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Thrips are tiny (.5 to 2 mm) plant feeding insects; approximately 4500 species are known, and some are serious agricultural pests. Kladothrips is an Australian genus of at least 35 species which form galls on Acacia trees. In Biol J Linn Soc 2006 88:555 researchers from Flinders University, Australia, apply mtDNA analysis to show that two gall morpho-types of Kladothrips rugosus represent different species. 

Originally described in 1907, K. rugosus is widely distributed across south and western Australia. Two gall types were noted, but no morphologic differences could be found in the thrips themselves. McLeish, Chapman, and Mound found pairwise uncorrected mtCOI p-distances were 0.0-0.6% within gall morphotypes, and 7.4-7.8% between, similar to distances within and among other gall thrips species. The authors aver the usual taxonomic distaste for distance measures (“Distance values are not intended as a means of identifying different species here, which is a problematic approach for species depiction, but as useful descriptors of genetic variation”). I translate this as distance measures can be used help discover new species, but are verboten in official species descriptions. 

The only morphologic differences are that “abdominal segments I-III are as brown as IV-VII, the metathorax is scarcely paler than the brown mesothorax and prothorax, and the sculptured reticles on the posterior half of of tergites II-III are all small and equiangular.” Phew! Not many persons could decipher such abstruse morphologic terminology, whereas DNA-based identification promises more democratic access to species identification. The main limiting factors are technological and likely solvable: establishing reference libraries and developing inexpensive DNA analytic methods. 

The authors found a third genetic cluster in K. rugosus, but were unable to discover any morphologic characters, so did not describe this as a new species. This seems scientifically inconsistent, and the authors seem to agree: “This lack of morphologic divergence has evident problems for traditional taxonomy..we suggest that “morpho-taxonomy” is little more than an historical artifact in the methodology of species recognition, despite commonly providing the most practical methods”

I hope the large data sets emerging from the barcode initiative and other genetic surveys will enable taxonomists to develop consistent methods of species delimitation, whether in thrips or thresher sharks, and the sequences themselves or their diagnostic nucleotide characters will be routinely incorporated into species descriptions.

Insiders can be mistaken, in science and in other fields. At the beginning of the Human Genome Project, “the great majority of scientists dismissed the original proposal with hostility or indifference” (Great 15-year project to decipher genes stirs opposition. New York Times, June 5, 1990). The Times article details some of the initial negative reactions:

“Even if scientists manage to finish the genome project, it will have generated enormous reams of uninterpretable and often useless data”.

“The human genome project is bad science, it’s unthought-out science, it’s hyped science” said Dr. Martin Rechsteiner, a biochemist at the University of Utah. Some critics have begun aggressive letter-writing campaigns, urging colleagues who harbor similar sentiments to write Congress.

“Everybody I talk to thinks this is an incredibly bad idea,” said Dr. Michael Syvanen, a microbiologist at the Medical School of the University of California at Davis and a stout antagonist of the genome project.

Professional societies weighed in as well. A resolution adopted by the Council of the American Society for Biochemistry and Molecular Biology, and endorsed by the Federation of American Societies for Experimental Biology stated: “A large scale, massive effort to ascertain the sequence of the entire genome cannot be adequately justified at the present time… The Council wants to state in the clearest possible terms our opposition to any current proposal that envisions the establishment of one or a few large centers that are designed to map and/or sequence the human genome.” https://www.fasebj.org/cgi/reprint/1/6/502 

This history comes to mind in reading the article by Hickerson, Meyer, and Moritz in October 2006 Syst Biol 55:729. According to their analysis, mathematical modelling predicts that DNA barcoding will often fail to discover young species. Their analysis is based on a classical model of speciation (Bateson-Dobzhansky-Muller) and “well-established population genetic theory”. I should tread lightly here, not being a population biologist! To my reading, these mathematical models are either unsupported or disproved by experimental evidence. The BDM model of biological species formation is “well-characterized, tractable, and its dynamics captures a range of speciation times implicit across many pre- and post-zygotic isolation models”, ie good for modelling, but is not derived from actual genetic data on differences between sister species. Genetic surveys including growing barcode libraries demonstrating limited intraspecific variation in diverse species across enormous differences in population size and generation time indicate that “well established population genetic theory” does not explain intraspecific mitochondrial diversity (Bazin et al 2006 Science 28:570).

Instead of making predictions about why barcoding will fail, I hope the same mathematic rigor will be applied to understanding why barcoding works as well as it does, why the variation within most species is low, why the distances between most species are large, and what determines the exceptions.

In October Proc R Soc B Gomez et al apply DNA barcoding to the cosmopolitan marine bryozoan Celleporella hyalina. Morphologic identification in this genus uses scanning electron microscopy measurements of the 0.2 mm autozooid and its 0.05 mm orifice. To eliminate potential variability associated with colonial development or environmental plasticity, these morphologic measurements are made on cloned F1 progeny grown under controlled laboratory conditions. This example highlights how standard morphologic techniques can be cumbersome and costly, and require highly-trained personnel and expensive equipment. It is unlikely this sort of morphologic identification process can be sped up, while DNA analysis is getting faster, cheaper, and more portable.

The researchers from University of Hull, University of Wales, and Universidad Catolica de la Santisima Concepcion in Chile analyzed mtCOI barcodes in 176 colonies from 33 sites around the globe, revealing at least 10 deeply divergent lineages. Mating compatability in 26 pairwise combinations showed complete reproductive isolation in 23 cases, and 3 were inconclusive due to self-fertilization. Only one of the genetically divergent, reproductively incompatible groups could be reliably separated by morphologic analysis.

It is obviously impractical to do mating studies for routine identification of bryozoans. Instead, standardized genetic analysis, ie DNA barcoding, can first help discover species (as in this case by highlighting lineages that were then subjected to other forms of biological analysis), and then be applied to assign unknown specimens to the newly revealed species. The authors conclude “DNA barcoding clearly identifies biologically meaningful groups in the C. hyalina complex” and speculate that biodiversity is similarly underestimated in other sessile marine invertebrates, including sponges and corals. “Failure to recongize cryptic speciation among sessile benthos therefore may seriously underestimate marine biodiversity as well as impeding attempts to predict the response of marine benthos to environmental change.” I conclude that DNA barcoding is the fastest way forward to help discover and then routinely identify what appear to be the vast numbers of cryptic animal species.  

The Sponge Barcoding Project https://www.spongebarcoding.org/ aims to barcode all described sponges, about 8,000 species in the phylum Porifera. The initial phase of 3 years will focus on 2,000 species covering all genera.

Sponges are thought to be the earliest living branch on the multicellular animal tree and are difficult even for experts to identify. In addition to their ecological importance, sponges are sources for novel pharmaceuticals and biomaterials (eg Sipkema et al 2005 Biotech Bioengineer 90:201).

Like some corals, some sponges show very few differences in mitochondrial DNA with the standard COI barcode (corals, Shearer et al 2002 Mol Ecol 11: 2475; sponges, Erpenbeck et al 2006 Mol Ecol Notes 6: 550). The latter study suggests that the 3′ end of COI may provide greater resolution for Porifera and Cnidaria. An important goal of the initial phase of the project is to determine the best strategy for obtaining species-level identifications, one that provides sufficient resolution to separate most of the closely-related species and still takes advantage as much as possible of the benefits of standardization on 5′ COI.

I note that in animals closely related sister species are often largely or completely allopatric. In such cases, combining genetic barcode data with GIS coordinates may improve the certainty of some identifications.

For fun, I close with a sponge video: