The SRALP and the SRNLP: A New Hope

This is the first installment of a fresh three-part series on the Snake River Physa controversy, prompted by the 2021 publication of new research on the subject by a fish guy named Michael K. Young and colleagues at the National Genomics Center for Wildlife and Fish Conservation in Missoula [1].

And because I look at the world through the eyes of a college professor, my first instinct is to assign homework.  I have previously posted six essays on Physa natricina: an introduction to the controversy in 2008, a broadening in 2010, and my four-part series on the “SRALP” (Snake River acuta-like Physa) in 2013, by the end of which I was so frustrated with the willful ignorance, professional malpractice, and borderline fraud perpetrated by our colleagues in the environmental community of the arid West I wrote, “I am done with it.”  But research published more recently has given me cause for new hope.

Figure 2.1 of Gates & Kerans [7]

So if you, dear reader, are seriously interested in the Snake River Physa controversy, I would (indeed!) encourage you to visit footnote [2] at the bottom of this essay and review my six previous essays on the subject before reading further into this, the seventh.  Then feel free to skip the next seven paragraphs and resume this month’s essay at the topic sentence, “And from that basement, the situation deteriorated.” But for the benefit of the rest of you, more casually interested, let me summarize, as briefly as I can.

We entered the Snake River Physa controversy, way back in 2005, with our eyes wide open.  We knew that Dwight Taylor’s (1988) description of Physa natricina [3], “Shell ovoid, solid, with broadly rounded anterior end and acute spire,” “length 5.4 – 6.9 mm,” found only “on boulders in the deepest accessible portion of the Snake River near rapid margins” [4] in Gooding, Elmore, and Owyhee Counties, Idaho, was motivated by water resource politics, cynically calculated to stop an impoundment project planned by the Idaho Power Company (IPC).  The concept of “endangerment” is entirely political, not testable by science.  One might argue that science is sullied by association with controversies of this sort.  I certainly did, in my essay of [12Mar08].

But as of 2010, when an email arrived on my desktop at the College of Charleston, calling me into a deeper involvement with the Snake River Physa controversy, I was still naïve enough to believe that the world of science, in which I live, might be compatible with the world of public policy, in which laws are made and regulations enforced.  No, I did not imagine that science could be brought to bear on questions of any political relevance.  I am not a Democrat.  But maybe, I thought back in 2010, science can piggyback on the public dole without becoming corrupted by it.  Just because we know the reason that Dwight Taylor described Physa natricina in 1988, doesn’t mean that he was wrong, does it?  Might the massive resources of the federal government and private industry be directed toward testing an hypothesis of purely scientific interest without entanglement, corruption, self-dealing and bias?

Is that weirdly shaped little physid population hugging those rocks in the raging torrents of the Snake River indeed a valid biological species, narrowly endemic to three counties of Idaho?  Or is it conspecific with the cosmopolitan Physa acuta, invasive on five continents, as suggested by Rogers and Wethington in 2007 [6]?  Or might those enigmatic little snails be neither?  A regional endemic, locally common in the shallow margins of the river, perhaps?  That was the “Hypothesis #2 of 3” I advanced in [14Sept10].

My faithful readership may remember a four-part series I posted in 2013 detailing my 2010 invitation to review a report filed by Kiza Gates & Billie Kerans on a Physa study conducted at the Minidoka Dam [7], one hundred river miles upstream from the type range of P. natricina [5Feb13], my field experiences hunting Physa in the shadow of that dam with Dr. J. B. Burch, with subsequent solo tour of the waters downstream [1Mar13], and our confrontation at a meeting convened by the US Bureau of Reclamation in Boise [2Apr13].

All I could find in the Snake River shallows as far upstream as the Minidoka Dam in September of 2010 was a sparse population of Physa gyrina, a rather different animal that really does not bear on the Physa natricina controversy at all, but keeps gumming up the works, somehow.  Further downstream, however, and for several hundred miles across the bottom of Idaho, I was able to confirm that the shallows of the Snake River are infested with Physa indistinguishable to my eyes from trash Physa acuta.  These snails I began calling SRALP, “Snake River acuta-like Physa.”

