Cytoplasmic Male Sterility in the Snake River Physa

Editor’s Note – This is the fourth installment of my three part series on the Snake River Physa controversy.   So if you’re interested in all the public policy craziness surrounding the nominally endangered Physa natricina, I would recommend that you back up to my posts of [14May24], [11June24], and [2July24] before proceeding.  If you’re just interested in the science, on the other hand, you might want to refresh your memory with  my [9June22] essay on cytoplasmic male sterility.

Last month we reviewed a mtDNA sequence dataset collected by Mike Young and colleagues [1] from “The Twelve Phascinating Physa of Bliss,” a small sample taken by IPC/FWS biologists from the tailwaters of the Bliss Dam in the Snake River of Idaho in 2019.  That sample included N = 4 snails bearing a CO1 sequence so strange and divergent that our buddy Mike hesitated even to assign it to the genus Physa.  He called the four snails bearing that sequence “Snake River Candidate Species 3,” or SRCS3 for short.

Blasting Mike’s SRCS3 sequences against the entire worldwide NCBI GenBank, we confirmed that OK510774 (taken as typical for the set of four) was more similar to a planorbid from Bangladesh than to any other physid sequence ever reported, “with five phascinating exceptions.”  SRCS3 was approximately 93% similar to two Physa sequenced in Singapore [2], and three Physa sequenced in South Africa [3].

With those little scraps of data in front of us last month, I speculated that SRCS3 might be a strain of Physa acuta demonstrating cytoplasmic male sterility (CMS).  And at that point I abruptly shifted focus to a remarkable paper published in 2022 by my good friend Patrice David and colleagues, reporting very similar levels of mtDNA sequence divergence in a French strain of Physa acuta unable to mate in the male role, but nevertheless fully fertile as female [4].  Could the Snake River – Singapore – South Africa sequence signal the existence of a second case of CMS, a mitotype strikingly different both from the normal, simultaneously hermaphroditic (N) strain and the divergent, male-sterile (D) discovered by Patrice and his team?

Yes.  Two days after I posted last month’s essay I sent an email to Patrice, subject line “Shout-out on the FWGNA blog,” the entire body of which simply read, “I thought you might be interested to see how your 2022 paper on cytoplasmic male sterility could have an impact on conservation biology here in the USA.”  And Patrice replied with a pdf reprint that knocked my socks off [5].

The paper was published in Evolution by Patrice’s student Fanny Laugier, working with a team of nine coauthors from Montpellier and Villeurbanne [6].  Although available in preprint since March, it just appeared in the physical journal last month.  But let’s back up two steps before we leap forward three.

Cytoplasmic male sterility is well studied in plants.  And given the accelerated rates of mutation demonstrated by mitochondria hosting CMS genes, I do not suppose it is surprising that natural populations of gynodioecious plants often host multiple, independently evolving CMS lines.

And as I mentioned in my essay of [9June22] natural populations of gynodioecious plants hosting CMS mitochondria have also often evolved nuclear genes that restore male fertility.  This results from the selective advantage that a fully functional hermaphrodite has over other members of its population reproducing strictly as a single sex [7].

So, reasoning from numerous well-documented cases in plants, Fanny and her team returned to the Physa populations around Lyon originally studied by Patrice and his colleagues to look for additional CMS strains.  And sure enough, prospecting around with a clever PCR test, they found seven individual snails in two populations bearing a “mitotype K,” startlingly different from both normal hermaphroditic N and the CMS mitotype D they had reported in 2022.

My readership might also remember from [9June22] that CMS mitotype D was, around the entire mitochondrial genome, approximately 44% different from the normal Physa acuta mitotype N.  The 20% CO1 sequence divergence between those two mitotypes was actually less than average.  So the newly discovered mitotype K ultimately proved to be 35% - 57% divergent from N and 35% - 57% divergent from D (ten genes), with CO1 sequence divergences 23% and 28%, respectively.  This is the phenomenon I have termed “mitochondrial superheterogeneity” in many previous posts on this blog [8].

And can you smell what our French chefs are cooking?  Focusing now on the CO1 sequence, the French CMS strain bearing the newly discovered mitotype K matched Ting Hui Ng’s [2] Singapore sequence and Molaba’s [3] South Africa sequence 100%, almost identically.  And the match with Mike Young’s [1] SRCS3 sequence from the Bliss Rapids was 93%, just as I reported last month.  Fanny Languier, Patrice David, and their colleagues had discovered a strain of Physa acuta bearing a wildly divergent mitochondrion worldwide in its distribution.

Laugier [6] Figs. 1B and 1C, modified.

But that is not the headline news.  Here is the headline.  Mitotype K Physa acuta were not male-sterile!  Our French colleagues cultured up a big batch of Mitotype K Physa and were easily able to cross them with their albino N laboratory line [9], both lines copulating readily in both the male and the female role.

So again, reasoning from many years of accumulated research on cytoplasmic male sterility in plants, Fanny and her team suspected that nuclear genes might have evolved in the mitotype K line to restore male function.  And they launched a 17 – generation introgression experiment to insert mitochondrial lineages derived from their wild-caught (pigmented) K line into the “naïve” nuclear background of their (albino) laboratory line N.

And sure enough!  After just 5 generations of introgression, 69% of the naïve snails bred to bear K-type mitochondria had lost their ability to mate as males, with no such loss whatsoever in control lines bearing the N-type mitochondria.  After 11 generations, the proportion of naïve male-sterile K snails stabilized at around 60%.  No loss in female function was ever detectable in any line.  In my 5July24 email back to Patrice, I wrote:

“Wow, nuclear restorers!  It's a shame we work with crap-brown little trash snails.  If snails were maize, wheat, or rice [10], we'd be rich.”

What wonderful science!  Deductive reasoning, tested by rigorous experimentation carefully designed to proceed from the known to the unknown.  Conducted for the joy of it, for the exploration of evolutionary mechanisms, for the pushing back of the darkness.  The construction of testable hypotheses about the natural world, period, full stop, nothing more and nothing less.  Pure and unsullied science, utterly useless and wonderful!

Laugier [6] Fig. S1, modified.

And yet, it turns out, completely by accident, useful.  Ting Hui’s study in Singapore was directed toward invasive species, the Molaba study in South Africa was parasitological, and Mike Smith’s study on the Snake River directed toward conservation.  Fanny’s results contribute toward an understanding of all those results, and more.

And here is Lesson Number One.  Gene sequences are not species.  A species is a population or group of populations reproductively isolated from all others [11].  Sequence divergence is typically correlated with reproductive isolation [12], of course, no different from morphological divergence.  But gene trees are not species trees, and genes are not species.

