{"id":1071,"date":"2016-12-02T21:30:35","date_gmt":"2016-12-02T21:30:35","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/wm-biology2\/?post_type=chapter&#038;p=1071"},"modified":"2024-04-25T17:53:23","modified_gmt":"2024-04-25T17:53:23","slug":"phylogenetic-trees","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/wm-biology2\/chapter\/phylogenetic-trees\/","title":{"raw":"Phylogenetic Trees","rendered":"Phylogenetic Trees"},"content":{"raw":"<div class=\"textbox learning-objectives\">\r\n<h3>Learning Outcomes<\/h3>\r\n<ul>\r\n \t<li>Explain the purpose of phylogenetic trees<\/li>\r\n<\/ul>\r\n<\/div>\r\nIn scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. <strong>Phylogeny<\/strong> describes the relationships of one organism to others\u2014such as which organisms it is thought to have evolved from, which species it is most closely related to, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.\r\n\r\nScientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A\u00a0<strong>phylogenetic tree<\/strong> is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a \u201ctree of life\u201d can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure\u00a01).\r\n\r\n[caption id=\"attachment_1482\" align=\"aligncenter\" width=\"1024\"]<img class=\"wp-image-1482 size-large\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/110\/2016\/05\/02192630\/Figure_20_01_01-1024x308.jpg\" alt=\"The phylogenetic tree in part a is rooted and resembles a living tree, with a common ancestor indicated as the base of the trunk. Two branches form from the trunk. The left branch leads to the domain Bacteria. The right branch branches again, giving rise to Archaea and Eukarya. Smaller branches within each domain indicate the groups present in that domain. The phylogenetic tree in part B is unrooted. It does not resemble a living tree; rather, groups of organisms within the Archaea, Eukarya, and Bacteria domains are arranged in a circle. Lines connect the groups within each domain. The groups within Archaea and Eukarya are then connected together. A line from the Archaea\/ Eukarya domains, and another from the Bacteria meet in the center of the circle. There is no root, and therefore no indication of which domain arose first.\" width=\"1024\" height=\"308\" \/> Figure\u00a01. Both of these phylogenetic trees shows the relationship of the three domains of life\u2014Bacteria, Archaea, and Eukarya\u2014but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba)[\/caption]\r\n\r\nA\u00a0phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains\u2014Bacteria, Archaea, and Eukarya\u2014diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and minuscule these groups are compared with other organisms. Unrooted trees don\u2019t show a common ancestor but do show relationships among species.\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Carl Woese and the Phylogenetic Tree<\/h3>\r\nIn the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The organizational scheme was based mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which are used by modern systematics. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains\u2014Bacteria, Archaea, and Eukarya. The first two are prokaryotic groups of\u00a0microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms together with the four original kingdoms (excluding bacteria). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (Figure\u00a01a). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape).\r\n\r\nWoese's tree was constructed from comparative sequencing of the genes that are universally distributed, present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese's approach was revolutionary because comparisons of physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (Figure\u00a02). The comparison of homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified the separation of the prokaryotes into two domains: bacteria and archaea.\r\n\r\n[caption id=\"attachment_1521\" align=\"aligncenter\" width=\"990\"]<img class=\"size-large wp-image-1521\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/110\/2016\/05\/02202719\/Figure_01_02_17abcd-990x1024.png\" alt=\"Photo depict: A: bacterial cells. Photo depict: B: a natural hot vent. Photo depict: C: a sunflower. Photo depict: D: a lion.\" width=\"990\" height=\"1024\" \/> Figure\u00a02. These organisms\u00a0represent different domains. The (a) bacteria in this micrograph belong to Domain Bacteria, while the (b) extremophiles (not visible) living in this hot vent belong to Domain Archaea. Both the (c) sunflower and (d) lion are part of Domain Eukarya. (credit a: modification of work by Drew March; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Leszek Leszcynski)[\/caption]\r\n\r\n<\/div>\r\n<div class=\"textbox tryit\">\r\n<h3>Try It<\/h3>\r\nhttps:\/\/assess.lumenlearning.com\/practice\/341237c1-8a92-41cd-b73b-891e5aca2d9a\r\n<\/div>","rendered":"<div class=\"textbox learning-objectives\">\n<h3>Learning Outcomes<\/h3>\n<ul>\n<li>Explain the purpose of phylogenetic trees<\/li>\n<\/ul>\n<\/div>\n<p>In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. <strong>Phylogeny<\/strong> describes the relationships of one organism to others\u2014such as which organisms it is thought to have evolved from, which species it is most closely related to, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.<\/p>\n<p>Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A\u00a0<strong>phylogenetic tree<\/strong> is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a \u201ctree of life\u201d can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure\u00a01).<\/p>\n<div id=\"attachment_1482\" style=\"width: 1034px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1482\" class=\"wp-image-1482 size-large\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/110\/2016\/05\/02192630\/Figure_20_01_01-1024x308.jpg\" alt=\"The phylogenetic tree in part a is rooted and resembles a living tree, with a common ancestor indicated as the base of the trunk. Two branches form from the trunk. The left branch leads to the domain Bacteria. The right branch branches again, giving rise to Archaea and Eukarya. Smaller branches within each domain indicate the groups present in that domain. The phylogenetic tree in part B is unrooted. It does not resemble a living tree; rather, groups of organisms within the Archaea, Eukarya, and Bacteria domains are arranged in a circle. Lines connect the groups within each domain. The groups within Archaea and Eukarya are then connected together. A line from the Archaea\/ Eukarya domains, and another from the Bacteria meet in the center of the circle. There is no root, and therefore no indication of which domain arose first.