Friday, May 2, 2014

Towards a Bivalve Tree of Life



An important paper entitled “Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters” was recently published this year in Invertebrate Systematics.  This paper led by Rüdiger Bieler and Paula M. Mikkelsen and their team of 18 collaborators represents a significant product of their Bivalvia project (BivAToL), which is part of the Assembling the Tree of Life program sponsored by the National Science Foundation.  This paper, which uses an exemplar-based approach to generate morphological and molecular data from specimens from the same population or even the same specimen goes a long way towards providing the necessary phylogenetic infrastructure (sensu Bieler et al., 2013 and my April 2013 blog posting) for those interested in using bivalves as model organisms in a wide range of evolutionary and ecological studies. 

The BivAToL team examined stomach morphology and other features of the alimentary tract, the morphology of gills and labial palps, shell microstructure, and sperm ultrastructure.  Molecular markers included two nuclear ribosomal genes (18S and 28S rRNA), one nuclear protein encoding gene (histone H3), one mitochondrial ribosomal gene (16S rRNA) and one mitochondrial protein-encoding gene (cytochrome c oxidase subunit I; COI).  Four additional nuclear protein-encoding genes were also generated for a subset of taxa.  This impressive assemblage of data was analyzed using a variety of methods including parsimony, maximum likelihood and Bayesian inference with molecular data alone and in combination with the morphological characters.   The results consistently recovered the monophyly of Autobranchia, Pteriomorphia, Heterochonchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and a new clade Imparidentia (=Euheterodonta excluding Anomalodesmata).  The authors also discussed the origin and diversification times for each of the major clades and provided a classification scheme for the six major monophyletic groups of modern Bivalvia.  This important paper is certain to stimulate much more research on bivalve systematics and and other interesting evolutionary questions.

Literature Cited

Bieler, R., P. M. Mikkelsen, T. M. Collins, E. A. Glover, V. L. González, D. L. Graf, E. M. Harper, J. Healy, G. y. Kawauchi, P. P. Sharma, S. Staubach, E. E. Strong, J. D. Taylor, I. Tȅmkin, J. D. Zardus, S. Clark, A. Guzmán, E. McIntyre, P. Sharp, and G. Giribet.  Investigating the bivalve tree of life – an exemplar –based approach combining molecular and novel morphological characters.  Invertebrate Systematics 28:32-115.

Bieler, R., P. M. Mikkelsen, and G. Giribet.  2013.  Bivalvia-A discussion of known unknowns.  American Malacological Bulletin 31(1):123-133.

Tuesday, December 17, 2013

A New Classification of the Chromodorid Nudibranchs



With over 300 described species, the chromodorid nudibranchs are one of the most species rich families of gastropods.  Their bright colors and interesting morphology appeal to underwater photographers and scientists alike.  Their aposematic coloration has also drawn the attention of scientists interested in natural products chemistry.  In spite of their conspicuousness and appeal, there has been no comprehensive, well-supported phylogeny of the chromodorid nudibranchs.  This hinders progress being made in other biological disciplines where one may assume that species from the same genus represent a monophyletic group.  In a recent issue of PlosOne, Rebecca Johnson and Terrence Gosliner set out to remedy this situation and generate a phylogeny of the chromodorid nudibranchs and present a classification that accurately reflects the evolutionary history of the group.  

In the paper entitled “Traditional Taxonomic Groupings Mask Evolutionary History: A Molecular Phylogeny and New Classification of the Chromodorid Nudibranchs,” Johnson and Gosliner assembled the most comprehensive dataset to date including 244 specimens (142 new), representing 157 species (106 new) chromodorid species and several other taxa.  They used two mitochondrial genes (16S rRNA and cytochrome oxidase I) to reconstruct a phylogeny of the group.  The results revealed that currently recognized genera were either polyphyletic or nested within another genus rendering the other genus paraphyletic.  Extensive homoplasy of morphological attributes that have been thought to be synapomorphies for a particular genus seems to be the cause of the unnatural groupings that have been recognized in the past.  This pattern of polyphyly of recognized genera has been observed for unionid bivalves as well (Campbell et al., 2004).  