So, as I pointed out in last month’s essay [2July24], the Snake River line of Physa acuta that Mike Young and colleagues called SRCS3 is not the same as the French mitotype K.  The two lines are 7% different, as though they arose from a single mutation in some mitochondrial DNA repair gene sometime in the past and have subsequently diverged.  Could such a mutation have occurred more than once in the evolutionary history of the Physidae, here in North America, where Physa seem to have first evolved?  You betcha.

There is no reason that the CO1 gene sequence that Gates, Kerans and colleagues [13] recovered from the stunted Physa below the Minidoka Dam, roughly 15% different from the N line at Bliss (OK510580), couldn’t be evidence of yet another CMS strain in Physa acuta.  Gates and Kerans identified that sequence as “Physa natricina.”  But gene sequences are not species.  Species are defined by reproductive isolation.  And we have no data on reproductive relationships between the Minidoka population and the dirt-common Physa acuta downstream whatsoever.  And plenty of evidence otherwise [14].

Nor is there any reason in the world that the peculiar mitotype shared by Mike Young’s SRF14, the Owyhee Wet Rock Physa of eastern Oregon [15] and scattered in odd lot Physa populations from California to British Columbia couldn’t be evidence of a CMS strain in Physa gyrina.  MtDNA sequence data, and the gene trees we make with them, are (at best) weak null models of population relationships, correlated with speciation, nothing more [16].

Do not misunderstand me.  I am not demanding controlled breeding studies between every pair of the 2.2 x 10^6 species described from Planet Earth.  But for nominally endangered species, such as Physa natricina, before we enact pages of Federal regulations and spend millions of dollars on conservation, we could at least run a couple of $12 allozyme gels and test for evidence of assortative mating [17]  with a nuclear polymorphism or two, am I right?

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] Ng, T.H., Tan, S.K. & Yeo, D.C. (2015) Clarifying the identity of the long-established, globally-invasive Physa acuta Draparnaud, 1805 (Gastropoda: Physidae) in Singapore. BioInvasions Rec. 4, 189–194.

[3] Molaba, G.G. et al. (2023) Molecular detection of Fasciola, Schistosoma and Paramphistomum species from freshwater snails occurring in Gauteng and Free State provinces, South Africa.  Veterinary Parasitology 320: 109978.  https://doi.org/10.1016/j.vetpar.2023.109978

[4] David, Patrice, Cyril Degletagne, Nathanaëlle Saclier, Aurel Jennan, Philippe Jarne, Sandrine Plénet, Lara Konecny, Clémentine François, Laurent Guéguen, Noéline Garcia, Tristan Lefébure, Emilien Luquet (2022) Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination.  Current Biology 32: 2325 - 2333.  https://doi.org/10.1016/j.cub.2022.04.014.  For a review, see:

• Cytoplasmic Male Sterility in Physa! [9June22]

[5] Patrice went on to apologize “I told my PhD student Fanny a dozen times to send this to you, that you would probably make good use of it because it was solving a controversy, apparently she didn’t, so I do it myself.” Yes, please send me your reprints!  I lost my library privileges when I was banned from campus in 2016.  I really haven’t had access to most of the scientific literature published since.

[6] Laugier, Fanny, Nathanaëlle Saclier, Kévin Béthune, Axelle Braun, Lara Konecny, Tristan Lefébure, Emilien Luquet, Sandrine Plénet, Jonathan Romiguier, and Patrice David (2024) Both nuclear and cytoplasmic polymorphisms are involved in genetic conflicts over male fertility in the gynodioecious snail, Physa acuta.  Evolution 78 (7): 1227–1236. https://doi.org/10.1093/evolut/qpae053

[7] Yes, mitochondria bearing CMS genes are “selfish” in the sense of the Richard Dawkins (1976) classic.   Don’t get me started on Richard Dawkins.

[8] Mitochondrial superheterogeneity (mtSH), where two or more of the members of a single population demonstrate greater than 10% divergence in any single-copy mtDNA gene, not sex linked, seems to be remarkably common in freshwater gastropods.  In pulmonate populations, I wouldn’t be surprised if most or all mtSH is ultimately traceable to CMS.  In prosobranch populations, however, I think mtSH is a signature of great age, plus low-frequency long distance dispersal, the “Jetlagged Wildebison Model.”  Here is a sample of my previous posts on mtSH:

• The Snails the Dinosaurs Saw [16Mar09]
• Mitochondrial superheterogeneity: What we know [15Mar16]
• Mitochondrial superheterogeneity: What it means [6Apr16]
• Mitochondrial superheterogeneity and speciation [3May16]
• Mitochondrial heterogeneity in Marstonia lustrica [3Aug20]

[9] Dillon, R.T. and A.R. Wethington (1992) The inheritance of albinism in a freshwater snail, Physa heterostropha. Journal of Heredity 83:208-210. [pdf]  For nice review, see:

• Albinism and sex allocation in Physa [5Nov18]

[10] The clever manipulation of cytoplasmic male sterility, together with nuclear restorers, has been one of the more important methods by which plant breeders have achieved the outcrossing of normally self-pollinating crop plants.  I am quite sure that a lot of money has been made with that genetic technology.  With Physa acuta, however, the prospects are not as lucrative.

[11] This is the biological species concept, most closely associated with the work of Ernst Mayr.  It should need no restatement, much less a defense.  But the best paper Jerry Coyne ever wrote was a defense of both Mayr and his species concept, here:

• Coyne, J. A. (1994) Ernst Mayr and the origin of species.  Evolution 48: 19 – 30.

[12] Dillon, R. T., A. R. Wethington, and C. Lydeard (2011)  The evolution of reproductive isolation in a simultaneous hermaphrodite, the freshwater snail Physa.  BMC Evolutionary Biology 11:144. [html] [pdf].  For a review, see:

• What is a species tree? [12July11]

[13] 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.  For a review, see:

• The Mystery of the SRALP: No Physa acuta were found [2May13]

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

• Red flags, water resources, and Physa natricina [12Mar08]

[15] Moore, A.C., J.B. Burch, and T.F. Duda Jr. (2015) Recognition of a highly restricted freshwater snail lineage (Physidae: Physella) in southeastern Oregon: convergent evolution, historical context, and conservation considerations.  Conservation Genetics 16: 113 – 123.

