[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-0-en-105":3,"doc-seo-595489-105":59,"doc-detail-595489-en":130},{"code":4,"msg":5,"data":6},0,"success",[7,13,18,23,28,33,38,43,48,51,55],{"id":8,"doc_module":4,"doc_module_name":9,"category_name":10,"show_sort_weight":11,"slug":12},1,"Document","Story & Novel",90,"story-novel",{"id":14,"doc_module":4,"doc_module_name":9,"category_name":15,"show_sort_weight":16,"slug":17},2,"Literature",80,"literature",{"id":19,"doc_module":4,"doc_module_name":9,"category_name":20,"show_sort_weight":21,"slug":22},4,"Exam",70,"exam",{"id":24,"doc_module":4,"doc_module_name":9,"category_name":25,"show_sort_weight":26,"slug":27},5,"Comic",60,"comic",{"id":29,"doc_module":4,"doc_module_name":9,"category_name":30,"show_sort_weight":31,"slug":32},6,"Technology",50,"technology",{"id":34,"doc_module":4,"doc_module_name":9,"category_name":35,"show_sort_weight":36,"slug":37},7,"Healthcare",40,"healthcare",{"id":39,"doc_module":4,"doc_module_name":9,"category_name":40,"show_sort_weight":41,"slug":42},8,"Research & Report",30,"research-report",{"id":44,"doc_module":4,"doc_module_name":9,"category_name":45,"show_sort_weight":46,"slug":47},9,"Religion & Spirituality",20,"religion-spirituality",{"id":46,"doc_module":4,"doc_module_name":9,"category_name":49,"show_sort_weight":46,"slug":50},"World Cup","world-cup",{"id":52,"doc_module":4,"doc_module_name":9,"category_name":53,"show_sort_weight":52,"slug":54},10,"Lifestyle","lifestyle",{"id":56,"doc_module":4,"doc_module_name":9,"category_name":57,"show_sort_weight":24,"slug":58},19,"General","general",{"code":4,"msg":60,"data":61},"ok",{"site_id":62,"language":63,"slug":64,"title":65,"keywords":66,"description":67,"schema_data":68,"social_meta":123,"head_meta":125,"extra_data":127,"updated_unix":129},105,"en","exploring-evolutionary-patterns-in-genetic-sequence-a-computer-exercise","Exploring Evolutionary Patterns in Genetic Sequence - A Computer Exercise","","The paper addresses the need for hands-on molecular evolutionary sequence analysis for undergraduates, leveraging comparative data resources such as NCBI GenBank. It targets widespread student misconceptions about evolution that impede learning of genetic sequences, mutation, and evolutionary processes. It presents a flexible computer laboratory exercise using freely available software to analyze GenBank or online sequences, supporting varying instructor complexity and improving introductory biology students’ understanding of sequence variation and analytical foundations.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/exploring-evolutionary-patterns-in-genetic-sequence-a-computer-exercise/595489/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/exploring-evolutionary-patterns-in-genetic-sequence-a-computer-exercise/595489.png","ImageObject",300,407,{"name":92,"@type":93},"Well Done","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-30","2026-10-15",true,{"@type":102,"interactionType":103,"userInteractionCount":24},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"Why does the exercise emphasize evolutionary context for sequence analysis?","Question",{"text":112,"@type":113},"The document argues that students need active, hands-on analysis within an evolutionary framework to better understand mutation, genetic sequence variation, and evolutionary processes, rather than relying only on lectures or memorization.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"What is the role of synonymous and nonsynonymous substitutions in the analysis?",{"text":117,"@type":113},"Synonymous substitutions are treated as expected to occur at a baseline random rate and are generally unaffected by selection, while nonsynonymous substitutions may reflect selection pressure depending on the locus and evolutionary scenario.",{"name":119,"@type":110,"acceptedAnswer":120},"How does the dN/dS ratio help interpret selection outcomes?",{"text":121,"@type":113},"The dN/dS ratio is described as a baseline-neutral measure of how mutation types arise and persist; excess nonsynonymous substitutions can suggest positive selection, while excess synonymous substitutions may indicate balancing selection maintaining amino acid polymorphism.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},595489,1792637123,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":24,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":24,"language":139,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":140,"faqs":141,"seo_title":142,"seo_description":67,"update_tm":143,"read_time":144,"preview_page_count":4},5909892210082,"https://ap-avatar.wpscdn.com/avatar/56001069da27c9f41e8?x-image-process=image/resize,m_fixed,w_180,h_180&k=1789614185077863061","Exploring Evolutionary Patterns in Genetic Sequence: A Computer Exercise  \nAlice M. Shumate1 and Aaron J. Windsor2  \n1Department of Biological and Allied Health Sciences, Fairleigh Dickinson University, 285 Madison Avenue, Madison, NJ 07940; 2Department of Biology, Duke University, Durham, NC 27708  \nEmail: [ashumate@fdu.edu](ashumate@fdu.edu)  \nAbstract: The increase in publications presenting molecular evolutionary analyses and the availability of comparative sequence data through resources such as NCBI‘s GenBank underscore the necessity of providing undergraduates with hands-on sequence analysis skills in an evolutionary context. This need is particularly acute given that students have been shown to bring misconceptions about evolution to the classroom, and these misconceptions can hinder their learning about genetic sequences, mutation, and evolutionary processes. However, undergraduate institutions sometimes lack sophisticated analytical software in student computer laboratories. Here we present a computer laboratory exercise utilizing freely available analysis software, and which is designed to analyze sequences that can be obtained from GenBank or other online sources. The exercise is flexible in its complexity, allowing instructors to modify the lab to suit the needs and skills of their classes, and was significantly helpful to introductory biology students in understanding the basics of sequence variation and analysis.  \nKeywords: genetic data, DNA sequence, evolution, computer exercise, sequence alignment, phylogeny, population genetics  \nINTRODUCTION  \nThe integration of exploratory labs in undergraduate science courses is based upon the ideas that students learn science best by doing, and that difficult concepts are best internalized by thinking, discussing, and working with them actively, instead of simply hearing about and/or memorizing them (von Glaserfeld, 1995; D'Avanzo, 2003) . The challenge in designing laboratory activities is to foster active exploratory discussion and debate from which all students benefit.  \nCollaborative learning and discussion can be particularly important when students are working with difficult concepts, or those about which they have some misconceptions. It is common for students to hold onto misconceptions in the face of data that fail to support them (D'Avanzo, 2003), and also for the retention of misconceptions to hinder development of a correct understanding of such concepts (Driver, 1995) . This has been a particular problem for the field of evolutionary biology, to which students bring a wide array of misconceptions (Anderson, Fisher, and Norman, 2002; Garvin-Doxasand Klymkowsky, 2008) . In particular, analysis of evolutionary patterns in genetic sequence is problematic, as it relies heavily on a central understanding of mutation as a random process, while students want to assign a driving force of positive change to evolution (Anderson, Fisher, and Norman, 2002; D'Avanzo, 2003; Garvin-Doxas and Klymkowsky, 2008) . We tend to discuss these ideas theoretically in class, without always giving our students active exercises working with genetic  \nsequence data, in order to force them to challenge, and move past, their misconceptions.  \nPopulation genetic analyses of nucleotide sequence data rely on the fact that the genetic code is degenerate, meaning that there are multiple nucleic acid substitutions that do not change the amino acid specified by a codon. Such silent mutations are called synonymous substitutions, and under most conditions are expected to occur at a random, baseline, rate that represents the rate of mutation, and thereafter be unaffected by selection pressure. On the other hand, substitutions that code for a different amino acid (nonsynonymous substitutions) could be subject to selection pressure. If no selection is taking place at a locus, variations are selectively neutral, and the ratio of nonsynonymous to synonymous substitutions (the dN/dS ratio) should repre","cbCaioc6t6Mc7FgW","https://ap.wps.com/l/cbCaioc6t6Mc7FgW","pdf",191438,"English","# Introduction\n## Population genetics and neutral models\n## Selection signatures and dN/dS interpretation\n## Rationale for active laboratory learning","[{\"question\":\"Why does the exercise emphasize evolutionary context for sequence analysis?\",\"answer\":\"The document argues that students need active, hands-on analysis within an evolutionary framework to better understand mutation, genetic sequence variation, and evolutionary processes, rather than relying only on lectures or memorization.\"},{\"question\":\"What is the role of synonymous and nonsynonymous substitutions in the analysis?\",\"answer\":\"Synonymous substitutions are treated as expected to occur at a baseline random rate and are generally unaffected by selection, while nonsynonymous substitutions may reflect selection pressure depending on the locus and evolutionary scenario.\"},{\"question\":\"How does the dN/dS ratio help interpret selection outcomes?\",\"answer\":\"The dN/dS ratio is described as a baseline-neutral measure of how mutation types arise and persist; excess nonsynonymous substitutions can suggest positive selection, while excess synonymous substitutions may indicate balancing selection maintaining amino acid polymorphism.\"}]","Exploring Evolutionary Patterns in Genetic Sequence - A Computer Exercise | PDF",1792081239,13]