One appealing outcome of the study by Johnson and Gosliner (2012) is that they took the time to propose a new classification of the group based on their findings.  As Johnson and Gosliner (2012) indicate, “the translation of phylogenetic hypotheses into classifications is the best way to communicate results to a larger community” and “communicating these new hypotheses is one of the main contributions systematics can make to the scientific community.”  Their study now provides a sound phylogenetic framework from which morphological, chemical and behavioral attributes can be examined.       

Literature Cited
Cambpell, D. C., J. M. Serb, J. E. Buhay, K J. Roe, R. L. Minton, and C. Lydeard.  2005.  Phylogeny of North American amblemines (Bivalvia, Unonoida): prodigious polyphyly proves pervasive across genera.  Invertebrate Biology 124:131-164.
Johnson, R. F., and T. M. Gosliner.  2012.  Traditional taxonomic groupings mask evolutionary history: a molecular phylogeny and new classification of the chromodorid nudibranchs.  PlosOne 7(4):e33479.

Tuesday, November 26, 2013

Increased Litter Decomposition Rates by Terrestrial Gastropods in Hawaii



Terrestrial gastropods are often a major component of various terrestrial ecosystems.  It is thought that litter-dwelling terrestrial gastropods contribute to the cycling of nutrients either directly or indirectly through metabolism and modifying habitat to enhance micro-arthropod or microbial activity, respectively.  However, their role in ecosystem processes is poorly known particularly in tropical forests.  In a recent issue of Biotropica, Wallace M. Meyer III, Rebecca Ostertag, and Robert H. Cowie shed some light on this very issue in a paper entitled “Influence of Terrestrial Molluscs on Litter Decomposition and Nutrient Release in a Hawaiian Rain Forest.”  Meyer et al. (2013) used a field mesocosm approach to examine (1) whether the presence of terrestrial gastropod species increased rates of leaf litter decomposition, (2) whether different terrestrial gastropod species influence the rates of nutrient release differently, and (3) whether terrestrial gastropods facilitate recruitment of mesoinvertebrates.  The results of the experiments showed that the presence of gastropods increased litter decomposition rates and that the highest decomposition rates were those with the greatest gastropod biomass.  Furthermore, although there were differences in the rates of release of some nutrients among treatments, the different gastropod species appeared to influence nutrient release in a similar way.  Finally, there was no evidence that terrestrial gastropods facilitated mesoinvertebrate recruitment.

The authors have shown empirically that terrestrial gastropods can play a major role in litter decomposition.  One interesting aspect of the study is that it was done using the five most abundant species of gastropods in the Hawaiian rain forest: the native Succinea cepulla and four non-native species (Arion intermedius, Deroceras leave, Oxychilus alliarius, and Limax maximus).    The native species had the lowest density among the gastropods studies and is comparatively rare.  Indeed, Hawaii presents a particularly compelling case because some 65-90 percent of the 750+ species (over 99% endemic) are now considered extinct (Solem, 1990; Cowie et al. 1995; Cowie, 2001; Lydeard et al., 2004) so there is the distinct possibility that invasive gastropod species are now conducting important ecological processes that were once carried out by native species and potentially benefitting otherwise native ecosystems.  Regrettably, important information is lacking to fully address this issue such as species richness and densities in historical, native communities.

Literature Cited
Cowie, R. H., N. L. Evenhuis, and C. C. Christensen.  1995.  Catalog of the native aland and freshwater molluscs of the Hawaiian Islands.  Backhuys Publishers, Leiden, The Netherlands.
Cowie, R. H.  2001.  Invertebrate invasions on Pacific islands and the replacement of unique native faunas: a synthesis of land and freshwater snails.  Biol. Invasions 3:119-136.
Meyer III, W. M., R. Ostertag, and R. Cowie.  2013.  Influence of terrestrial molluscs on litter decomposition and nutrient release in a Hawaiian rain forest.  Biotropica 45(6):719-727.
Lydeard, C., R. H. Cowie, W. F. Ponder, A. E. Bogan., P. Bouchet, S. A. Clark, K. S. Cummings, T. J. Frest, O. Gargominy, D. G. Herbert, R. Hershler, K. E. Perez, B. Roth, M. Seddon, E. E. Strong, and F. G. Thompson.  2004.  The global decline of nonmarine mollusks.  Bioscience 54:321-330.
Solem, A.  1990.  How many Hawaiian land snail species are left? And what we can do for them.  Bishop Museum of Occasional Papers 30:27-40.