[16] I have made this argument as many times as the number of essays listed under the label “Gene trees” above.  For an overview, see:

• Gene trees and species trees [13July08]

[17] For an explanation of gametic phase disequilibrium, its power to distinguish species, and its extension to character phase disequilibrium, see:

• What is character phase disequilibrium? [4Jan22]
• Character phase disequilibrium in the Gyraulus of Europe [4Feb22]
• Just 125 Species of Pyrgulopsis in the American West [7Sept22]

The Twelve Phascinating Physa of Bliss

Editor’s Note – This is the third episode in a three part series on the Snake River Physa controversy, prompted by the recent paper of M. K. Young and colleagues [1].  If you’re new to this blog, and seriously interested in the science, I would recommend that you back up two months and read my essays of [14May24] and [11June24] before continuing onward.  I’ve also written six older posts on the subject 2008 – 2013, but no point in going back that far, screw it.

In August of 1979 the Idaho Power Company (IPC) received a permit to study the construction of a proposed A. J. Wiley Hydroelectric Project on the Snake River at RM 565, about 1.5 miles west of the little town of Bliss [2].  The proposed dam would have impounded a narrow reservoir as deep as 85 feet nearly eight miles upstream, to the foot of the Lower Salmon Falls Dam.  Inundated would have been the childhood home of a lichen biologist named Dr. Peter Bowler.

By 1992, Bowler had developed a second career as a malacologist, thick as thieves with Dwight Taylor, Terry Frest, and Ed Johannes.  A new species of Physa had been described, Physa natricina, which although found as a fossil throughout northern Utah and southern Idaho, was known alive only from RM525 to RM571 of the Snake River [3].  The “Snake River Physa” had been fast-tracked onto the Federal Endangered species list [4], and the A.J. Wiley Project had been permanently shelved.

The Snake River at RM 570

So last month we reviewed the exciting story of heroic efforts by IPC biologists working in the tailwaters of the Swan Falls Dam, RM 420 – 449, ultimately yielding hundreds of small physids matching the Physa natricina phenotype in at least some respects [11June24].  Because the IPC sample was taken 76 miles downstream from the type range, however, we referred to this population as “Snake River natricina-like Physa,” or SRNLP for short.  Ultimately, the SRNLP from RM 420 – 449 proved a genetic match with Physa acuta, a trash snail invasive on five continents [1].

This is not the situation at RM 675, however.  Previously we have reviewed very similar efforts by biologists engaged by the U.S. Bureau of Reclamation in the tailwaters of the Minidoka Dam 100 miles upstream of the type range of Physa natricina [5].  There, the SRNLP bear a unique mtDNA haplotype, not matching Physa acuta.

Between the Swan Falls Dam and the Minidoka Dam, in the actual type range of Physa natricina, previous research results have been equivocal.  Rogers and Wethington examined hundreds of physids sampled from this stretch of river by IPC biologists 1995 -2007, ultimately unable to distinguish the entire lot from Physa acuta [6].  John Keebaugh disagreed, selecting a small subsample as bona fide Physa natricina.  But the genetic results from the Keebaugh subsample were dubiously reported and never vouchered [7].

Are there no reliable genetic data for Snake River physids sampled between RM 525 and RM 571?  Well, yes, there are.  Twelve very interesting and extraordinarily diverse mtDNA sequences from the tailwaters of the Bliss Dam at RM 559, to be precise.

The Snake River in Idaho, modified from Gates et al [7]

It materializes that the Idaho Power Company has interests that extend beyond the conservation biology of freshwater gastropods.  Sport fishing is an important part of the local economy of the small communities along the Snake River, for example, and mercury levels in the game fish a matter of some concern to the IPC [8].  IPC biologists also have an ongoing project to survey mercury levels in the macrobenthos, as a component of the diet of the white sturgeon.

And so it came to pass that on 17Sept19 a team of IPC and USFWS biologists gathered to sample macrobenthos from the tailwaters of the Bliss dam at RM 559 with a suction dredge.  Their sample came from wadable depths – not the middle of the river – and Physa were not the target [9].  But the 12 individual Physa recovered as bycatch were sent to Mike Young and colleagues at the National Genomics Center for Wildlife and Fish Conservation in Missoula for analysis, along with that big sample of P. acuta from the Swan Falls tailwaters we obsessed over last month [1].  And the results were fascinating:

P. gyrina, Snake R. [10]

N = 1 Physa gyrina.  This is the most widespread of the Snake River physids, inhabiting the main stem throughout the state of Idaho, upstream beyond the Minidoka Dam and into many of the tributaries.  Populations of P. gyrina are not as invasive as P. acuta, however, demonstrating slower growth rates, larger sizes at first reproduction, and lower fecundities per unit body mass.  The CO1 sequence similarity between the singleton P. gyrina recovered by IPC biologists at Snake River mile 559 (SRP199 = OK510769) and the type P. gyrina sequence from Council Bluffs, Iowa (AY651187) is 99.0%.  Good.  No surprises there.

N = 5 Physa acuta.  Arbitrarily selecting the first-listed of the five sequences in this most common category of physids recovered from the Bliss tailwaters, the divergence of SRP001 (= OK510580) from the P. acuta type sequence (River Garonne, AY282589) is 4.7%, and the divergence with our typical P. acuta sequence from the Swan Falls tailwaters (SRP051 = OK510624) is 3.4%.  Apparently, a population of very ordinary, typical [11] Physa acuta was found, again.  This is additional confirmation, if any was needed, that the range of a trash snail invasive on five continents does in fact extend 76 miles up the Snake River from Swan Falls to the type locality of Physa natricina.  Fine.  No surprises there, either.

N = 4 Snake River Candidate Species 3 (“SRCS3”).  Four individual physids sampled from the Snake River at RM 559 bore a haplotype so divergent from all other sequences in the worldwide database that Mike Young, bless his heart, considered the evidence “consistent with their assignment to a separate genus.”  Ultimately, however, Mike decided simply to nominate this subset of four as #3 in his slate of 18 new “candidate species” for the physinine malacofauna of North America.

P. acuta, Snake R. [13]

Picking the first SRCS3 sequence from my buddy Mike’s Supplementary Table 2 as typical (SRP206 = OK510774), we can immediately confirm nearly negligible CO1 sequence similarities of 76.1% with Bliss acuta (OK510580) and 75.8% with Bliss gyrina (OK510769).  Indeed, blasting OK510774 against the entire NCBI GenBank database, we discover that Mike’s SRCS3 is more similar to Indoplanorbis exustus from Bangladesh than to (essentially) any other physid sampled from anywhere else in the world, with five phascinating exceptions.

