Dr. Rob Dillon, Coordinator





Friday, February 15, 2019

Dates of Publication

Editor’s Note – This brief post is offered as an appendix to my essay of 6Feb19, “Ferrissia fragilis (Tryon 1863).”

Several of you have pointed out, in separate correspondence with me over the last week, that taxonomic priority is established not by date of oral presentation, but by date of publication.  This does not change the order of the three freshwater limpet descriptions I reviewed in my essay of 6Feb19, nor indeed anything in my essay at all.  But for the record, the precise, formal publication dates of the three limpet taxa I discussed in that essay were: 
  • Gundlachia californica Rowell, (31)May1863
  • Ancylus fragilis Tryon, 13July1863
  • Gundlachia meekiana Stimpson, (31)Dec1863
Our good buddy Dr. Harry Lee, from Jacksonville (FL), is quite the gifted scholar.  Yesterday morning he sent me a thoroughly-researched letter on the subject, together with supporting documentation, which I have made available from the links below: 
  • Letter from H. G. Lee, regarding the nomen Ferrissia fragilis [pdf]
  • Extract from Levinton et al. (2010) [pdf
And to be clear.  Just because I myself am not a priest, nor a scribe, nor a Pharisee does not mean that I don’t value the services they can provide.  Everybody appreciates a scribe now and then.  Thanks, Harry!

Wednesday, February 6, 2019

Ferrissia fragilis (Tryon, 1863)


At 9:30 on the starry but moonless night of April 16, 1863, seven armored gunboats under the command of Admiral David Porter, accompanied by three army transports and a steam ram, began a stealthy voyage down the Mississippi under the guns of Vicksburg.  Water-soaked bales of hay were stacked around their boilers and pilot houses, and coal barges lashed to their starboard flanks.  At 11:10 PM, all hell broke loose [1].

Wikimedia Commons
On the evening of April 20, four days later, the regular biweekly meeting of the California Academy of Natural Sciences convened at 622 Clay Street, San Francisco, seven members present, Dr. Trask in the chair.  Dr. Cooper communicated the description of a new mollusk, recently discovered by Rev. Joseph Rowell in the waters of the Feather River, Gundlachia californica [2].  Images of the little limpet, “length about sixteen one-hundredths of an English inch,” showed a shell apex distinctly different from the embryonic shell origin.  Philip Lutley Sclater, Esq., of London was elected a corresponding member, three species of reptiles from San Mateo added to the cabinet, and the Academy adjourned.

Shortly after 5:00 on the evening of May 2, 1863, the troops on the right flank of General Joseph Hooker’s army at Chancellorsville, VA, stacked their rifles and began to prepare their suppers.  They were amused to see large numbers of deer and rabbits break out of thickets to the west and come bounding toward them.  The men cheered and waved their caps at the startled forest creatures, until the next thing they saw froze the laughter in their throats.  Total casualties at the end of the battle were 3,500 killed and 19,000 wounded.

May 2, Just before dawn.  Wikimedia commons
A bit more than two weeks later, on the afternoon of May 26, 1863, The Academy of Natural Sciences of Philadelphia convened for its regular weekly meeting, 19 members present, Mr. Lea in the chair.  The agenda was lengthy: 9 papers presented and ordered to be published, including an ambitious contribution by T. B. Wilson & J. Cassin proposing a third kingdom of life, the Primalia.  Mr. George W. Tryon read a paper describing seven new species of freshwater gastropods, finishing with Ancylus fragilis [3].  The 4 millimeter limpet, apex elevated, acute and “curved backwards,” had been sent to him from California by Rev. J. Rowell.

On June 3, 1863, General Robert E. Lee began to concentrate his army of 75,000 at Culpeper, in preparation for an invasion northward.  And on the morning of June 8, Union General Alfred Pleasonton probed south across the Rappahannock with six brigades of cavalry, approximately 10,000 horsemen, to gauge Lee’s disposition.  Around noon Pleasonton encountered a roughly equal force of confederate cavalry under Gen. Jeb Stuart at Brandy Station.  Sabers, pistols, and carbines flashing in the sun, the largest cavalry engagement ever fought on American soil was underway.

Cavalry Charge Near Brandy Station, by Edwin Forbes.
Two weeks later, on the afternoon of June 17, the Boston Society of Natural History convened at Tremont Street, Prof. Wyman in the chair.  Mr. Stimpson read a paper on the genus Gundlachia, in which he counted five species, including G. californica, described just two months prior [4].  He went on to describe a sixth species, G. meekiana, collected from the vicinity of Washington DC, similar in all respects to G. californica, but with a less ovate aperture.  One additional paper was read, two communications received, six donations to the museum logged, and the Society adjourned.

Admittedly, the little brown pulmonate limpet that we today call Ferrissia fragilis is not the most striking element of the North American malacofauna.  It is, however, the fourth most common freshwater gastropod in the Eastern United States, behind Physa acuta, Campeloma decisum, and Menetus dilatatus [5].  Populations of Ferrissia fragilis are ubiquitous on aquatic vegetation and organic debris in every lake, pond, and riverine backwater nationwide, Canada to Mexico, sea to shining sea.  Including at the mouth of Pennypack Creek, in north Philadelphia.

Why do you suppose that these exceptionally abundant and wide-ranging little gastropods were completely overlooked by every American biologist working in every puddle of fresh water for half a century, and then simultaneously discovered by three completely separate societies of learned men, meeting in San Francisco, Philadelphia, and Boston, during a single eight-week period of 1863?  What might account for the sudden, passionate interest among young well-born gentlemen of the urban North in freshwater limpets?  I will leave that question to the speculation of my readership.

The Bartow County Yankee Killers [6]
I will, however, take a paragraph to remind you all of several previous essays touching upon Ferrissia fragilis [7].  You may recall, from my essays of 10June09 and 9Nov12, that the freshwater limpets were a particular research interest of Bryant Walker’s (1856 – 1936), and that the definitive monograph was contributed by Paul Basch in 1963 [8].  Both Walker and Basch recognized Ferrissia fragilis as a widespread and important element of the North American malacofauna, and listed californica (Rowell 1863) and meekiana (Stimpson 1863) as junior synonyms of fragilis (Tryon 1863).  And you may also remember my essay of 8Dec10 reviewing the excellent work of Andrea Walther and colleagues [9] synonymizing several additional well-known names under fragilis, including walkeri (Pilsbry & Ferris 1906) and mcneilli (Walker 1925).  So that today, the FWGNA Project recognizes just two species of Ferrissia: rivularis and fragilis.

Up until recently it has been quite easy to ignore the extraordinarily trivial and obscure detail that the meeting of the California Academy which heard the description of G. californica preceded the meeting of the ANSP which heard the description of A. fragilis by five weeks.  For some reason I cannot fathom, however, here in 2019 it has become less easy.

The issue of the American Malacological Bulletin freshly arrived on my desk last month included a research note announcing the “discovery of the freshwater limpet, Ferrissia californica (Rowell, 1863)” on the Island of Montserrat [10].  Tryon’s nomen “fragilis” does not appear in title, abstract, key words, or the first five paragraphs of its introduction.

Do systematic biologists of the 21st century feel some heightened sense of obligation to the Rev. Rowell, now asleep in Christ for 100 years?  Have our oaths to uphold the International Code of Zoological Nomenclature suddenly become more solemn?  Is the iron fist of the ICZN Commission grown more fearsome?

I do not know.  I am neither priest nor scribe nor Pharisee, I am a scientist.  The names I assign to populations of freshwater gastropods are hypotheses of evolutionary relationship – my best hypothesis, without compromise.  If I find that more than one name has been assigned to a population or group of populations, each of which conveys the same evolutionary hypothesis, I will select the name that, in my judgement, conveys my hypothesis to the broadest audience. 

That name, in the case of the 4 mm freshwater limpets with the eccentric shell apex, is Ferrissia fragilis (Tryon, 1863).  The letter of some legalistic code about which I was not consulted, administered by some commission I do not recall electing, does not enter into the calculation.

