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Lumpsuckers are globular, scaleless marine fish with bony tubercles on head and body, and a ventral sucking disc, derived from specialized pelvic fins, which allows them to adhere to environmental substrates. The genus Eumicrotremus comprises 16 species distributed in the Arctic and northern Atlantic and Pacific oceans; the commonest and most widespread in the north Atlantic is the Spiny lumpsucker E. spinosus, which was first described by Fabricius in 1776. A new subspecies E. s. eggvinii was described in 1956, based on a single specimen, and this was later elevated to species level “on the basis of wrinkled skin, numerous dermal warts and a large sucking disk, in addition to the low number of bony tubercles.”

In August 2007 J Fish Biol 71A: 111, researchers from University of Bergen, Norway, analyze DNA and morphologic characters of E. eggvinii (n=16) and E. spinosus (n=67).  All specimens were easily classified by morphologic characters. However, the two species had identical mitochondrial DNA sequences (COI barcode region, COII, cytb) and identical nuclear gene Tmo-4C4. Further genetic testing revealed that E. eggvinii were all males, and E. spinosus were all females. The authors conclude that the two morphologically distinct “species” represent the sexually dimorphic forms of E. spinosus. 

In this study by Byrkjedal et al, identical mtDNA sequences suggested synonymy, and this in turn suggested that morphologic divergence might represent sexual dimorphism, confirmed by further genetic testing. To my reading, this study suggests DNA testing needs to be as commonplace in taxonomy as recording size, shape, and coloration, and counting rays in fins and placement of tubercles. Every new species should have a representative DNA sequence as part of the species description. For animals, the standard should be a COI barcode. One of the remaining impediments to widespread adoption is that simple protocols for sequencing COI barcode region need to be better disseminated. In this study, the researchers were able to recover COI barcode region using primers designed for invertebrates (Folmer et al 1994), although others have published primer pairs that have greatly increased effectiveness with diverse fish (Ward et al 2005, Ivanova et al 2007). Compiling primer pairs and amplification protocols and displaying this information prominently on the various barcoding web sites will help (see for example SpongeBOL home page www.spongebarcoding.org link to illustrated primer primer!). I close with note this is post #100 since the first DNA barcode blog entry of March 15, 2006!

In 17 September 2007 Zootaxa (open access full article) researchers from Museo Nacional de Ciencias Naturales-CSIC, Madrid, make a plea for routinely incorporating standardized DNA sequence analysis, ie DNA barcoding, into modern taxonomic practice. In their view, “integrative taxonomists should use and produce DNA barcodes.” Of course, this is already happening in many areas, but new practices diffuse slowly through the fragmented world of taxonomy, and so Padial and de la Riva’s exhortation is an important step. With growing DNA barcode libraries and increasingly inexpensive sequencing technologies, DNA testing will likely be the fastest way to sort specimens into species and will enable identification of multiple forms that now go unnamed or misidentified while waiting for an expert, waiting for eggs and larva to mature, or waiting to find an identifiable adult male or a recognizable fragment in stomach contents.

One might view taxonomic science as an effort to construct detailed, reliable “maps” of species and their historical relationships. Adopting Padial’s and de la Riva’s advice to routinely “use and produce DNA barcodes” will speed taxonomic research and, more importantly, will naturally produce a “map of species” with general scientific and public utility. Few persons can have the requisite knowledge to distinguish larval fish for example, whereas anyone can submit a sample for DNA sequence analysis. In this way, a DNA barcode library is a map of species, one that anyone can read with the right device, a DNA sequencer. Of course, more work is needed to identify the best approaches for assigning sequences to named species and for flagging divergent sequence clusters that might represent new species. With improved analytic software and as more species and specimens per species are analyzed, the reliability of DNA barcode maps will increase. Based on results so far, I expect rapid growth in mail-order identification services, analogous to today’s DNA ancestry companies, that do DNA barcode analysis of submitted specimens, and, as others have envisioned, soon enough there will be table-top or hand-held devices that pinpoint where the specimen in hand belongs on the biodiversity map. Best wishes to all this holiday season!