Mike Young’s SRCS3 sequences are 93.2% similar to a pair of CO1 sequences uploaded by Ting Hui Ng and colleagues from their famous survey of freshwater gastropods in the ornamental pet trade of Singapore (KP182981 and KP182982).  I reviewed Ting Hui’s paper shortly after its 2016 publication [14], adding a footnote to her earlier paper focusing on Singapore Physa in particular [15], and a footnote connecting the Singapore Physa to the situation in the Snake River of Idaho, which now looks genuinely prophetic [16].

Mike Young’s SRCS3 sequences are also 92.1 – 93.9% similar to a set of three sequences very recently uploaded to GenBank by Gantshe Molaba and colleagues [17] from a 2023 parasitological study in South Africa (ON953193, ON953197, ON953200).  The South African sequences and the Singapore sequences are virtually identical.

What is going on here?  In Singapore and in South Africa and now in the Snake River, physids bearing an extravagantly divergent haplotype have been recovered together with Physa acuta bearing a typical haplotype, and in none of these cases did the authors of the papers report any corresponding morphological distinction between divergent and typical snails.

This situation looks precisely like the situation in France, and indeed right here in Charleston, South Carolina, elegantly demonstrated by our good friend Patrice David and his colleagues [18] to be a signature of cytoplasmic male sterility.  Patrice has hypothesized that mutation in some component of the mitochondrial DNA repair mechanism has simultaneously increased mitochondrial mutation rates in such lines and robbed their bearers of fertility in the male function.  But because they retain female function and mate freely with typical P. acuta (serving as male), they have not speciated.  They are still Physa acuta.

From David et al. [18]

Male-sterile variants of P. acuta are also at least as invasive as typical P. acuta, possibly even more so.  It is impossible to resist pointing out that the middle Snake River Valley is home to scores of fish hatcheries and fish farms, jostling each other for every cubic foot of the spring water that gushes forth from its scenic canyon walls, yielding truckloads of rainbow trout, cutthroat trout, salmon and steelhead.  It was almost certainly these hatcheries, and the fisheries they support, that introduced Potamopyrgus into the American West back in 1987.  Surely, they could bring exotic Physa into this country as well, yes?

Sure, maybe.  But we should also immediately note that Physa acuta is a North American native, and it is just as likely that we exported a male sterile variant to Singapore as Singapore exported one to us.  And the Snake River strain is not the Singapore strain.  They are 6.8% different, as though they sprang from a single mitochondrial mutation, and have subsequently diverged.

And the hypothesis that SRCS3 really is a valid biological species cannot be ruled out.  I’ve been footnoting the possibility of a second acuta-like Physa in the Pacific Northwest for years now – even suggesting Haldeman’s (1843) concolor as a possible name for the critter [19].  Wouldn’t it be great to do some old-fashioned breeding studies here?  Informed by old-fashioned nuclear markers – allozymes, microsatellites, anything?  I have a dream.

N = 2 Snake River Form 14 (“SRF14”).  Mike Young, bless his heart, declined to nominate the two individual snails (SRP200 and SRP201) recovered from the Bliss tailwaters bearing CO1 sequence OK510770 as a “candidate species” unto themselves, instead referring to them as “Form 14” of the 34 “forms” of physinine snails he ultimately distinguished in his stupendous gene tree.  His OK510770 sequence is 92.6% similar to Bliss gyrina (OK510769) and just 83.6% similar to Bliss acuta (OK510580).

Blasting the CO1 sequence Mike Young obtained from his two SRF14 individuals against the entire NCBI GenBank database, we discover that OK510770 is 95 - 96% similar to a set of 13 sequences obtained by University of Michigan (UMMZ) researcher A. C. Moore, with Jack Burch and Tom Duda, from a “highly restricted freshwater snail lineage” they introduced to the world in 2014 as the “Owyhee Wet-Rock Physa,” or OWRP for short [20].

The Owyhee River enters the Snake River in eastern Oregon at RM 395, downstream 165 miles from the Bliss Dam.  (See map below.)  It would be quite the adventure, but if one could float those 165 miles down the Snake to the Oregon border then pioneer back up the Owyhee approximately 130 miles through deep, arid canyons one would arrive at a geothermal spring complex inhabited by a population of Physa that apparently reminds everybody, both in their morphology and in their life habit, of the federally endangered Physa zionis of Utah.

Fig 1 of Moore et al [20] modified

Both the Owhyee Wet-rock Physa and Physa zionis are tiny, stunted little things, with grotesquely expanded body whorls, even more stunted and even more grotesque than Physa natricina.  What is the chance that Mike Young’s SRF14 might be Dwight Taylor’s long-sought and much-endangered species?

The evidence does not point in that direction.  As most of my (highly specialized) readership will be aware, pulmonate snails of the family Physidae bear several distinct types of penial morphology.  The most common type was called “Type C” by George Te in 1975 [21] – bearing a one part, muscular penial sheath.  Type C physids include Physa acuta, Physa natricina [22], and Physa zionis.  Also quite common in North America are physids bearing “Type B” penial morphology – a two part penial sheath – such as demonstrated by Physa gyrina.  If that distinction is unfamiliar to you, and you have more than a casual interest in the Snake River Physa controversy, I would assign the 2007 paper of Wethington & Lydeard [23] for homework.

Wethington & Lydeard showed that penial morphology correlates with molecular phylogeny.  So, although neither the IPC/USFWS team that fished them from the Bliss rapids nor Mike Young, bless his heart, dissected any of the 12 fascinating physids under discussion here, nor (indeed!) did the UMMZ group dissect any of their Owyhee Wet Rock Physa, it turns out that both the SRF14 sequence and the 13 OWRP sequences all clustered together with Type B Physa gyrina, not with Type C Physa acuta/natricina/zionis.

So, the next four paragraphs will be a digression, but indulge me.  The UMMZ group sequenced 13 Owhyee Wet-rock Physa for three genes, ultimately obtaining five slightly different CO1 sequences (KF305393 – 405).  While a match to P. zionis was not confirmed, those sequences did demonstrate a 95% match to a set of 11 CO1 sequences (KF305406 – 416) obtained from a population identified as Physa gyrina inhabiting Aqua Fria Creek, about 20 miles west of Yosemite National Park in central California.

And in 2018, four years after the publication of the OWRP paper, our hardworking friends at the Centre for Biodiversity Genomics (CBG) in Guelph uploaded to GenBank a “Physidae sp.” sequence collected from a beaver pond by the Similkameen River in southern British Columbia (MG421809) that also demonstrated a 95% match to the OWRP.  The Similkameen River flows south into the Okanogan River, joining the Columbia River in central Washington.

Now for the punch line.  It materializes that Mike Young’s SRF14 sequence, collected by IPC/USFWS biologists from the Bliss Rapids of the Snake River, is a stunning 99.7% similar to that “Physidae” sequence collected by the CBG from the beaver pond by the Similkameen 500 miles to the northwest.

