{"id":25358,"date":"2025-09-22T12:14:54","date_gmt":"2025-09-22T19:14:54","guid":{"rendered":"https:\/\/dornsife.usc.edu\/news\/?p=25358"},"modified":"2025-09-29T11:57:01","modified_gmt":"2025-09-29T18:57:01","slug":"genomic-reference-dna-affects-genetic-research-results","status":"publish","type":"post","link":"https:\/\/dornsife.usc.edu\/news\/stories\/genomic-reference-dna-affects-genetic-research-results\/","title":{"rendered":"Want to save an endangered species? Start with the right DNA blueprint"},"content":{"rendered":"\n\n\n    \n                                \n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--article-hero \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--article-hero\"\n    \n      >\n\n    \n<div class=\"inner-wrapper\">\n          \n<div class=\"f--field f--image\">\n\n    \n    \n    \n    \n    \n    \n              \n      <img\n                            data-src=\"https:\/\/dornsife.usc.edu\/news\/wp-content\/uploads\/sites\/7\/2025\/09\/mooney-grey-fox-dornsife-768x432.jpg\"\n          data-srcset=\"https:\/\/dornsife.usc.edu\/news\/wp-content\/uploads\/sites\/7\/2025\/09\/mooney-grey-fox-dornsife-1920x1080.jpg 1920w,https:\/\/dornsife.usc.edu\/news\/wp-content\/uploads\/sites\/7\/2025\/09\/mooney-grey-fox-dornsife-1280x720.jpg 1280w,https:\/\/dornsife.usc.edu\/news\/wp-content\/uploads\/sites\/7\/2025\/09\/mooney-grey-fox-dornsife-768x432.jpg 768w\"          data-sizes=\"(min-width:1200px) 75vw, (min-width:768px) 83vw, 100vw\"          class=\"lazyload\"\n        \n                  alt=\"A golden retriever, left, juxtaposed with a gray fox, right, with an illustration of DNA between them\"\n        \n        \n                                      \/>\n\n    \n    \n  \n  \n\n<\/div>\n  \n      <div class=\"image-caption\">\n          \n<div class=\"f--field f--description\">\n\n    \n  Researchers commonly use the domestic dog genome as a reference for studying gray fox genetics. (Composite: Letty Avila. Image sources: iStock; Wikimedia Commons.)\n\n\n<\/div>\n    <\/div>\n  \n  <div class=\"text-wrapper\">\n          <nav aria-label=\"Breadcrumb\" class=\"breadcrumbs\">\n        <ul>\n                      <li><a href=\"\/news\/stories\/\">News<\/a><\/li>\n                      <li><a href=\"\/news\/stories\/\/?category=science-and-technology\">Science and Technology<\/a><\/li>\n                  <\/ul>\n      <\/nav>\n    \n              \n<div class=\"f--field f--page-title\">\n\n    \n  <h1>Want to save an endangered species? Start with the right DNA blueprint<\/h1>\n\n\n<\/div>\n    \n          <div class=\"subtitle\">\n            \n<div class=\"f--field f--description\">\n\n    \n  Most species still lack their own sequenced genome. New research led by USC Dornsife shows that when studies rely on similar but different species, findings from genetic data can be distorted by up to 60% \u2014 putting vulnerable species at greater risk.\n\n\n<\/div>\n      <\/div>\n    \n           <strong class=\"author-field\"><span >By<\/span><a href=\"mailto:communication@dornsife.usc.edu\">USC Dornsife News<\/a><\/strong>\n    \n          <span class=\"post-date-field\">September 22, 2025<\/span>\n      <\/div>\n<\/div>\n\n\n  <\/div><\/div>\n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--social-share \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--social-share\"\n    \n      >\n\n    \n  <div class=\"content-wrapper\">\n    <span class=\"a2a_kit a2a_kit_size_32 addtoany_list\" style=\"line-height: 32px;\">\n      <span class=\"title\">\n        Share\n      <\/span>\n                        <a class=\"a2a_button_copy_link\" target=\"_blank\" href=\"\/#copy_link\" rel=\"nofollow noopener\" 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       <a class=\"a2a_button_email\" target=\"_blank\" href=\"\/#email\" rel=\"nofollow noopener\" title=\"E-mail\">\n            <span class=\"a2a_svg a2a_s__default a2a_s_print\">\n              <svg height=\"12\" viewBox=\"0 0 18 12\" width=\"18\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><path d=\"m8.14285714 9.42857143c-.17142857 0-.34285714 0-.51428571.08571428l7.28571427 6.34285719c.3428572.2571428.6857143.2571428.9428572 0l7.2857142-6.34285719c-.0857142-.08571428-.2571428-.08571428-.4285714-.08571428zm-1.28571428 1.11428567v.1714286 8.5714286c0 .6857143.6 1.2857143 1.28571428 1.2857143h14.57142856c.6857143 0 1.2857143-.6 1.2857143-1.2857143v-8.5714286c0-.0857143 0-.0857143 0-.1714286l-7.2 6.3428572c-.7714286.6857143-1.8857143.6857143-2.6571429 0z\" fill-rule=\"evenodd\" transform=\"translate(-6 -9)\"\/><\/svg>\n            <\/span>\n            <span class=\"a2a_label visually-hidden\">Email<\/span>\n          <\/a>\n                  <\/span>\n  <\/div>\n\n  <\/div><\/div>\n \n\n\n      \n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--article-highlights \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--article-highlights\"\n    \n      >\n\n    \n<div class=\"inner-wrapper\">\n          \n<div class=\"f--field f--section-title\">\n\n    \n  <h2>\n          Key points:\n      <\/h2>\n\n\n<\/div>\n    \n      <ul>\n              <li><p>Since few species have their own sequenced genome, scientists often use the DNA of a related species as a stand-in \u2014 a shortcut that can distort research findings.<\/p>\n<\/li>\n              <li><p>A new study published in <em>Cell <\/em>shows that, in animals such as gray foxes, using something other than a species-specific genome can miss up to a third of genetic variations \u2014 a problem that threatens nearly all species without their own sequenced genome.<\/p>\n<\/li>\n              <li><p>Such errors could mislead conservation efforts, diverting resources to the wrong places and leaving truly at-risk species unprotected.<\/p>\n<\/li>\n          <\/ul>\n  <\/div>\n  \n\n  <\/div><\/div>\n\n\n\n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <p>When scientists want to trace how a species has changed over time \u2014 and predict its prospects for survival \u2014 they turn to DNA. But what if the genetic map guiding them belongs to the wrong animal?<\/p>\n<p>A <a href=\"https:\/\/www.cell.com\/cell\/abstract\/S0092-8674(25)01026-8\" target=\"_blank\" rel=\"noopener\">new study<\/a> led by researchers at the USC Dornsife College of Letters, Arts and Sciences shows that using the wrong \u201creference genome\u201d \u2014 the master sequence scientists rely on to compare DNA \u2014 can significantly distort the picture. For the gray fox, one of North America\u2019s most common wild canids, mapping against a dog or Arctic fox genome, instead of its own, made populations look smaller, less diverse and even in decline when they were actually stable or growing.<\/p>\n<p>\u201cIt turns out the reference you use really changes the story you tell about a species,\u201d said <a href=\"https:\/\/dornsife.usc.edu\/profile\/jazlyn-mooney\/\">Jazlyn Mooney<\/a>, Gabilan Assistant Professor of <a href=\"https:\/\/www.qcb-dornsife.usc.edu\/\">Quantitative and Computational Biology<\/a> at USC Dornsife and corresponding author of the study published in <em>Cell<\/em>. \u201cIf you use the wrong reference, you can end up with misleading answers about a species\u2019 history or health, and even its chances of long-term survival.\u201d<\/p>\n<h2>Scientists put a reference genome to the test<\/h2>\n<p>Every genetic study needs a starting point: a reference genome, usually built by sequencing the DNA of one individual of a species. When scientists study additional individuals, they align the new DNA against that reference for comparison.<\/p>\n<p>But many species, especially those less studied, lack their own reference. In these cases, researchers turn to the next best option \u2014 a close relative. For decades, the domestic dog\u2019s genome has stood in for foxes, wolves and wild dogs.<\/p>\n<p>Mooney and her colleagues wondered just how much that choice matters. Would using a genetically distant blueprint simply blur the details, or could it actually rewrite the story?<\/p>\n<p>The team re-analyzed DNA from 12 gray foxes \u2014 six from eastern North America and six from the West \u2014 comparing how their genomes aligned to three different references: the gray fox itself, the domestic dog and the Arctic fox.<\/p>\n<p>They asked:<\/p>\n<ul>\n<li>How much genetic variation appears?<\/li>\n<li>What does the data reveal about past population sizes?<\/li>\n<li>Are current populations growing or shrinking?<\/li>\n<li>Which genes seem to be under natural selection, hinting at adaptation?<\/li>\n<\/ul>\n<p>The answers depended heavily on which genome served as the map.