Sponges are difficult to identify and classify. Many sponges “have a depauperate suite of morphologic characters and/or are plagued by morphological homoplasies” and vary according to environmental conditions, challenging identification at species level and stymying attempts to reconstruct evolutionary lineages.  In Dec 2007 J Marine Biol Assoc UK researchers from Geoscience Centre Gottingen, Germany, and Queensland Museum, Australia, report on how DNA can help. Worheide and Erpenbeck describe the nascent Sponge Barcoding Project www.spongebarcoding.org, which aims to collect DNA signature sequences [COI barcodes] from all 8,000 known marine intertidal, deep sea, and freshwater sponge taxa.  According to the authors “DNA barcoding will open up a new dimension and quality in biodiversity research and will become of vital importance for the survival and acknowledgement of sponge taxonomy and increase its reputation over the coming decades.” In addition to assisting species-level identifications, the authors posit the necessity of “DNA-assisted” taxonomy of sponges given the inability to construct convincing higher order classifications with morphologic characters.

An accompanying article analyzes COI barcode results for 166 specimens belonging to 65 species of Caribbean sponges. Similar to findings in other animal groups, the 584 bp COI fragment produced a gene tree similar to that with 28s rRNA, a slowly-evolving nuclear gene. In a ML analysis, some species had overlapping or shared sequences, which the authors point out may mean these are not “good species”, specimen identifications are incorrect, or that these species cannot be distinguished by a COI barcode alone. The sequences are published in GenBank and available individually through the Sponge Barcode website, and I hope the authors will also make their sequence and specimen data available on the Published Projects section of BOLD. This will allow access to the analytic and display software on the BOLD site, enable easy comparison of the sponge data set with that of other animals, and facilitate testing of other methods particularly for those species which are not distinguished in ML analysis.  

Birds are relatively large, conspicuous, vocal, and mostly diurnal creatures, making it relatively easy for humans to tell apart. Even so, new species continue to be discovered; these usually represent distinct forms within what were thought to be single species. In 27 February 2007 Mol Phylogenetics Evol, Arpad Nyari, University of Kansas, reports on molecular and vocal differentiation in a widespread South American songbird, the Thrush-like Schiffornis Schiffornis turdinus. S. turdinus is a “dull-colored, secretive bird distributed throughout Neotropical humid lowland forests from southeastern Mexico south to northern Bolivia and the Atlantic Forest of southeastern Brazil.”  The thirteen recognized subspecies show “subtle differences in plumage hue and intensity, and body size”. How to sort out which forms might represent distinct species?

Nyari analyzed 38 individuals representing 10 of the 13 subspecies, plus 3 congeneric individuals of S. virescens or S. major. 8 of the 41 specimens were from University of Kansas, and the remainder were loaned from 6 museum collections in the US and Brazil, which highlights the distributed nature of avian tissue collections and the benefit of sharing resources. 2475 bp of mtDNA including COI barcode region, ND2, and cytochrome b were sequenced as molecular markers. Vocalizations were downloaded from Macaulay Library of Natural Sounds, Cornell University and spectrographs analyzed with RAVEN bioacoustic software which is provided on the Cornell site. The ability to combine these disparate data sets hints at power of making biological data widely available. Molecular analysis revealed 7 distinct geographically restricted clades, 5 of which had characteristic vocalizations. On this basis, S. turdina is recommended to be split into 5 species.  When analyzed separately, the COI barcode region (615 bp) recovered the same 7 clades as the full 2475 bp. As in other studies, the branching order among clades and congenerics was better shown with the larger data set.  

To my reading, this and other studies suggest that large-scale COI barcode screening of avian tissue collections will be a scientifically productive and efficient approach that will speed discovery of new bird species and advance understanding of avian diversity. As in Kerr et al’s recent study of North American birds, it seems likely that many or most of the new bird species awaiting discovery will be found among birds similarly inconspicuous as S. turdinus.