Do the four populations mapped above, inhabiting wet rocks on the eastern edge of Oregon, a creek in central California, a beaver pond in southern British Columbia, and now discovered in the Bliss rapids of the Snake River of Idaho, represent a single previously unrecognized species of Type B Physa, extraordinarily variable, widespread across western North America?  Or might they have evolved from a male-sterile variant of Physa gyrina, as SRCS3 seems to have evolved from Physa acuta?

Again, as was the case with SRCS3 and P. acuta, Mike Young’s SRF14 population is sympatric with a population of Physa gyrina of the typical phenotype, bearing mitochondria of the typical haplotype.  Dare I dream that some worthy and industrious graduate student might someday survey these populations for variation at some sort of nuclear marker or markers and look for reproductive isolation, or lack thereof?  Followed by some breeding studies, perhaps?

There was a time in my career when I could have answered every question posed in this entire essay with a day in the field, four days in the lab, and $100 for reagents and expendable supplies.  Get a nice, big sample of Physa from the Bliss Dam tailwaters, paying attention to microhabitat.  Examine their anatomy and shell morphology critically, sort them into Type B and Type C subsets.  Within those subsets, are nuclear markers segregating in Hardy-Weinberg equilibrium?  How many biological species of Physa are we dealing with here?  Give me another six months and a student or two, and the breeding experiments done would have been done.  How many million dollars and years of wandering in a wilderness of ignorance and superstition might timely reference to a scientist, who actually knows something about the biology of the living, breathing animals he is studying, have saved?

N = 0 Minidoka SRNLP.  Although otherwise bearing a stunningly diverse array of mitochondria, our little sample of 12 physids from the tailwaters of the Bliss Dam did not include any bearing a CO1 sequence matching that of the peculiar little misshapen Physa recovered from the Minidoka Dam tailwaters 116 miles upstream, ascribed by Gates, Kerans and Keebaugh to Physa natricina [7].  True, the IPC/USFWS biologists did not sample midstream, where Physa bearing such haplotypes were recovered at Minidoka.  This is a weak test, indeed.

But these are all the relevant data we have, for 18 years of effort by multiple teams of hardworking, well-meaning biologists and millions of dollars flushed down the toilet.  So, since Physa acuta do indeed appear to be common in the shallows of the Snake River in the type range of Physa natricina, and since populations identified as Physa natricina in the Swan Falls tailwaters, both in the shallows and at midstream, are synonymous with P. acuta, the strongest hypothesis at present remains that the population Dwight Taylor described as Physa natricina in its RM 525 – 571 type range is a junior synonym of Physa acuta, as suggested by Rogers and Wethington in 2007.  And the SRNLP population in the roiling tailwaters of the Minidoka Dam is Something-Else-God-Knows-What.

To summarize.  On [12Mar08] I posted the following overly optimistic observation:

“Science is a self-correcting process. It is gratifying to see two of our own, Rogers and Wethington, designing the research program and publishing the paper that has turned us back from our 20-year blunder. But at such a cost! Literally millions of dollars have been wasted monitoring, managing, and protecting a snail that anyone on six continents could find in the ditch behind his local McDonalds, licking special sauce off the hamburger wrappers.”

Now 16 more years have passed, the Rogers and Wethington paper ignored, and millions of additional dollars wasted.  In 2008 I was laboring under the assumption that the world of science and the world of public policy could find some common frame in which to communicate.  Although I went on to write, “Science and politics do not mix,” in retrospect, I should have written that science and public policy cannot mix.

I am playing bluegrass music.  The natural resource agencies are playing baseball [24].  And the Idaho Power Company, just trying to run a business heaven help them, is standing in the batter’s box with a fiddle.

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] Malde, H. E. (1981)  Geologic factors pertinent to the proposed A. J. Wiley Hydroelectric Project, No. 2845, Bliss, Idaho.  U.S. Department of the Interior, Open File Report 81-569.  75 pp.

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

[4] 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)

[5] Gates, K. K., and B. L. Kerans (2010) Snake River Physa, Physa (Haitia) natricina, Survey and Study.  Report to the US Bureau of Reclamation under agreement 1425-06FC1S202.  87 pp.  For a review of this report, see:

• 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]

[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.  For a review, see:

• Red Flags, Water Resources, and Physa natricina [12Mar08]

[7] 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. For reviews, see:

• The Mystery of the SRALP: No Physa acuta were found [2May13]
• The SRALP and the SRNLP: A New Hope [14May24]

[8] Willaker, J.J., C.A. Eagles-Smith, J.A. Chandler, J. Naymik, R. Myers and D.P. Krabbenhoft (2023) Reservoir stratification modulates the influence of impoundments on fish mercury concentrations along an arid land river system.  Environmental Science & Technology. DOI: 10.1021/acs.est.3c04646

[9] This is a personal communication from my friend Jim Chandler at IPC.  No reports or publications are as yet available for the sturgeon/food web/methylmercury research project.

[10] The specimen of P. gyrina figured above was collected by RTD from wetlands below the Minidoka Dam on 19Sept2010.

[11] Actually, I think the Snake River population of P. acuta may represent the “Clade B” form of Ebbs, Loker, and Brant [12].  The sequence similarity of OK510580 to Clade B sequence MF694449 from Montana was 98.2%.

[12] Ebbs, E.T., Loker, E.S. & Brant, S.V. (2018) Phylogeography and genetics of the globally invasive snail Physa acuta Draparnaud 1805, and its potential to serve as an intermediate host to larval digenetic trematodes. BMC Evol Biol 18, 103. https://doi.org/10.1186/s12862-018-1208-z

[13] The specimen of P. acuta figured above was collected by RTD from the Snake River at Bliss, 19Sept2010.

[14] Ng, Ting Hui, Tan SK, Wong WH, Meier R, Chan S-Y, Tan HH, Yeo DCJ (2016) Molluscs for Sale: Assessment of Freshwater Gastropods and Bivalves in the Ornamental Pet Trade. PLoS ONE 11(8): e0161130. https://doi.org/10.1371/journal.pone.0161130.  For a review, see:

• What’s Out There? [9Oct17]

[15] Ng, T.H., Tan, S.K. & Yeo, D.C. (2015) Clarifying the identity of the long-established, globally-invasive Physa acuta Draparnaud, 1805 (Gastropoda: Physidae) in Singapore. BioInvasions Rec. 4, 189–194.

