{"id":13406,"date":"2020-12-16T15:28:25","date_gmt":"2020-12-16T15:28:25","guid":{"rendered":"https:\/\/wildsalmoncenter.org\/?p=13406"},"modified":"2026-03-24T19:16:06","modified_gmt":"2026-03-24T19:16:06","slug":"first-salmon-last-chance-part-iii","status":"publish","type":"post","link":"https:\/\/wildsalmoncenter.org\/2020\/12\/16\/first-salmon-last-chance-part-iii\/","title":{"rendered":"First Salmon, Last Chance | Part 3"},"content":{"rendered":"\n

The Key in the Code<\/h2>\n\n\n\n
<\/div>\n\n\n\n

On the banks of Oregon\u2019s Rogue River, six children gawk at a very dead fish. Wriggling in oversize lifejackets, they cluster around a taller boy, who rolls the carcass onto a river rock.<\/span><\/p>\n\n\n

\n
\"\"
Late September, 2020: examining a Chinook carcass on the north bank of Oregon’s Rogue River.<\/figcaption><\/figure>\n<\/div>\n\n\n

The fish is mottled gray, probably stinky, and, from the kids\u2019 expressions, pretty fascinating.<\/span><\/p>\n\n\n\n

From his passing raft, Wild Salmon Center Science Director Dr. Matt Sloat can just make out the buck\u2019s hooked kype, jaw hanging wide like the small fry around him.<\/span><\/p>\n\n\n\n

\u201cLooks like you found a salmon,\u201d he calls. <\/span>\u201cHe came here all the way from the ocean. Pretty cool, huh?\u201d<\/span><\/p>\n\n\n\n

As his raft drifts past, the kids turn back to prodding their science experiment. <\/span><\/p>\n\n\n\n

This is not, perhaps, the most dignified end for a salmon, whose hero\u2019s journey home likely spanned thousands of miles and myriad challenges<\/a>. But it might be a fittingly forensic one for the scientific mystery he represents<\/strong>.<\/span><\/p>\n\n\n\n

From the raft, everything here looks fine: spawning fish, happy fishers, curious kids. It\u2019s a beautiful, late September afternoon, but Dr. Sloat is worried.<\/span><\/p>\n\n\n

\n
\"\"
As spring Chinook populations decline across the Pacific Northwest, the spring run on Oregon’s Rogue River\u2014a popular destination for anglers\u2014is considered one of the world\u2019s last, best, and healthiest.<\/span> (PC: Ken Morrish.)<\/figcaption><\/figure>\n<\/div>\n\n\n

Once, he might have told the kids that they\u2019d found a spring Chinook. Because that was the salmon you\u2019d typically find this far upstream. For generations, the upper Rogue\u2019s spring Chinook run has been its most prized, for anglers and salmon managers alike. Today, with springer populations in decline across the Pacific Northwest, the Rogue\u2019s spring run is considered one of the world\u2019s last, best, and healthiest.<\/span><\/p>\n\n\n\n

But Dr. Sloat knows something here is shifting, just beneath the water\u2019s surface. He can\u2019t be sure, any more, what run of salmon he’s seeing.It\u2019s a vexing mystery. And one we wouldn\u2019t know existed, if it weren\u2019t for the genetic detectives.<\/strong><\/span><\/p>\n\n\n\n

\n

On the Rogue, something is shifting, just beneath the water\u2019s surface.<\/span><\/p>\n<\/blockquote>\n\n\n\n

\n\n\n\n

<\/p>\n\n\n\n

Genetic science has come a long way since the mid-2000s, before Dr. Michael Miller earned his scholarly honorifics.<\/span><\/p>\n\n\n\n

\u201cA genome is like a big instruction manual that tells you how to make an organism,\u201d explains Dr. Miller, a genetics professor at UC-Davis. \u201cAt the time, we didn\u2019t have a fully decoded sequence. We didn\u2019t have the full book. Imagine that you have only certain sentences, and you don\u2019t know their order.\u201d<\/span><\/p>\n\n\n\n

As geneticists cracked open those first sentences, Dr. Miller, then a doctoral candidate at the University of Oregon, focused on decoding snippets of steelhead DNA. His goal was a career in conservation genetics, using insights from DNA to help protect threatened species. Species like the springers he hooked as a kid on Oregon\u2019s Molalla River<\/strong>. <\/span><\/p>\n\n\n

\n
\"\"
Dr. Michael Miller. (PC: Mikal Jakubal.)<\/figcaption><\/figure>\n<\/div>\n\n\n

\u201cSpring Chinook are most near and dear to my heart,\u201d says Dr. Miller. \u201cBut back then, doing high resolution genetic analysis on salmon wasn\u2019t feasible.\u201d<\/span><\/p>\n\n\n\n

In those heady early days\u2014when as he says, analyzing DNA was \u201cthousands of times more expensive and time-consuming\u201d\u2014the field\u2019s limited tools could fuel some questionable correlations. <\/span><\/p>\n\n\n\n

One leap, in particular, troubled the young graduate student. Data showed that in individual rivers, spring and fall Chinook shared big chunks of DNA. From this, researchers came to a conclusion that still influences salmon management policies.<\/strong> They argued that spring Chinook populations emerge from a river\u2019s fall Chinook population\u2014and that they\u2019ve always done so: splitting off many times, in many rivers. For managers, this created a sense of safety. If spring Chinook went extinct, the geneticists reassured, they could reevolve from a river\u2019s fall run.<\/span><\/p>\n\n\n\n

\n

In those heady early days, the field\u2019s limited tools could fuel some questionable correlations. <\/span>One leap, in particular, troubled the young graduate student.<\/span><\/p>\n<\/blockquote>\n\n\n\n

\u201cYou know, that argument was reasonable at the time,\u201d says Dr. Miller. Early genetic approaches could only look at overall relatedness, not specific genes. The two runs are related, he stresses; a river\u2019s spring and fall Chinook sometimes interbreed, but usually only at low levels in healthy rivers. <\/span><\/p>\n\n\n\n

But this conclusion missed one important thing. \u201cRelatedness,\u201d he says, \u201cdoesn\u2019t mean that they\u2019re not genetically distinct in critical ways.\u201d<\/span><\/p>\n\n\n\n

Dr. Miller suspected that a critical divergence lurked somewhere in the springer genome\u2014a hunch from growing up with this fish<\/strong>. When he started fishing for fall Chinook, too, the space between the two felt huge: run times separated by months, different spawning grounds, vastly different fat storage (and resulting flavors). Spring Chinook’s uniqueness was a no-brainer, he thought\u2014at least for anyone who\u2019d ever handled one.<\/span><\/p>\n\n\n\n

\u201cWhen genetic methods mature,\u201d he thought, \u201cI\u2019m going to figure this out.\u201d<\/span><\/p>\n\n\n\n