Friday, October 25, 2013

Great Unanswered Questions Continued - Deep Molluscan Phylogenetics




The January 2013 issue of American Malacological Bulletin included eight papers from 11 presentations from the James H. Lee symposium, “Great Unanswered Questions in Malacology,” which was held at the 77th Annual American Malacological Society meeting in Pittsburgh, Pennsylvania, July 23-27 2011.  The organizers, Timothy Pearce and Charles Sturm, introduced each paper (Pearce and Sturm, 2013).  I highlighted one paper previously in my April blog posting, but one that I would like to highlight further as the topic for this blog posting is entitled “Recent advances and unanswered questions in deep molluscan phylogenetics” by Kevin M. Kocot (Kocot, 2013).  Kocot provides a terrific brief review of the leading hypotheses of molluscan phylogeny that have been proposed based on morphological and sequence data such as nuclear small subunit (SSU or 18S) and large subunit (LSU or 28S) ribosomal gene sequences.  Many of these hypotheses have been debated about over many years with each hypothesis having a leading advocate or group of advocates supporting them.  Regrettably, molecular sequence data, which often provides useful data when morphology conflicts offered little information to resolve any of the conflicts and often resulted in bizarre findings such as the lack of monophyly of the Bivalvia and Gastropoda or a paraphyletic Mollusca.  Recently, with the development of phylogenomics, large amounts of nuclear protein-coding gene data derived from genomes and transcriptome data instead of PCR to amplify targeted gene fragments has been generated and found useful in examining the relationships of animals.  In 2011, two papers were published applying phylogenomics to the test of examining deep molluscan relationships (Kocot et al. 2011, Smith et al., 2011) and one examined PCR-amplified regions of seven genes in a target-gene approach (Vinther et al. 2011).  

A consensus tree based on the findings of the three studies was provided as follows:  (((Gastropoda, Bivalvia, Scaphopoda)(Cephalopoda, Monoplacophora))(Polyplacophora,(Neomeniomorpha, Chaetodermomorpha))).  Unlike some previous hypotheses, it is evident that the Aplacophora is monophyletic and sister to Polyplacophora rather than being a paraphyletic grade that was basal and plesiomorphic.  This finding alters our notion of character states for an hypothetical ancestral mollusk.  Also, there is no support for the recognition of the Cyrtosoma (Gastropoda + Cephalopoda), which alters our notion from a comparative framework for those interested in neurobiology of Cephalopods, which may actually be sister to Monoplacophora (although Monoplacophora was only examined in one of the three studies – Smith et al., 2011).

The fact that there was general agreement among the three studies is comforting and leads one to think perhaps we are making progress towards understanding deep phylogenetic relationships of the Mollusca, but many more molecular studies need to be done and sample sizes increased to determine whether the consensus tree will stand the test of time.  Also, in addition to molecular sequence data, as Kocot concludes “more traditional morphological and developmental studies will undoubtedly continue to improve understanding of molluscan evolution while simultaneously raising new questions about this fascinating group of animals.”   
Literature Cited

Kocot, K. M.  2013.  Recent advances and unanswered questions in deep molluscan phylogenetics.  American Malacological Bulletin 31(1):195-208.

Kocot, K. M., J. T. Cannon, C. Todt, M. R. Citarella, A. B. Kohn, A. Meyer, S. R. Santos, C. Schander, L. L. Moroz, B. Lieb, and K. M. Halanych.  2011.  Phylogenomics reveals deep molluscan relationships.  Nature 477:452-456.

Pearce, T. A. and C. F. Sturm.  2013.  Introduction to the James H. Lee symposiu, “Great Unanswered Questions in Malacology,” 77th annual meeting of the American Malacological Society.  American Malacological Bulletin 31:105-107.

 Smith, S. A., N. G. Wilson, F. E. Goetz, C. Feehery, S. C. S. Andrade, G. W. Rouse, G. Giribet, and C. W. Dunn.  2011.  Resolving the evolutionary relationships of molluscs with phylogenomic tools.  Nature 480:364-367.

Vinther, J. , E. A. Sperling, D. E. G. Briggs, and K. J. Peterson.  2011.  A molecular palaeobiological hypothsis of the origin of aplacophoran molluscs and their derivation from chiton-like ancestors.  Proc. Of the Royal Society B: Biol. Sciences 279:1259-1268.