[16] If you write five crazy things per month for 25 years, eventually at least one will turn out to be a prophecy.  See footnote [6] of my [9Oct17] post for an example.

[17] Molaba, G.G. et al. (2023) Molecular detection of Fasciola, Schistosoma and Paramphistomum species from freshwater snails occurring in Gauteng and Free State provinces, South Africa.  Veterinary Parasitology 320: 109978.  https://doi.org/10.1016/j.vetpar.2023.109978

[18] David, Patrice, Cyril Degletagne, Nathanaëlle Saclier, Aurel Jennan, Philippe Jarne, Sandrine Plénet, Lara Konecny, Clémentine François, Laurent Guéguen, Noéline Garcia, Tristan Lefébure, Emilien Luquet (2022) Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination.  Current Biology 32: 2325-2333.  https://doi.org/10.1016/j.cub.2022.04.014.  For a review, see:

• Cytoplasmic Male Sterility in Physa! [9June22]

[19] The hypothesis “that some physid bearing a type-C penial morphology, but not correctly identified as either P. natricina or as P. acuta, might inhabit rivers of the Pacific Northwest” was Hypothesis #2 (of 3) in my post of [14Sept10].

[20]  Moore, A.C., J.B. Burch, and T.F. Duda Jr. (2015) Recognition of a highly restricted freshwater snail lineage (Physidae: Physella) in southeastern Oregon: convergent evolution, historical context, and conservation considerations.  Conservation Genetics 16: 113 – 123.

[21] Te, G. A. (1975) Michigan Physidae, with systematic notes on Physella and Physodon (Basommatophora: Pulmonata).  Malacological Review 8: 7-30.  For a review, see:

• To Identify a Physa, 1975 [6May14]

[22] Figure 6 in Dwight Taylor’s original description [3] clearly shows a type-C penial morphology.  And Jack Burch’s Fig 2.3 confirms that the SRNLP population in the Minidoka tailwaters are also type-C Physa [5].

[23] Wethington, A.R., & C. Lydeard (2007) A molecular phylogeny of Physidae (Gastropoda: Basommatophora) based on mitochondrial DNA sequences.  Journal of Molluscan Studies 73: 241 - 257. For a review, see:

• The Classification of the Physidae [12Oct07]

[24] The relationship between the worldview of science and the worldview of public policy is analogous to the relationship between music and sports.  They have different languages, cultures, and values.  They are not “compatible” in any sense, neither are they “incompatible” in any sense, because they are absolutely, utterly different.  Nothing I have written in this essay, nor indeed  any scientific findings of any sort, can ever have any effect on public policy.  I play the banjo, and the USFWS plays baseball.

Most of advocates for science in public policy are harmless naïfs, enamored of big government, Democrats the lot of them.  I worked with a building full of that sort 1982-83, as a AAAS Congressional Fellow on Capitol Hill.  They write reports which nobody reads.  No harm in that.

But should any person step forward, claiming to be a scientist, promising to conduct research to inform some issue of public importance, in exchange for contract money or grant, beware!  This is a charlatan, and pseudoscience is his snake oil.   

The SRALP and the SRNLP: Physa acuta were found

Editor’s Note: This is the second essay in a fresh series on the Snake River Physa controversy, prompted by the 2021 publication of new genetic data by M. K. Young and colleagues [1].  If this is your first visit to the FWGNA blog, I would suggest that you back up to last month’s post at minimum [14May24].  And if you have a serious interest in the subject, from last month’s essay you can follow links to six previous posts on Physa natricina and the Snake River, 2008 – 2013.

Located 35 miles south of Boise on the Snake River at River Mile (RM) 458, the Swan Falls Dam is something of a museum piece.  It was constructed in 1901 by local mining companies as a demonstration of the potential for waterpower to drive industry in a land that was just beginning to assert its potential.  That dam and its generating plant were consolidated into the newly incorporated Idaho Power Company, IPC, in 1916.

Swan Falls Dam

Physa natricina, described in 1988 from the Snake River upstream at RM525 – RM571 [2], was entered onto the federal endangered species list in 1992 [3].  And at that point, alas, IPC found itself in the Physa business, as well as in the power business.  IPC biologists initiated a comprehensive Physa survey and monitoring program in 1995, beginning way downstream at the Oregon border (RM 340) extending upstream to the Lower Salmon Falls Dam (RM 573), using a broad range of sampling techniques, including Venturi loop dredging apparatus operated by tethered divers in deeper and more rapid waters.  By 2007, over 1,500 Physa specimens had been collected from these 233 miles of river, identified to genus (only) and deposited in the Orma J. Smith Museum of Natural History (ALBRCIDA) in Caldwell, Idaho.

In 2007, our colleagues Christopher Rogers and Amy Wethington examined this gigantic collection of preserved gastropods and compared them, critically and completely, to the type specimens of Physa natricina deposited by Dwight Taylor in connection with his 1988 description [4].  They found no individual snail matching all eight of Taylor’s diagnostic characters completely.  Indeed, none of Taylor’s paratypes matched all eight characters of his holotype.  Taylor’s “diagnostic characters” were variable.  And that variation extended seamlessly from his holotype Physa natricina to merge with the (extremely variable) North American invasive species Physa acuta, which is what the great majority of those 1,500 snails collected between RM 340 and RM 573 between 1995 and 2007 appeared to be.

Rogers and Wethington synonymized Dwight Taylor’s narrowly endemic P. natricina under the cosmopolitan P. acuta, suggesting as they did that the stunted morphology and unusually large body whorl demonstrated by individuals sampled from stones in exposed environments in the middle of the Snake River might be an ecophenotypic response to life in rapid currents.

Our scene now shifts to the Minidoka Dam, way upstream at RM 675, a hundred miles above any place that Dwight Taylor or IPC ever surveyed for Physa.  The Minidoka Dam is also a museum piece, built by the brand new US Bureau of Reclamation in 1906 to supply water for irrigation.  In 2005 the USBR contracted with a pair of biologists from Montana State University, Kiza Gates and Billie Kerans, “to thoroughly survey the USBR P. natricina recovery area from RM 663-675 and determine if any P. natricina populations or colonies exist” [5].  These surveys, conducted by tethered divers operating Venturi suction dredges, extended through the field seasons of 2006 – 2008. 

Gates & Kerans ultimately recovered 274 physids with shell morphology matching the description of Physa natricina in at least some respects, of which roughly 15 were sequenced for two mtDNA genes by two different laboratories.  Concatenated, these sequences averaged 17% different from a set of reference Physa acuta fished from GenBank.  The gray literature report of Gates & Kerans [5], released in 2010, “confirmed the original description of P. natricina as a distinct species and the existence of a population below Minidoka Dam.”