But let me hasten to make another point, and to make it as forcefully as I have made the previous one.  I would not presume to impose my selection of any scientific name on anyone else.  In fact, I earnestly hope that other scientists will develop other hypotheses about the evolutionary relationships of the populations I refer to Ferrissia fragilis.  Such a situation would be the mark of an active science.  And if it is the judgement of some other worker that Rowell’s nomen californica transmits information more effectively than Tryon’s fragilis, far be it from me to second-guess.

I have no problem with synonyms.  I do not think that taxonomic synonyms necessarily lead to scientific confusion, any more than I expect the college dean to become confused if I tell him to kiss my peachy-pink posterior or my rosy-red ass, on the way out the door.  Synonyms are pervasive in the English language, and we are richer for it.

Indeed, I think it will be a service to preserve both names.  So just this morning I have added Rowell’s “Ferrissia californica” directly under the header “Ferrissia fragilis” at the top of my FWGNA page.  And entered the nomen into the list of synonyms available from the website pull-down.  And written the present essay, wherein both names are connected.  In this fashion, the future generation of graduate students, perhaps na├»ve about the fragilis/californica situation, will be able to google-up and connect their disparate literatures.

And finally.  Difficult though it may be to understand [11], some non-negligible fraction of my colleagues have, from time to time, associated into committees to develop formal lists of accepted or approved names that we, “the community,” will be sanctioned to apply to the diverse biota of this, our great country.  I would suggest that all members of such committees re-read the first six paragraphs of the present essay.  And get a life, every one of you.


Notes

[1] This account of the action at Vicksburg, together with those of Chancellorsville and Brandy Station following, are extracted from Shelby Foote’s (1963) classic The Civil War, A Narrative.  Volume II, Fredricksburg to Meridian. Vintage Books, 988 pp.

[2] Rowell, J (1863) Description of a new Californian Mollusc.  Proceedings of the California Academy of Sciences Series 1, 3: 21 – 22.

[3] Tryon, G. W. (1863) Descriptions of new species of fresh water Mollusca, belonging to the families Amnicolidae, Valvatidea, and Limnaeidae; inhabiting California.  Proc. Acad. Natl. Sci. Phila. 15: 147 – 150.

[4] Stimpson, W. (1863) Malacozoological Notices No. 1, On the genus Gundlachia.  Proc. Boston Nat. Hist. Soc. 9: 249 -252.

[5] This result is from 18,974 records of 99 species in four regions: the Atlantic, the Ohio, East Tennessee, and (very preliminarily) The Cumberland.  Download the presentation here:
  • The freshwater gastropods of The Ohio: An interim report [27June17]
[6] From left, Daniel, John, and Pleasant Chitwood of Company A, 23rd Georgia Infantry.  Daniel and John were captured at Chancellorsville on May 2, 1863.  This image scanned from Miller, W J. & B. C. Pohanka (2006).   An Illustrated History of the Civil War.  Barnes & Noble.

[7] My previous essays on Ferrissia:
  • Just One Species of Ferrissia [10June09]
  • Two Species of Ferrissia [8Dec10]
  • Bryant Walker’s Sense of Fairness [9Nov12]
[8] Basch, P.F. (1963) A review of the recent freshwater limpet snails of North America (Mollusca: Pulmonata). Bull. Mus. Comp. Zool. Harvard Univ. 129: 399–461.

[9] Walther, A. C., J. B. Burch and D. O’Foighil (2010) Molecular phylogenetic revision of the freshwater limpet genus Ferrissia (Planorbidae:Ancylinae) in North America yields two species: Ferrissia (Ferrissia) rivularis and Ferrissia (Kincaidilla) fragilis. Malacologia 53: 25-45.

[10] Coote, T, K. A. Schmidt, R. E. Schmidt, & E. R. McMullin (2018) Discovery of the freshwater limpet, Ferrissia californica (Rowell, 1863) (Gastropoda: Planorbidae), from streams of Montserrat, West Indies, a new addition to the Caribbean fauna.  American Malacological Bulletin 36: 291 – 295.