The Snake River, modified from Fig 3 of Gates et al [8]

In 2010 I was trying to test, or (rather) trying to spur Gates, Kerans, and the team of scientists who had been expressly contracted by the U.S. Bureau of Reclamation for these purposes to test, the 2007 Rogers and Wethington hypothesis that the stunted, oddly shaped little physids inhabiting rocks in the middle of the Snake River, identified by Dwight Taylor as Physa natricina, might genetically match the SRALP.  My hosts had already collected a fair sample of snails that they had identified as “Physa natricina” from the waters below the Minidoka Dam at RM 675 and sequenced a subset for two mtDNA genes [7].  These turned out to be genetically distinctive from Snake River P. gyrina, which is completely irrelevant, and from P. acuta sampled across the continental divide in Wyoming, which is just a little bit less irrelevant.  So, I brought with me a live sample of acuta-like SRALP Physa I collected fresh from the Snake River at RM 600 to the meeting of the Bureau of Reclamation in Boise and challenged – nay, begged – my hosts to sequence them.  And waited three years.

And in 2013, my hopes were dashed [2May13].  Gates, Kerans and their colleagues [8] blithely reported that “No Physa acuta were found,” refusing to sequence my SRALP samples or any Physa of any acuta-like morphology from anywhere down the length of the Snake River, cynically ginning up an elaborate process to avoid testing any hypothesis that might challenge the specific status of Physa natricina.  I was beyond disappointed – I was furious.

And from that basement, the situation deteriorated.  In their 2013 paper, Gates and Kerans, together with John Keebaugh of the Orma J. Smith Museum at The College of Idaho (ALBRCIDA), and  S. K. Kalinowski of Montana State University, reported the confirmation of snails that they identified as “Physa natricina” all the way down the length of the Snake River in Idaho, beyond Boise to the Oregon border.  This result is not surprising, on the face of it.  Dwight Taylor recorded all his modern collections “from the vicinity of Bliss to Hammett, Idaho,” roughly halfway between Minidoka and Boise, RM 525 – 571.

And indeed, the ALBRCIDA collection, where all Snake River physid samples have been deposited for many years, does hold many small-bodied Physa with inflated apertures, matching Taylor’s 1988 holotype as well as any of his paratypes, collected throughout most of the length of the Snake River in Idaho.  Quoting the 2013 paper by Gates, Kerans and colleagues verbatim: “Fifty-two specimens matching P. natricina shell characteristics were found in ALBRCIDA samples.  The furthest downstream P. natricina was collected at RK 592 (RM 367) in 2001 and the furthest upstream from RK 900 (RM 559) in 2002 (Fig. 3).”  Fine.

The problem is in the reporting of the sequence data.  There is an irregularity hidden so deeply in the paper by Gates, Kerans and colleagues [8] that I missed it entirely in my 2013 review, and only spotted it quite recently, as I was trying to correlate their results with the 2021 results of Mike Young and colleagues [1].  Watch this closely.

Gates, Kerans & colleagues selected N = 15 physids matching the P. natricina phenotype from the Minidoka Dam tailwaters for sequencing, which they listed in their Table 1, 15 physids matching the P. natricina phenotype from museum collections further downstream, which they listed in their Table 2, and 5 Physa gyrina, for a total of 35 individuals.  Here is how they reported their results, verbatim [9]:

“Only two of the five molecular markers surveyed produced amplicons suitable for sequencing, CO1 and mitochondrial ribosomal subunit 16S.  Twenty specimens produced readable sequences at the 16S locus with an aligned sequence length of 375 base pairs (bp) (GenBank Accession # GU830927 – GU830941 and JF806430 – JF806434). Only 16 out of 35 samples produced readable sequences at the CO1 locus with an aligned sequence length of 634 bp (GenBank Accession # GU830942 – GU830952 and JF806435 – JF806439).”