\" width=\"1024\" height=\"308\" \/><\/p>\n<p id=\"caption-attachment-1482\" class=\"wp-caption-text\">Figure\u00a01. Both of these phylogenetic trees shows the relationship of the three domains of life\u2014Bacteria, Archaea, and Eukarya\u2014but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba)<\/p>\n<\/div>\n<p>A\u00a0phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains\u2014Bacteria, Archaea, and Eukarya\u2014diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and minuscule these groups are compared with other organisms. Unrooted trees don\u2019t show a common ancestor but do show relationships among species.<\/p>\n<div class=\"textbox key-takeaways\">\n<h3>Carl Woese and the Phylogenetic Tree<\/h3>\n<p>In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The organizational scheme was based mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which are used by modern systematics. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains\u2014Bacteria, Archaea, and Eukarya. The first two are prokaryotic groups of\u00a0microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms together with the four original kingdoms (excluding bacteria). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (Figure\u00a01a). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape).<\/p>\n<p>Woese&#8217;s tree was constructed from comparative sequencing of the genes that are universally distributed, present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese&#8217;s approach was revolutionary because comparisons of physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (Figure\u00a02). The comparison of homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified the separation of the prokaryotes into two domains: bacteria and archaea.<\/p>\n<div id=\"attachment_1521\" style=\"width: 1000px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1521\" class=\"size-large wp-image-1521\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/110\/2016\/05\/02202719\/Figure_01_02_17abcd-990x1024.png\" alt=\"Photo depict: A: bacterial cells. Photo depict: B: a natural hot vent. Photo depict: C: a sunflower. Photo depict: D: a lion.\" width=\"990\" height=\"1024\" \/><\/p>\n<p id=\"caption-attachment-1521\" class=\"wp-caption-text\">Figure\u00a02. These organisms\u00a0represent different domains. The (a) bacteria in this micrograph belong to Domain Bacteria, while the (b) extremophiles (not visible) living in this hot vent belong to Domain Archaea. Both the (c) sunflower and (d) lion are part of Domain Eukarya. (credit a: modification of work by Drew March; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Leszek Leszcynski)<\/p>\n<\/div>\n<\/div>\n<div class=\"textbox tryit\">\n<h3>Try It<\/h3>\n<p>\t<iframe id=\"assessment_practice_341237c1-8a92-41cd-b73b-891e5aca2d9a\" class=\"resizable\" src=\"https:\/\/assess.lumenlearning.com\/practice\/341237c1-8a92-41cd-b73b-891e5aca2d9a?iframe_resize_id=assessment_practice_id_341237c1-8a92-41cd-b73b-891e5aca2d9a\" frameborder=\"0\" style=\"border:none;width:100%;height:100%;min-height:300px;\"><br \/>\n\t<\/iframe>\n<\/div>\n\n\t\t\t <section class=\"citations-section\" role=\"contentinfo\">\n\t\t\t <h3>Candela Citations<\/h3>\n\t\t\t\t\t <div>\n\t\t\t\t\t\t <div id=\"citation-list-1071\">\n\t\t\t\t\t\t\t <div class=\"licensing\"><div class=\"license-attribution-dropdown-subheading\">CC licensed content, Shared previously<\/div><ul class=\"citation-list\"><li>Biology 2e. <strong>Provided by<\/strong>: OpenStax. <strong>Located at<\/strong>: <a target=\"_blank\" href=\"http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8\">http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8<\/a>. <strong>License<\/strong>: <em><a target=\"_blank\" rel=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\">CC BY: Attribution<\/a><\/em>. <strong>License Terms<\/strong>: Access for free at https:\/\/openstax.org\/books\/biology-2e\/pages\/1-introduction<\/li><\/ul><\/div>\n\t\t\t\t\t\t <\/div>\n\t\t\t\t\t <\/div>\n\t\t\t <\/section>","protected":false},"author":17,"menu_order":9,"template":"","meta":{"_candela_citation":"[{\"type\":\"cc\",\"description\":\"Biology 2e\",\"author\":\"\",\"organization\":\"OpenStax\",\"url\":\"http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8\",\"project\":\"\",\"license\":\"cc-by\",\"license_terms\":\"Access for free at https:\/\/openstax.org\/books\/biology-2e\/pages\/1-introduction\"}]","CANDELA_OUTCOMES_GUID":"587cb8be-737c-484b-8f10-a678d310c4dc, 2c80d138-783d-4e4e-a367-10192d704df5","pb_show_title":"on","pb_short_title":"","pb_subtitle":"","pb_authors":[],"pb_section_license":""},"chapter-type":[],"contributor":[],"license":[],"class_list":["post-1071","chapter","type-chapter","status-publish","hentry"],"part":1054,"_links":{"self":[{"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/pressbooks\/v2\/chapters\/1071","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/pressbooks\/v2\/chapters"}],"about":[{"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/wp\/v2\/types\/chapter"}],"author":[{"embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/wp\/v2\/users\/17"}],"version-history":[{"count":9,"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/pressbooks\/v2\/chapters\/1071\/revisions"}],"predecessor-version":[{"id":8246,"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/pressbooks\/v2\/chapters\/1071\/revisions\/8246"}],"part":[{"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/pressbooks\/v2\/parts\/1054"}],"metadata":[{"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/pressbooks\/v2\/chapters\/1071\/metadata\/"}],"wp:attachment":[{"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/wp\/v2\/media?parent=1071"}],"wp:term":[{"taxonomy":"chapter-type","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/pressbooks\/v2\/chapter-type?post=1071"},{"taxonomy":"contributor","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/wp\/v2\/contributor?post=1071"},{"taxonomy":"license","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/wm-biology2\/wp-json\/wp\/v2\/license?post=1071"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}