[11] I myself probably do understand it, however.  I think committees form to standardize the names of the diverse elements of the American biota to facilitate governmental regulation.  And with governmental regulation comes governmental funding.  I don’t want to be cynical – I’m pretty sure my colleagues on such committees think that they are furthering the cause of conservation, and that whatever taxpayer’s dollars might be expended on their salaries are well-justified.  I used to think that, too.

Monday, January 14, 2019

The best estimate of the effective size of a gastropod population, of any sort, anywhere, ever


First, a quick refresher on week #4 of your population genetics class.  One of the assumptions of Hardy-Weinberg equilibrium is that population size is effectively infinite.  If that assumption is met (together with all the other ones) gene frequencies will not change.  But if the population is small, gene frequencies will change by sampling error, for the same reason that if I flip a fair coin twice, there a 50% chance of that either the head will not be represented, or the tail.  That phenomenon is called “genetic drift.”

So, suppose we were standing on the edge of a huge field of peas, say 100,000 plants, polymorphic at the seed color locus – green and yellow – meeting all the Hardy-Weinberg assumptions (no selection, no migration, random mating and all that, Note 1).  And suppose we sampled 100 plants, and shucked a bunch of pods, and estimated the frequencies [2] of the green and yellow genes in the remaining 99,900.  And then we waited a year, let all 99,900 plants reproduce, cover the field with a new generation, and sampled another 100.  And we didn’t obtain exactly the same gene frequencies in year 2 that we did in year 1.

Much of the reason that the year-2 gene frequencies didn’t match the year-1 frequencies would certainly be our own sampling error – that we sampled a finite number from year 1 and a finite number from year 2.  But part of that allele frequency variance (new term) might also be due to the sampling error of the peas themselves – only a finite number of peas reproduced to yield the year-2 population.  Might we have been wrong about that 99,900 estimate?  Maybe, effectively, there weren’t 100,000 peas in the field at all?

The Duck Pond at Quarterman Park
So effective population size (Ne) is the size of an idealized population that demonstrates the same allelic frequency variance as the population under study.  There are many possible reasons why Ne is always less than or equal to N, the headcount (or stem count) population size.  Often much less.

Well, I hate to be pedantic, but there’s another (equivalent, but somewhat more difficult) definition of Ne.

Suppose we were to sample 100 peas from our population at a single date but analyzed gene frequencies at two polymorphic loci, not just one.  So, say seed color (green/yellow) and seed shape (wrinkled/smooth).  There is no reason to expect any relationship between seed color and seed shape – knowing green shouldn’t allow you to predict wrinkled.  That is true regardless of whether the seed color locus and the seed shape locus are on the same chromosome or not, because (in a large, randomly-breeding population) crossing-over would ultimately erase any initial relationship between the alleles.

But what if you did find a relationship between seed color and seed shape in the pea field?  This is often called “gametic phase disequilibrium” to distinguish it from the (hard) linkage disequilibrium you might discover between loci on the same chromosome using a controlled cross.  That would mean that the population wasn’t infinitely large and randomly-breeding.

So finally.  Effective population size is the size of an idealized population that demonstrates the same allelic frequency variance or the same gametic phase disequilibrium as the population under study.  Geeze, that turned out to take longer to explain than I imagined when I started this essay eight paragraphs ago.  I appreciate your forbearance.

Effective population size is a parameter in every model of theoretical population genetics ever published, neutral or otherwise.  That number is really, REALLY important.  And also, really difficult to obtain.

I only know of ten estimates of Ne in gastropod populations ever published, in total, for all environments: 2 marine, 4 terrestrial, and 4 freshwater [3].  And frankly, many of those ten are pretty darn spurious.

OK, I’m going to change subjects entirely here.  But don’t forget all the boring population genetics stuff you had to slog through above, because you’re going to need it again, shortly.

I taught Genetics Laboratory 305L at The College of Charleston for 33 years.  And Investigation #9 in my Genetics 305L lab manual was “The analysis of genetic polymorphism in a natural population using allozyme electrophoresis.”  I needed a sample of 31 individual somethings from some polymorphic population for each section, which toward the latter half of my career [4], became three sections per semester, two semesters per year, that’s N = 186 somethings.  And after years of messing around with pleurocerid snails and Mercenaria hard clams, those somethings became Physa acuta.