<\/p>\n<blockquote><p><em>This is the kind of thing that could change conservation decisions.<\/em><\/p><\/blockquote>\n<p>With the gray fox\u2019s own genome, researchers detected 26%\u201332% more genetic differences among individuals and about a third more rare variants (the subtle DNA changes that reveal how populations have been evolving recently).<\/p>\n<p>Estimates of population size were also 30%\u201360% higher. In the western United States, for instance, the gray fox genome showed stability and growth, while the dog and Arctic fox genomes suggested decline.<\/p>\n<p>The wrong reference also threw off measures of how DNA shuffles during reproduction. With the dog or Arctic fox genomes, the numbers sometimes doubled or even tripled compared with the gray fox genome, especially near the ends of chromosomes.<\/p>\n<p>\u201cThis is the kind of thing that could change conservation decisions,\u201d Mooney said. \u201cIf you think a population is shrinking when it\u2019s not, or vice versa, you might end up protecting the wrong group or missing an opportunity to safeguard genetic diversity.\u201d<\/p>\n<p>The study also showed that using the wrong reference could create <a href=\"https:\/\/dornsife.usc.edu\/news\/stories\/island-fox-brains-proportionally-larger-than-mainland-foxes\/\">misleading signs of natural selection<\/a>. The dog and Arctic fox genomes identified twice as many potential DNA \u201chot spots\u201d\u2014 regions that looked like they might be adaptive \u2014 compared with the gray fox genome. Many of these signals were false alarms, caused by the mismatch between species.<\/p>\n<h2>Why the right reference genome matters for conservation \u2014 and people<\/h2>\n<p>The study\u2019s implications go well beyond foxes. Conservation biologists use genetic data to decide which populations to protect, how to design breeding programs and whether endangered species are at risk of inbreeding. If the genetic picture is distorted, those decisions may rest on shaky ground.<\/p>\n<p>That could affect high-profile species such as the Ethiopian wolf, the African wild dog or even the tiny Channel Island foxes off Southern California\u2019s coast. For animals already on the edge, a flawed map could mean misjudging their vulnerability.<\/p>\n<p>\u201cMaintaining the world\u2019s biodiversity isn\u2019t just about saving animals for their own sake,\u201d Mooney said. \u201cBiodiversity supports clean water, food security and climate stability. If conservation plans are based on incomplete or biased genetic information, we risk mismanaging species and weakening the natural systems people depend on.\u201d<\/p>\n<p>These findings echo a lesson from human genetics: For years, the human reference genome drew mostly from just a few people, limiting research across populations. More recent efforts are building references that better reflect global diversity.<\/p>\n<h2>Scientists call for better genomic maps<\/h2>\n<p>The researchers argue that the solution is to invest in building species-specific reference genomes. Assembling a high-quality genome sequence is expensive, and nearly 99% of species still lack one, but the payoff could be crucial.<\/p>\n<p>For species without their own reference, Mooney and her team point to new computational methods and building high quality genomes that capture more of a species\u2019 diversity \u2014 as ways to reduce bias.<\/p>\n<p>\u201cWe\u2019re not saying every species will be as impacted as gray foxes,\u201d Mooney said. \u201cBut our study shows the risks are real, and can lead you astray.\u201d<\/p>\n<p>The gray fox study stands as both a warning and a call to action: choosing the wrong reference doesn\u2019t just blur the details \u2014 it can redraw a species\u2019 past and future.<\/p>\n<h2>About the study<\/h2>\n<p>In addition to corresponding author Mooney, the research team includes first author and former USC Dornsife postdoctoral fellow Maria Akopyan, now at the University of California, Riverside; USC undergraduate Matthew Genchev; and Assistant Professor Ellie Armstrong of UC Riverside.<\/p>\n<p><em>Editor\u2019s Note: Darrin S. Joy contributed to this article.<\/em><\/p>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n\n\n\n  \n        \n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--article-related-stories \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--article-related-stories\"\n    \n      >\n\n    \n  <div class=\"inner-wrapper\">\n              \n<div class=\"f--field f--section-title\">\n\n    \n  <h2>\n          Related Articles\n      <\/h2>\n\n\n<\/div>\n    \n                  <article>\n              \n<div class=\"f--field f--cta-title\">\n\n    \n  <h3>\n          <a href=\"https:\/\/dornsife.usc.edu\/news\/stories\/biological-aging-twin-study-linking-childhood-to-midlife-cognition\/\" \n                        class=\"\" \n      >What your DNA \u2013 and childhood \u2013 reveal about midlife decrease in IQ<\/a>\n      <\/h3>\n\n\n<\/div>\n        <\/article>\n              <article>\n              \n<div class=\"f--field f--cta-title\">\n\n    \n  <h3>\n          <a href=\"https:\/\/dornsife.usc.edu\/news\/stories\/protein-droplets-protect-heterochromatin-from-dna-repair-errors\/\" \n                        class=\"\" \n      >USC Dornsife study reveals how protein droplets help cells master difficult DNA repair<\/a>\n      <\/h3>\n\n\n<\/div>\n        <\/article>\n              <article>\n              \n<div class=\"f--field f--cta-title\">\n\n    \n  <h3>\n          <a href=\"https:\/\/dornsife.usc.edu\/news\/stories\/understanding-america-study-expansion-alzheimers-dementia\/\" \n                        class=\"\" \n      >$59 million boost enhances USC Dornsife\u2019s Understanding America Study and nationwide research<\/a>\n      <\/h3>\n\n\n<\/div>\n        <\/article>\n            <\/div>\n\n\n  <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>Most species still lack their own sequenced genome. New research led by USC Dornsife shows that when studies rely on similar but different species, findings from genetic data can be distorted by up to 60% \u2014 putting vulnerable species at greater risk.<\/p>\n","protected":false},"author":14,"featured_media":25359,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[16],"tags":[116,86,60],"class_list":["post-25358","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science-and-technology","tag-genetics-and-genomics","tag-quantitative-and-computational-biology","tag-research"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Want to save an endangered species? Start with the right DNA blueprint<\/title>\n<meta name=\"description\" content=\"USC Dornsife research shows studies relying on stand-in reference DNA can distort findings and put vulnerable species at greater risk\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/dornsife.usc.edu\/news\/stories\/genomic-reference-dna-affects-genetic-research-results\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Genomic reference DNA affects genetic research results\" \/>\n<meta property=\"og:description\" content=\"USC Dornsife research shows studies relying on stand-in reference DNA can distort findings and put vulnerable species at greater risk\" \/>\n<meta property=\"og:url\" content=\"https:\/\/dornsife.usc.edu\/news\/stories\/genomic-reference-dna-affects-genetic-research-results\/\" \/>\n<meta property=\"og:site_name\" content=\"USC Dornsife News\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/uscdornsife\" \/>\n<meta property=\"article:published_time\" content=\"2025-09-22T19:14:54+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2025-09-29T18:57:01+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/dornsife.usc.edu\/news\/wp-content\/uploads\/sites\/7\/2025\/09\/mooney-grey-fox-dornsife.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"2000\" \/>\n\t<meta property=\"og:image:height\" content=\"1150\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Darrin Joy\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@uscdornsife\" \/>\n<meta name=\"twitter:site\" content=\"@uscdornsife\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/dornsife.usc.edu\/news\/stories\/genomic-reference-dna-affects-genetic-research-results\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/dornsife.usc.edu\/news\/stories\/genomic-reference-dna-affects-genetic-research-results\/\"},\"author\":{\"name\":\"Darrin Joy\",\"@id\":\"https:\/\/dornsife.usc.edu\/news\/#\/schema\/person\/851085523b73581e3387a7fc90cadb96\"},\"headline\":\"Want to save an endangered species? 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