errata 25300

modules/m45419/index.cnxml

@@ -104,7 +104,7 @@ The diversity of life on Earth is a result of mutations, or random changes in he
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                 <caption>These images represent different domains. The scanning electron micrograph shows (a) bacterial cells belong to the domain Bacteria, while the (b) extremophiles, seen all together as colored mats in this hot spring, belong to domain Archaea. Both the (c) sunflower and (d) lion are part of domain Eukarya. (credit a: modification of work by Rocky Mountain Laboratories, NIAID, NIH; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Frank Vassen)</caption></figure><note id="fs-idm108538560" class="evolution non-majors"><title>Carl Woese and the Phylogenetic Tree</title>
             <para id="fs-idm10904720">The evolutionary relationships of various life forms on Earth can be summarized in a phylogenetic tree. A <term id="term-00019">phylogenetic tree</term> is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of branch points, or nodes, and branches. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch can be considered as estimates of relative time.</para>
-    <para id="fs-idm71571824">In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. 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—Bacteria, Archaea, and Eukarya. Woese proposed the domain as a new taxonomic level and Archaea as a new domain, to reflect the new phylogenetic tree (<link target-id="fig-ch01_01_10"/>). 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). Various genes were used in phylogenetic studies. Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, found in some slightly altered form in every organism, conserved (meaning that these genes have remained only slightly changed throughout evolution), and of an appropriate length.</para>
+    <para id="fs-idm71571824">In the past, biologists grouped living organisms into six kingdoms—animalia, plantae, fungi, protista, archea, and bacteria. 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—Bacteria, Archaea, and Eukarya. Woese proposed the domain as a new taxonomic level and Archaea as a new domain, to reflect the new phylogenetic tree (<link target-id="fig-ch01_01_10"/>). 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). Various genes were used in phylogenetic studies. Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, found in some slightly altered form in every organism, conserved (meaning that these genes have remained only slightly changed throughout evolution), and of an appropriate length.</para>
             <figure id="fig-ch01_01_10"><media id="fs-idm169160320" alt="This phylogenetic tree shows that the three domains of life, bacteria, archaea and eukarya, all arose from a common ancestor.">
                     <image mime-type="image/jpg" src="../../media/Figure_01_01_10.jpg" width="500"/>
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modules/m45511/index.cnxml

@@ -12,6 +12,6 @@
 <figure id="fig-ch13_00_01" class="splash"><media id="fs-idm92564624" alt="A photo collage of images from the chapter. Clockwise from top left are: ringworm in skin; trypanosomes (pink ribbon-like parasites) in a smear of blood viewed under a light microscope; an electron micrograph of tree mold, showing a long, slender stalk that branches into long chains of spores that look like a string of beads; a wedge of cheese; a scanning electron micrograph of MRSA bacteria, which looks like clusters of spheres clinging to a surface; grapes with white and brown fungus; pale pink, cup-shaped fungi growing on a log; a scanning electron micrograph of corkscrew-shaped bacterium; coral fungus, a yellowish-orange fungus that grows in a cluster and is lobe-shaped.">
         <image mime-type="image/jpeg" src="../../media/Figure_13_00_01-7708.jpg" width="500"/>
         </media>
-<caption>Living things are very diverse, from simple, single-celled bacteria to complex, multicellular organisms. (credit "ringworm": modification of work by Dr. Lucille K. Georg, CDC; credit "Trypanosomes": modification of work by Dr. Myron G. Schultz, CDC; credit “tree mold”: modification of work by Janice Haney Carr, Robert Simmons, CDC; credit "coral fungus": modification of work by Cory Zanker; credit "bacterium": modification of work by Dr. David Cox, CDC; credit "cup fungus": modification of work by "icelight"/Flickr; credit "MRSA": modification of work by Janice Haney Carr, CDC; credit "moldy grapefruit": modification of work by Joseph Smilanick)</caption></figure><para id="fs-idm6124544">Until the late twentieth century, scientists most commonly grouped living things into five kingdoms—animals, plants, fungi, protists, and bacteria—based on several criteria, such as absence or presence of a nucleus and other membrane-bound organelles, absence or presence of cell walls, multicellularity, and mode of nutrition. In the late twentieth century, the pioneering work of Carl Woese and others compared nucleotide sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a dramatically different way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The three domains are called Bacteria, Archaea, and Eukarya.</para><para id="fs-idm18202112">Two of the three domains—Bacteria and Archaea—are prokaryotic, meaning that they lack both a nucleus and true membrane-bound organelles. However, they are now considered, on the basis of membrane structure and rRNA, to be as different from each other as they are from the third domain, the Eukarya. Prokaryotes were the first inhabitants on Earth, perhaps appearing approximately 3.9 billion years ago. Today they are ubiquitous—inhabiting the harshest environments on the planet, from boiling hot springs to permanently frozen environments in Antarctica, as well as more benign environments such as compost heaps, soils, ocean waters, and the guts of animals (including humans). The Eukarya include the familiar kingdoms of animals, plants, and fungi. They also include a diverse group of kingdoms formerly grouped together as protists.</para>
+<caption>Living things are very diverse, from simple, single-celled bacteria to complex, multicellular organisms. (credit "ringworm": modification of work by Dr. Lucille K. Georg, CDC; credit "Trypanosomes": modification of work by Dr. Myron G. Schultz, CDC; credit “tree mold”: modification of work by Janice Haney Carr, Robert Simmons, CDC; credit "coral fungus": modification of work by Cory Zanker; credit "bacterium": modification of work by Dr. David Cox, CDC; credit "cup fungus": modification of work by "icelight"/Flickr; credit "MRSA": modification of work by Janice Haney Carr, CDC; credit "moldy grapefruit": modification of work by Joseph Smilanick)</caption></figure><para id="fs-idm6124544">Until the late twentieth century, scientists most commonly grouped living things into six kingdoms—animalia, plantae, fungi, protista, archea, and bacteria—based on several criteria, such as absence or presence of a nucleus and other membrane-bound organelles, absence or presence of cell walls, multicellularity, and mode of nutrition. In the late twentieth century, the pioneering work of Carl Woese and others compared nucleotide sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a dramatically different way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The three domains are called Bacteria, Archaea, and Eukarya.</para><para id="fs-idm18202112">Two of the three domains—Bacteria and Archaea—are prokaryotic, meaning that they lack both a nucleus and true membrane-bound organelles. However, they are now considered, on the basis of membrane structure and rRNA, to be as different from each other as they are from the third domain, the Eukarya. Prokaryotes were the first inhabitants on Earth, perhaps appearing approximately 3.9 billion years ago. Today they are ubiquitous—inhabiting the harshest environments on the planet, from boiling hot springs to permanently frozen environments in Antarctica, as well as more benign environments such as compost heaps, soils, ocean waters, and the guts of animals (including humans). The Eukarya include the familiar kingdoms of animals, plants, and fungi. They also include a diverse group of kingdoms formerly grouped together as protists.</para>
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modules/m62718/index.cnxml

