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
A 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 \u201cIt turns out the reference you use really changes the story you tell about a species,\u201d said Jazlyn Mooney<\/a>, Gabilan Assistant Professor of Quantitative and Computational Biology<\/a> at USC Dornsife and corresponding author of the study published in Cell. \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 Scientists put a reference genome to the test<\/p>\n 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 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 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 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 They asked:<\/p>\n How much genetic variation appears? The answers depended heavily on which genome served as the map.<\/p>\n This is the kind of thing that could change conservation decisions.<\/p>\n 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 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 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 \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
\nWhat does the data reveal about past population sizes?
\nAre current populations growing or shrinking?
\nWhich genes seem to be under natural selection, hinting at adaptation?<\/p>\n