Now my second-favorite population of Physa in the world [5] inhabits the Duck Pond at Quarterman Park in North Charleston.  Amy Wethington and I first sampled that population (“NPK”) in 1990 in conjunction with our study of sea island biogeography [6], and I knew it was polymorphic at three allozyme-encoding loci: Isocitrate dehydrogenase (Isdh, 3 alleles), 6-phosophogluconate dehydrogenase (6pgd, two alleles) and Esterase-3 (Est-3, two alleles, Note 7).

So, in May of 2009 I collected my first big sample of Duck Pond Physa for the students working on Genetics Lab Investigation #9.  In many respects the one-hectare pond at Quarterman Park is perfect Physa habitat – shallow, quiet, and very rich, fed by runoff from the neighborhood.  Every day the kids bring bags of stale bread to feed the ducks, which they empty and throw into the pond with all the other picnic garbage.  Occasional whiffs of sewage.  Physa paradise.

Physa paradise
Only three factors keep that pond from becoming a block of Physa solid enough to walk across.  One is the flocks of ducks and geese, which probably prefer the Physa over the bread.

A second is the general lack of habitat.  Some 15 – 20 years ago the City of North Charleston undertook a complete renovation of the Duck Pond, draining it and shoring up the walls with bulkheads.  So, the modern pond has no vegetation of any sort, nor indeed any littoral zone.  Physa are common only on the floating allochthonous debris and garbage that accumulates at the eastern end, by the drain, and rather rare elsewhere.

And a third is the summer maximum temperatures, which can be brutal.  The City of North Charleston also installed a couple fountain pumps during those renovations a few years ago, but during the hot months, I feel certain that all aerobic life must be confined to the top centimeter or two of the pond.  And concentrated at the eastern end.

All those stipulations registered, I had no problem collecting several hundred Physa at the Quarterman Park Duck Pond in the spring of 2009.  I knelt on the walkway at the eastern end of the pond and hand-plucked Physa off the floating debris.  Or sometimes I found it easier to wash higher concentrations of snails off large sticks and bread bags into my bucket.  The entire sample didn’t take more than 30 minutes to collect.

And in the fall of 2009, the students enrolled in my three sections of Genetics Lab 305L estimated gene frequencies at three loci in 93 of them.  And ditto for another N = 93 in the spring of 2010.  And I went back to the Duck Pond to fetch more.

This went on for seven years, from 2009 to 2015.  The actual date of the sampling varied a bit from year to year, depending on the density of the snail population, which in turn, seemed to vary with the weather.  I could always find at least a few Physa in the Duck Pond – any day, 12 months per year.  But to collect the hundreds I needed annually, I needed a bloom.

After a few years of experience, I began to notice a relationship between Physa blooms and the blooming of the azaleas.  In the Charleston area, as I am sure elsewhere, azaleas bloom in response to a pulse of warmth and sunshine – the stronger the pulse, the more brilliant the display.  The bloom typically takes place in March here and lasts for several weeks.  My annual observations suggested that the Physa bloom at the Quarterman Park Duck Pond typically commenced around the week the azaleas dropped their flowers – in early to mid-April.  The population typically expanded through May, contracted in June, and died back almost entirely in the summer.

The only exception happened in 2012, when no Physa bloom occurred at all.  The spring of 2012 was exceptionally hot in Charleston – the mean March temperature (65.3 degrees F) the second-highest value in the 80-year record of the National Weather Service.  I was never able to make a collection that year.  I visited the pond every couple weeks from March to July, and could always find a few snails, but never in the quantity that would prompt me to get on my knees and start washing bread bags into buckets.

So I was relieved of my duties at the College of Charleston in February of 2016, and ultimately banned from campus for a Woodrow Wilson quote [8], bringing my study to an end with the 2015 field season.  The paper reporting the results obtained by myself and my team of 540 undergraduates was published early last year in Ecology and Evolution, citation from Note [9] below.