@@ -212,7 +212,7 @@ The diversity of life on Earth is a result of mutations, or random changes in he
 <caption>This phylogenetic tree was constructed by microbiologist Carl Woese using data obtained from sequencing ribosomal RNA genes. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are prokaryotes, single-celled organisms lacking intracellular organelles. (credit: Eric Gaba; NASA Astrobiology Institute)
 </caption></figure><note id="fs-id2581806" class="evolution ost-assessed-feature"><title>Carl Woese and the Phylogenetic Tree</title>
 
-    <para id="fs-id2024686">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—Bacteria, Archaea, and Eukarya. The first two are prokaryotic cells with microbes 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 (<link target-id="fs-id1167066867652" class="has-default-text">see this figure</link>). 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).</para>
+    <para id="fs-id2024686">In the past, biologists grouped living organisms into six kingdoms—animalia, plantae, fungi, protista, archea, 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—Bacteria, Archaea, and Eukarya. The first two are prokaryotic cells with microbes 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 (<link target-id="fs-id1167066867652" class="has-default-text">see this figure</link>). 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).</para>
     <para id="fs-id2956594">Woese’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 (<link target-id="fig-ch01_02_09"/>). Comparing rRNA 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.</para><figure id="fig-ch01_02_09" orient="vertical" class="ost-tag-lo-apbio-ch01-s02-lo03 ost-tag-lo-apbio-ch01-s02-aplo-1-18"><media id="eip-idp79648976" alt="Photo depict: A: bacterial cells. Photo depict: B: a natural hot vent. Photo depict: C: a sunflower. Photo depict: D: a lion.">
      <image mime-type="image/png" src="../../media/Figure_01_02_17abcd.png"/>
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modules/m66428/index.cnxml

@@ -106,7 +106,7 @@
 
 <caption>Microbiologist Carl Woese constructed this phylogenetic tree using data that he obtained from sequencing ribosomal RNA genes. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are prokaryotes, single-celled organisms lacking intracellular organelles. (credit: Eric Gaba; NASA Astrobiology Institute)
 </caption></figure><note id="fs-id2581806" class="evolution"><title>Carl Woese and the Phylogenetic Tree</title>
-<para id="fs-id2024686">In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. They based the organizational scheme mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which modern systematics use. American microbiologist Carl Woese's pioneering work in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. The first two are prokaryotic cells with microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms (protists), together with the three remaining kingdoms (fungi, plants, and animals). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (<link target-id="fig-ch01_02_08"/>). 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).</para>
+<para id="fs-id2024686">In the past, biologists grouped living organisms into six kingdoms—animalia, plantae, fungi, protista, archea, and bacteria. They based the organizational scheme mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which modern systematics use. American microbiologist Carl Woese's pioneering work in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. The first two are prokaryotic cells with microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms (protists), together with the three remaining kingdoms (fungi, plants, and animals). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (<link target-id="fig-ch01_02_08"/>). 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).</para>
 <para id="fs-id2956594">Woese constructed his tree from universally distributed comparative gene sequencing that are present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese’s approach was revolutionary because comparing physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (<link target-id="fig-ch01_02_09"/>). Comparing rRNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified separating the prokaryotes into two domains: bacteria and archaea.</para><figure id="fig-ch01_02_09" orient="vertical"><media id="eip-idp79648976" alt="There are four photos shown. Photo A is a micrograph, showing tubelike bacteria. Photo B shows a steaming body of water, refered to as a hot vent. Some of the water is a typical blue, while the outer edges are rust colored. Photo C shows a tall sunflower, with a thick stem and bright yellow petals. Photo D shows a muscular lion that has a thick mane of hair around its neck and head.">
 <image mime-type="image/png" src="../../media/Figure_01_02_17abcd.png"/>
 </media>