construct internationally shared classification systems with each organism placed into increasingly more inclusive groupings.
The taxonomic classification system used in biology was developed by Carl Linnaeus, a Swedish scientist, using a hierarchical model where groups in the classification become more specific, until one branch ends as a single species.
In the Linnaean system, classification begins with domains, such as Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species.
Kingdoms include: Animalia, Plantae, Fungi, Protista, Archaea/Archaebacteria, and Bacteria or Eubacteria. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, or binomial nomenclature. Therefore, the scientific name of the dog, for example, is Canis lupus. The name at each level is also a taxon.
Homologous structures are features of organisms that overlap in morphology and genetically, such as the bones in bird and bat wings. Homologous structures share similar embryonic origin. An analogy or homoplasy is when features on two different organisms appear similar, such as wings of insects compared to wings of bats and birds.
Molecular systematics is a field of biology that studies the evolutionary relationships in taxonomy and biogeography between organisms by analyzing their DNA and RNA. Molecular systematics is also known as computational systematics, molecular genetics, or molecular evolution that help confirm classification taxonomy and identify errors.
Building Phylogenetic Trees Phylogenetic trees are built by sorting homologous and analogous traits. The homologous traits are organized by using cladistics, or hypothesizing relationships among organisms according to common traits. These organisms are sorted into clades, or organisms that descend from a common ancestor (and a single point on the phylogenetic tree). A single clade is a monophyletic group that has a common ancestor and all of its descendants.
Shared Characteristics Pattern of Classification of Organisms Cycle: 1 A change in an organism's genetic makeup leads to a new trait which becomes prevalent in the group. 2 Many organisms descend from this point and have this trait. 3 New variations continue to arise: some are adaptive and persist, leading to new traits. 4 With new traits, a new branch point is determined.
A shared ancestral character is when a characteristic is found in the ancestor of a group because all of the organisms in the taxon or clade have that trait. A shared derived character, however, is a trait derived at some point but is not included in all of the ancestors in the tree.
Maximum parsimony is the concept that phylogenetic trees likely occurred in the simplest or most obvious way. This concept is used to construct phylogenetic trees.
Charles Darwin sketched the first phylogenetic tree in 1837. However, evidence from modern DNA sequencing has caused skepticism about the validity about the standard classic phylogenetic tree model and limitations of this model have been discovered.
Horizontal gene transfer (HGT), or lateral gene transfer, is the transfer of genes between unrelated species. HGT is a concept that was not considered until recently, but HGT exists and makes phylogenetic trees more complicated. HGT is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parents to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes.
Many scientists believe that HGT and mutations are a significant source of genetic variation, which causes natural selection. HGT can occur between any two species that share an intimate relationship.
HGT in Prokaryotes is believed to be caused by these mechanisms: 1 transformation, where bacteria takes up naked DNA; 2 transduction, where a virus transfers the genes; 3 conjugation, where a hollow tube, or pilus transfers genes between organisms; 4 gene transfer agents (GTA), where small, virus-like particles transfer random genomic segments from one prokaryote species to another.
HGT in Eukaryotes was once thought to not exist, but was discovered later. HGT in eukaryotes is less evident and more difficult to observe. HGT has been observed in plants that cannot cross-pollinate like other plants. Scientists have claimed to observe HGT in aphids, as they have been observed to change color when ingesting fungi containing carotenoids that change their color from green to red-orange.
Genome fusion is a type of horizontal gene transfer (HGT) that occurs when two symbiotic organisms become endosymbiotic, and one species is taken inside another's cytoplasm, or one species lives inside another species, resulting in a genome that contains genes from both organisms. This process is considered to be the ultimate in HGT. Evolutionists believe that genome fusion is the mechanism of evolution of the first eukaryotic cells.
The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first, 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, which then acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell.
The eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity.
Some scientists propose discarding phylogenetic tree model because of HGT. Other scientists have proposed a phylogenetic model that resembles a web or a network in order to showcase the many species sharing genes by HGT mechanisms. Other scientists use phylogenetic trees and include horizontal gene transfer relationships on the chart.
The ring of life model is a phylogenetic model used by some scientists that proposes that all three domains of life (Archaea, Bacteria, and Eukarya) evolved from a single pool of primitive prokaryotes shown in the center of the ring. This model challenges the traditional tree of life model and is based on the idea that the evolution of life includes both Darwinian survival of the fittest and symbiotic cooperation.
All of these phylogenetic models of life (tree, web, ring) are methods used by proponents of evolution theory to explain the evolution of life and these models continue to be under development.