So, visiting GenBank today, we find that the JF sequences are the five for Physa gyrina.  The 15 GU accessions for 16S and the 11 accessions for CO1 are all Table 1 sequences, sampled from the Minidoka tailwaters (RM 670 – 674).  And no sequences whatsoever were uploaded for any alleged “Physa natricina” collected at any point further downstream, as listed on Table 2.  Apparently, none of the Table 2 physids yielded any “readable sequences.”  This is a significant irregularity, which the authors should have addressed forthrightly, rather than sweeping under the rug.  As a consequence, the Minidoka sequences have never been compared to bona fide Physa natricina sampled from the type range (RM 525 – 571).

Here I find it necessary to introduce a new term, “Snake River natricina-like Physa,” or SRNLP for short.  Until those stunted, oddly shaped little Physa recovered from the roiling tailwaters of the Minidoka Dam upstream at RM 670 – 674 can be matched genetically to the stunted, oddly shaped little Physa inhabiting the rapids of the Snake River in their RM 525 – 571 type range, the Minidoka Physa cannot, at the level of rigor demanded by this situation, be identified as Physa natricina.  They are SRNLP.

So now, the stage is set for some fresh data – those published by Mike Young and colleagues in 2021.   Does the SRNLP match the SRALP?  What policy implications might emerge from a match, or lack thereof?  Stay tuned!

Notes:

[1] Young, M.K., R. Smith K.L. Pilgrim, and M.K. Schwartz (2021)  Molecular species delimitation refines the taxonomy of native and nonnative physinine snails in North America.  Scientific Reports 11: 21739. https://doi.org/10.1038/s41598-021-01197-3

[2] Previous essays on the Physa natricina controversy:

• Red flags, water resources, and Physa natricina [12Mar08]
• Valvata utahensis and hypothesis #2 (of 3) [14Sept10]
• The mystery of the SRALP: A bidding… [5Feb13]
• The mystery of the SRALP: A twofold quest! [1Mar13]
• The mystery of the SRALP: Dixie-Cup showdown! [2Apr13]
• The mystery of the SRALP: “No Physa acuta were found.” [2May13]

If you are looking for something citable, all of these essays were subsequently published in Dillon, R.T., Jr. (2019d) Essays on Ecology and Biogeography.  Freshwater Gastropods of North America, Volume 4.  FWGNA Press, Charleston, SC.  257 pp.  [FWGNA Publications]

[3] Taylor, D. W. (1988) New species of Physa (Gastropoda: Hygrophila) from the western United States. Malacological Review 21: 43-79.

[4] The “deepest accessible” quote comes from the USFWS [5].  Taylor did not offer any habitat notes in his original 1988 description.

[5] US Fish & Wildlife Service (1992). Endangered and threatened wildlife and plants; Determination of endangered or threatened status for five aquatic snails in south central Idaho. 50 CFR Part 17. Federal Register 57(240)59244-57. (December 14, 1992)

[6] Rogers, D. C. & A. R. Wethington (2007) Physa natricina Taylor 1988, junior synonym of Physa acuta Draparnaud, 1805 (Pulmonata: Physidae). Zootaxa 1662: 45-51.

[7] Gates, K.K.,  & B.L. Kerans (2010)  Snake River Physa, Physa (Haitia) natricina, survey and study.  Unpublished report to the US Bureau of Reclamation, Boise, Idaho.  87 pp.

[8] Gates, K. K., B. L. Kerans, J. L. Keebaugh, S. K. Kalinowski & N. Vu (2013) Taxonomic identity of the endangered Snake River physa, Physa natricina (Pulmonata: Physidae) combining traditional and molecular techniques.  Conserv. Genet. 14: 159-169.

[9] I have corrected a pair of typographic errors in one of the accession numbers as published in [8].  Not "JF80634" but rather JF806434.