I should thank my good friend and former student Dr. John Robinson for putting me onto a really excellent freeware resource called “NeEstimator,” developed by Chi Do and colleagues [10].  The software calculates effective population size using both allelic frequency variance (which are called “two-sample methods”) and gametic phase disequilibrium (“one-sample methods”).  All the statistics and other gory details are available in my paper.

The bottom line turned out to be that Ne for the Physa population at the Quarterman Park Duck Pond was infinite in 2009 and 2010, dipped in 2011 to somewhere around Ne = 100, dipped again between 2011 and 2013 to around Ne = 50, popped up to around Ne = 200 in 2014, and then rebounded to infinite again in 2015.  These results are remarkably consistent across both my one-sample and the two-sample analyses, which are independent, and really tend to strengthen their mutual credibility.

I suppose the first explanation that might occur to one would be a population bottleneck in the 2012 year.  But bottleneck effects are notoriously long-lasting… once allelic diversity is lost, it takes many, many generations to regain it.

I think the key factor in the volatility of Ne demonstrated in this study may be cryptic population subdivision.  In retrospect, the striking dip in apparent population census size I observed in 2012 may have been localized at the east end of the pond, and its subsequent recovery due to immigration from elsewhere within a Physa population subdivided by distance.

Some of the most influential studies of population subdivision published ever have been conducted using land snail models. Cain and Currey (1963) described small-scale variation in the frequencies
of shell color morphs in the English land snail Cepaea as “area effects,” attributing the phenomenon to genetic drift [11].  Could freshwater gastropod populations perceive their environments much differently than Cepaea?

At minimum, these results should be received as a cautionary tale by those researchers, including yours truly, a sinner, who would represent the evolutionary relationships between populations by single samples, even as large as 200, even with multiple polymorphic loci, collected from single sites at single dates.

And as for the practice of sampling individual genes from individual snails from individual populations to represent an entire biological species?  That’s just plain White-House-stupid.


Notes

[1] I know that garden peas are self-pollinating.  Give me this one, for the sake of the example, OK?  Geeze, you must have really irritated your tenth-grade biology teacher.

[2] And I also realize that, because of dominance, you’d have to assume HWE to get gene frequencies at the seed color locus in garden peas.  Doggone it, now you’re beginning to piss me off.

[3] See the introduction section of my paper from note [9] below for the references.

[4] From 1983 into the mid-1990s, I only taught one section per semester – perhaps 15 students.  But the number of lab sections I taught per semester increased from two to three in the latter half of my career, as my lecture sections were assigned to adjunct faculty more sensitive to the self-esteem of the customers.

[5] My first-favorite Physa population inhabits the pond at Charles Towne Landing State Park.  See:
  • To Identify a Physa, 1989 [3Oct18]
  • Albinism and sex allocation in Physa [5Nov18]
[6] Dillon, R.T., and A.R. Wethington (1995) The biogeography of sea islands: Clues from the population genetics of the freshwater snail, Physa heterostropha. Systematic Biology 44:401-409.  [PDF]

[7] Dillon, R.T., and A.R. Wethington (1994) Inheritance at five loci in the freshwater snail, Physa heterostropha. Biochemical Genetics 32:75-82. [PDF]

[8] Who Decides What Must Be on a Syllabus?  Inside Higher Ed, 8Aug16.  [html]

[9] Dillon, R. T. (2018) Volatility in the effective size of a freshwater gastropod population.  Ecology and Evolution 8: 2746 - 2751. [https://doi.org/10.1002/ece3.3912]  [PDF]

[10] Do, C., Waples, R., Peel, D., Macbeth, G., Tillett, B., & Ovenden, J.  (2014) NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources, 14, 209–214. https://doi.org/10.1111/1755-0998.12157

[11] Cain, A. J. & Currey, J. D. (1963) Area effects in Cepaea. Phil. Trans. R. Soc. London Series B 246: 1-81.  Cain, A. J. & Currey, J. D. (1968) Studies on Cepaea III: Ecogenetics of a population of Cepaea nemoralis (L) subject to strong area effects.  Phil. Trans. R. Soc. London Series B: 253, 447-482.  Ochman, H., J. S. Jones & R. K. Selander (1983) Molecular area effects in Cepaea.  PNAS 80: 4189 – 4193.