The Snake River, modified from Fig 3 of Gates et al [6]

My concern, stated forcefully at a meeting convened by the USBR in Boise in September of 2010 [2Apr13], was that the physids Gates & Kerans were identifying as Physa natricina must be compared to the Snake River acuta-like Physa (“SRALP”) common as cockroaches in the shallows of the river downstream, not to random Physa acuta fished from GenBank, none sampled closer than Wyoming, on the other side of the continental divide.  My cries fell on deaf ears [6].

I might also have objected that the physids Gates & Kerans were identifying as “Physa natricina” must also be compared to bona fide Physa natricina sampled from the type range, RM 525 – 571, but I did not realize the significance of that problem until much more recently [14May24].  In retrospect, the Physa that Gates & Kerans did sample below the Minidoka Dam are best referred to as Snake River natricina-like Physa (SRNLP), just as the Physa they did not sample downstream were SRALP.

Setting all such pretty distinctions aside, however, sailing 215 river miles back downstream to the Swan Falls Dam, and picking up the story as told by Idaho Power in a 2011 gray literature report to the FWS [7]:

“Verified specimens of Snake River physa were very rare until recently, when the USBR discovered them in the upper Snake River (Gates and Kerans 2010). These new collections of Snake River Physa prompted IPC to re-evaluate specimens identified as Physidae from samples collected throughout the Middle and Lower Snake River from 1995–2003. John Keebaugh of the Orma J. Smith Museum of Natural History at the College of Idaho in Caldwell, Idaho, identified 51 (live when captured) Snake River Physa from 19,426 specimens identified as Physidae (Keebaugh 2008) (Table 2). These Snake River Physa were collected between Bliss Dam (RM 559.3) downstream to a site near the mouth of the Payette River (RM 367.9). Of the 51 Snake River Physa Keebaugh identified from IPC’s samples, 37 were collected in the (Swan Falls) Action Area (RM344 – RM469).”

The IPC went on to report that anatomical and genetic studies “conducted by Montana State University” had confirmed the Keebaugh identifications.  Those genetic results (from the laboratory of Steven Kalinowski) were dubiously transmitted in 2013 [6] and never vouchered.  But the bottom line is this.  A physid population morphologically indistinguishable from Physa natricina inhabits the rapids downstream from the Swan Falls Dam (RM 458).  This is a factual observation, with which all parties, Christopher Rogers, Amy Wethington, John Keebaugh, Gates, Kerans, and (most importantly) the U.S. Fish and Wildlife Service will all most certainly concur.

IPC biologists collecting suction dredge samples [8]

So, on the basis of what would seem to be universal scientific consensus, in 2011 the FWS required IPC to re-apply for its license to operate the Swan Falls Hydroelectric Project.  That new license, approved on September 28, 2012, contained an article that required a “snail protection plan focusing on Snake River Physa (Physa natricina),” directly analogous to the study that the US Bureau of Reclamation had undertaken in the tailwaters of the Minidoka Dam seven years earlier.  And in 2013 an elaborate five-year plan was approved [9], coauthored by IPC biologists Michael Stephenson [10] and Barry Bean.

But wait.  Because all the Physa populations inhabiting the length of the Snake River in Idaho have been the focus of intense legal and regulatory controversy for over 30 years now, exceptional rigor is demanded throughout.  And again, I must remind all parties that Dwight Taylor stated in his 1988 description that Physa natricina is “restricted to the Snake River from the vicinity of Bliss to Hammett, Idaho,” generally taken to range from RM 525 – 571.  So, the term we coined last month [14May24], “Snake River natricina-like Physa” (SRNLP) is the most appropriate name for both the stunted populations of Physa bearing shells with unusually large body whorls above that range, in the tailwaters of the Minidoka Dam at RM 675, and the stunted populations of Physa bearing shells with unusually large body whorls below that range, in the tailwaters of the Swan Falls Dam at RM 458.

Now moving forward.  The dawn of the 2014 field season saw IPC scuba divers, tethered to boats in the roaring Snake River rapids, sampling rocks and cobbles with Venturi power jet suction dredges at five selected sites between RM 400 and RM 445.  The total of 105 individual physids ultimately recovered [11] were sent to our good friend Hsiu-Ping Liu at the Metropolitan State University of Denver, who was able to obtain 16S mtDNA sequences from 59 of them [12].  The maximum sequence divergence across the entire set of 59 was just 3.6%.  Alas, Hsiu-Ping did not upload her sequences to GenBank or otherwise make them publicly available.  But comparing her big Swan Falls sample to an equally large sample of physids fished from GenBank, Hsiu-Ping concluded, “Based on the genetic evidence presented here, Idaho Power samples clustered with P. acuta.”  Physa acuta were found.

Idaho Power biologists used an identical tethered-diver technique in the 2015 field season, shifting their five sample sites to some extent, ultimately recovering another 59 individual Physa [13].  In 2016 they experimented with three new approaches, however: drift nets, sturgeon egg mats, and multiplate artificial (“Hester-Dendy”) substrate samplers [15].  Just two Physa were recovered in the nets, and just six in the mats, but promising results with the multiplate samplers [16] suggested a shift to that approach in subsequent years.  The 2016 field season was not subsequently counted among the five study years of the contracted project.

SRNLP from Swan Falls tailwaters [14]

In 2017, 2018, and 2019 IPC biologists deployed a two-part artificial substrate sampler of unusual design: a basket of large cobbles hooked to a multiplate Hester-Dendy apparatus [17].  Thirty such samplers were anchored at various spots in the Snake River rapids downstream of the Swan Falls Dam for two periods of five weeks, for each of the three study years remaining.  A total of 132 + 344 + 633 = 1,109 individual physids were recovered from the samplers, a subset of which [19] were sent to the laboratory of a fish guy named Michael K. (Mike) Young, bless his heart, at the USFS Rocky Mountain Research Station for mtDNA sequencing.

Mike and his colleagues [1] ultimately obtained CO1 sequences for 181 physids sampled from the Snake River rapids between RM 420 and RM 449.  These sequences were all fully reported and properly vouchered.  Eight sequences ultimately matched P. gyrina; let’s set those aside.  Then the maximum sequence divergence across the set of 173 that remained was just 4.82% [20].  This is the single largest survey of mtDNA sequence variation ever published for a population of pulmonate snails.

The sequence similarity between the downstream-most sample (SRP051 = OK510624) from RM 420 and the upstream-most sample (SRP182 = OK510755) from RM449 was 100%.  Let’s pick the longer of these two identical sequences, OK510624, as typical for SRALP in the Swan Fall tailwaters.

