Phylogenetic Sporting and the Genus Laevapex

Editor's Note.  This essay was subsequently published as: Dillon, R.T., Jr. (2019b)  Phylogenetic sporting and the genus Laevapex.  Pp 137-141 in TheFreshwater Gastropods of North America Volume 2, Essays on the Pulmonates.  FWGNA Press, Charleston.

Laurels are due to Andrea Walther, Taehwan Lee, Jack Burch and Diarmaid O'Foighil for their exemplary phylogenetic study of the ancylid genus Laevapex, published late last year in MP&E (1). In addition to contributing a thorough survey of DNA sequence variation and shell morphological diversity in this often-overlooked group of freshwater limpets, Andrea and her colleagues at the University of Michigan have posted a model of how modern molecular tools can combine with old-fashioned biology to provide fresh insights to important evolutionary processes.

As most of us are probably aware, the primary reference to the systematics of freshwater limpets in North America has long been the monograph of Paul Basch (2). Basch recognized two species of Laevapex, the ovate L. fuscus and the subcircular L. diaphanus. Andrea sampled 5 populations of the former and 5 populations of the latter. She also included in her analysis three less well-known taxa, L. peninsulae (two populations), L. arkansasensis (two populations) and Bob McMahon's unusual population from Oklahoma (3).

Andrea sequenced three genes: mitochondrial CO1, nuclear 28S, and nuclear ITS-2. Sample sizes were usually only one or two per population, but occasionally 10 - 12 or even as many as 28 individuals per population for the CO1 gene. She also performed an innovative geometric study of the digitized outlines of 76 representative Laevapex shells.

Her headline result was, "E Pluribus Unum." The five taxa of Laevapex were indistinguishable by their 28S and ITS-2 sequences, as well as by their shell morphometrics. They appeared polyphyletic in their CO1 sequences - all taxa generally mingled together on the main branch of the tree. Apparently the North American genus Laevapex comprises but a single polymorphic species, L. fuscus.

Perhaps of more general interest, however, was Andrea's discovery of several extremely divergent CO1 haplotypes in her large sample of Laevapex. The Baysian tree she derived from these data (her Figure 4) showed a highly divergent branch of four haplotypes jutting way off to the side of the main cluster - one diaphanus, one peninsulae, one arkansasensis and one Oklahoma. The CO1 haplotypes sequenced from these limpets were similar (but by no means identical) to one another, apparently bearing substantial nucleotide deletions relative to the 34 haplotypes in the main body of the tree (4).

I downloaded one of Andrea's divergent CO1 sequences from genebank, an L. diaphanus haplotype collected right here in South Carolina (DQ328243), as well as a typical sequence from a Virginia L. fuscus (DQ328225) for comparison. An alignment from the NCBI "Blast two sequences" utility showed that the typical and divergent sequences differed by about 10% of their nucleotides, where they matched. But there was a length of 20 nucleotides in the middle of the typical sequence that showed zero match to 11 nucleotides in the divergent. The CO1 protein being made by the South Carolina Laevapex is apparently deleted by three amino acids!

Horticulturists occasionally find that their trees and various other plants under cultivation produce "sports." These are branches of some obviously different genetic constitution, typically assumed to result from a somatic mutation or chromosomal rearrangement in the mother plant. By analogy, I suggest that the CO1 divergence documented by Andrea Walther and her colleagues in their small set of atypical Laevapex fuscus might be called "Phylogenetic Sporting."

Such sporting is not uncommon. Andrea listed seven previous examples from the freshwater gastropod literature alone, including the work by Bob Frankis and myself documenting 18.7% sequence divergence in a population of Goniobasis proxima (5). Several years ago our colleague Amy Wethington (6) discovered four individual Physa acuta in a local pond differing from the typical CO1 sequence by almost 30%.

What might be the origin of phylogenetic sporting? Again, Andrea and her colleagues did a thorough job of reviewing five possible explanations (7), ultimately unable to pick a single lead hypothesis for Laevapex. But at least one hypothesis can be ruled out quite decisively here, "cryptic speciation."

Sometimes I fear that the widespread application of DNA technology we have seen in systematic biology over the last few years has been more a curse than a blessing. The confusion that sequence data (and the methods developed to analyze it) have brought to the species concept is especially acute. Without question, there are professional evolutionary biologists among us today who would look at Andrea Walther's CO1 tree and conclude that her one limpet from Arkansas, her one limpet from South Carolina, her one limpet from Florida and her one limpet from Oklahoma together constitute an undescribed species. An embarrassment and a shame.

But returning to happier themes. In addition to her 15 populations of Laevapex, Andrea sequenced 11 populations of other ancylids and 4 populations of non-ancylid freshwater pulmonates, bringing her outgroup total up to match the total of her ingroups. I suppose it's not difficult to predict the next direction her research will be taking her.

For her Ph.D. dissertation, Andrea is extending her genetic survey to include Ferrissia, the five nominal species of which constitute by far the most enigmatic group of freshwater limpets in North America (8). In a nice article contributed to the current issue of the AMS Newsletter, Andrea reported preliminary results suggesting that the number of Ferrissia species has long been overestimated as well (9).

We'll keep you posted!
Rob


Notes

(1) Walther, A., T. Lee, J. B. Burch, and D. O'Foighil. 2006. E Pluribus Unum: A phylogenetic and phylogeographic reassessment of Laevapex (Pulmonata: Ancylidae), a North American genus of freshwater limpets. Molecular Phylogenetics and Evolution, 40: 501-516.

(2) 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.

(3) One could make a strong case that Bob McMahon's incisive morphometric study anticipated the conclusions of Walther and her colleagues by two years. See R. F. McMahon (2004) A fifteen-year study of interannual shell-shape variation in a population of freshwater limpets. Am. Malac. Bull. 19: 101- 109.

(4) I'm simplifying here a bit. One of the four sports did not appear deleted, and one of the "typicals" did. See the actual paper for the nitty-gritty.

(5) Dillon, R. T., Jr. & R. C. Frankis (2004) High levels of mitochondrial DNA sequence divergence in isolated populations of freshwater snails of the genus Goniobasis. Am. Malac. Bull. 19: 69-77.

(6) Wethington, A. R. (2003) Phylogeny, taxonomy, and evolution of reproductive isolation in Physa (Pulmonata: Physidae) Ph.D. thesis, University of Alabama.

(7) Natural selection not among them. It is interesting to see how far evolutionary biology has come since I was a graduate student 25 years ago.

(8) In fact, Andrea and her colleagues have already published two interesting papers on Ferrissia in Europe: Walther, A., T. Lee, J. B. Burch, and D. Ó Foighil. 2006. Acroloxus lacustris is not an ancylid: A case of misidentification involving the cryptic invader Ferrissia fragilis (Mollusca: Pulmonata: Hygrophila). Molecular Phylogenetics and Evolution, 39: 271-275. Walther, A., T. Lee, J. B. Burch, and D. Ó Foighil. 2006. Confirmation that the North American ancylid Ferrissia fragilis (Tryon, 1863) is a cryptic invader of European and East Asian freshwater ecosystems. Journal of Molluscan Studies, 72: 318-321

(9) We here in Charleston have also been doing a bit of research on Ferrissia in the past year as well, with intriguing results not quite ready for dissemination. Stay tuned!