Mike Young is a hard worker and was very patient with me over several weeks of incessant pestering, and he did his best with the tools the Good Lord packed in his tool box, bless his heart.  He dumped his block of 173 CO1 sequences from Snake River miles 420 – 449 into a gigantic cauldron of 920 physid CO1 sequences downloaded from every database you can imagine, from everywhere around the world, stirred it twice, and pushed the button on a stupendous, smoke-belching, oil-spewing, gear-grinding, tree-making machine.  Shoveled in some coal and gave her a kick.

Cobble Basket / Hester-Dendy sampler [18]

Carelessly tossed into the bubbling Cauldron O’sequences and piped into the Stupendous Tree-Making Machine was one sequence that actually mattered, AY282589, a CO1 sequence from the type locality of P. acuta in the River Garonne, France.  The sequence divergence between OK510624 and AY282589 was 2.4%.  Good, thank you Jesus, finally!  The Snake River acuta-like Physa, the SRALP, is indeed Physa acuta.  At least in the Swan Falls tailwaters, RM 420 – 449.  After all these years of Sturm und Drang. Why was that so hard?

In summary.  As of 2020, the Idaho Power Company had spent six years and millions of dollars for 105 + 59 + 8 + 132 + 344 + 633 = 1,281 Physa acuta, the world’s most cosmopolitan freshwater gastropod, the cockroach of malacology, invasive on five continents.  That is all – that is the complete yield for six years of intense (and sometimes dangerous) effort by a large, well-equipped team of dedicated biologists – with a smattering of P. gyrina easily set aside.

This screaming, flailing 1,281-trash-snail bellyflop will not have been a complete, utter, tragic, waste of time, effort, money and skin if we learn from it.  So, pay attention now.

If (1) A physid population morphologically indistinguishable from Physa natricina inhabits the Snake River rapids downstream from the Swan Falls Dam, and if (2) all the physids inhabiting the Snake River rapids downstream from the Swan Falls Dam are Physa acuta, then (3) the evidence at Swan Falls supports the Rogers and Wethington hypothesis that Physa natricina is a junior synonym of Physa acuta.  Well, to be as precise and rigorous as I can be, The SRNLP is Physa acuta at RM 420 – 449.

But to be clear.  Also dumped into Mike Young’s bubbling Cauldron O’sequences were all nine of the (qualified) CO1 sequences uploaded by Gates, Kerans, and colleagues for the SRNLP sampled from the Minidoka tailwaters 220 miles upstream [6], plus three Minidoka sequences Young and colleagues developed themselves.  Those 12 are (indeed) quite strikingly different from the 173 Physa acuta sampled from Swan Falls, and all other sequences in the worldwide Physa database.  So, the identity of the SRNLP at RM 675 remains unconfirmed.

Halfway between Swan Falls and Minidoka is the actual type range of bona fide Physa natricina, RM 525 - 571.  Does the stunted population of Physa bearing shells with unusually large body whorls in the roaring rapids of the Snake River where it actually matters genetically match the SRNLP population at Minidoka 675, or the P. acuta population at Swan Falls 449?  Or?  Tune in next time.

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

[3] 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)

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

• Red Flags, Water Resources, and Physa natricina [12Mar08]

[5] Gates, K. K., and B. L. Kerans (2010) Snake River Physa, Physa (Haitia) natricina, Survey and Study.  Report to the US Bureau of Reclamation under agreement 1425-06FC1S202.  87 pp.  For a review of this report, see:

• 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]

[6] 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.  [html]  For a review, see:

• The Mystery of the SRALP: No Physa acuta were found [2May13]

[7] Bean, B., and M. Stephenson (2011) Swan Falls Biological Assessment for the Snake River Physa.  (Swan Falls, FERC Project No. 503).  Idaho Power Company, Boise. 30 pp.

[8] “From left to right: Nick Gastelecutto, Michael Stephenson, and Dain Bates.”  This is Figure 2 from the IPC report of the 2014 results [11].

[9] Stephenson, M., and B. Bean (2013) Swan Falls Snake River Physa Protection Plan.  (Compliance Report, Swan Falls FERC Project No. 503, Article 405) Idaho Power Company, Boise.  78 pp.

[10] Michael Stephenson was at the forefront of the Swan Falls Physa project from its beginnings back in 2011 to the present day, designing the studies, spending long days in the field, and writing the reports.  He was tremendously helpful and forthcoming with me in the research for this blog post.  On the Altar of Science in the Temple of Public Policy, Michael’s his sacrifice has been heroic.  Good job, Old Buddy, and thanks.

[11] Bean, B. (2015)  Swan Falls Article 405 Snake River Physa Monitoring Report: 2014 Results.  (Compliance Report, Swan Falls FERC Project No. 503) Idaho Power Company, Boise. 32 pp.

[12] Liu, H-P. (2016) Report on taxonomic identity of the Snake River Physa using molecular techniques.  Appendix 4 (pp 65 – 73) in IPC report of 2015 results [13].

[13] Bean, B. (2016) Swan Falls article 405 Snake River Physa monitoring report: 2015 results.  (Compliance Report, Swan Falls FERC Project No. 503) Idaho Power Company, Boise. 80 pp.

[14] These images come from Appendix 3 of the IPC Report of the 2015 results [13].  Shell lengths (left to right) were given as 1.41 mm, 1.71 mm, 3.64 mm.

[15] Bean, B. (2017) 2016 Snake River Physa Studies in the Swan Falls Reach. (Compliance Report, Swan Falls FERC Project No. 503, Article 405)  Idaho Power Company, Boise. 16 pp.

[16] In 2016, IPC biologists actually deployed their experimental multiplate artificial substrate samplers way upstream at RM 674, below the Minidoka Dam, yielding “2 confirmed Physa natricina, as well as one putative Physa natricina,” which were returned to the river.

[17] Bean, B. (2018) Swan Falls Article 405 Snake River Monitoring Report: 2017 Results.  (Compliance Report, Swan Falls FERC Project No. 503) Idaho Power Company, Boise. 14 pp.

[18] This is Figure 2 of the IPC Report of the 2017 results [17].  Full caption: “Photo of gravel basket and Hester-Dendy artificial substrate samplers.”

[19] As a rule of thumb, the IPC selected individual physids “with a shell length/width ratio of less than 1.5” to forward on for genetic analysis.  I’m not sure where this rule came from.

[20] The team did not formally publish any statistics for their impressive block of 173 sequences.  Mike Young communicated the maximum sequence divergence value of 4.82% to me in personal correspondence.

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.