coralreeffish.com presents my research on coral reef fishes. Over the decades my interests have evolved from population biology of reef fishes (my PhD research on wrasses in Caribbean Panama, in the 1980s), to applying the daily otolith technique for aging reef fishes (particularly useful for larval stages and estimating the pelagic larval duration before settlement), leading to identifying and surveying larval fishes. Then, with the turn of the century, breakthroughs in high-volume DNA-sequencing technology opened a powerful new window into the identification and taxonomy of organisms. That led to a massive project to "barcode", i.e. sequence the same portion of the COI mitochondrial gene, for all organisms. The program was developed in Canada where the Barcode of Life database BOLD has millions of sequences.

Serendipitously, all of my fish collections I had systematically accumulated over decades were kept in ethanol, to preserve the otoliths I worked on, allowing them to be DNA-sequenced, even 40 years after they were preserved. In contrast, formalin, used to preserve fishes by almost everyone else at that time, degrades DNA and practically prevents using museum collections for DNA studies. Suddenly I had one of the largest collections of tropical marine fishes able to be sequenced, especially since my collections were mostly larvae and juveniles, permitting hundreds of specimens to be kept in a single jar, and I had hundreds of vials and jars.

From the start of the Barcode of Life program, I have sequenced the barcode gene for some of my old samples and many new specimens, and now have several thousand fishes sequenced. Most are from the Caribbean, where I worked for most of my early career, but I have also collected a comprehensive sample of tropical eastern Pacific fishes, particularly from Baja California and Galapagos.

At first, I used the DNA technique to identify my larvae to species, by matching them to known lineages, but soon discovered that our assumptions about shorefish species, how they are defined, and how they evolve, does not conform to what we are finding in barcoding studies, raising some very intriguing questions. My interest then gravitated to the evolutionary biology of reef fishes, specifically working on taxonomy, the study of describing and classifying species.

The first thing we all noticed as we developed a database for shorefishes was the consistency of DNA lineages between and among species is not what we expected: while many species do show a clean one-species, one-lineage pattern, exceptions pop up all over the place. Some species break up into multiple regional populations with different DNA lineages-- what does that mean? well, different lineages mean the two populations are not interbreeding, that they are to some degree genetically isolated, without gene flow between them-- one of the definitions of a species. However, to be an acceptable species, the two populations need to show some visible difference that defines them, an important requirement. Otherwise a few additional sequences can invalidate a species or create a new one, and how different two sets of sequences need to be to "qualify" as a species is unresolvable and ever-changing, depending on what gene segment is sequenced and what subjective amount of difference is proposed. That is so untenable, it would render taxonomy useless.

So, does it help resolve species to find a divergent DNA lineage? it alone does not determine species status, but it certainly helps decide if two populations are "sufficiently" diverging to be species. It is especially useful in practice-- in many cases, the DNA-lineage difference distinguishes sets of specimens that on closer examination are obviously different, in morphology (physical measurable differences), meristics (countable structures), and/or color patterns, thus revealing undetected "cryptic diversity", new undescribed species not recognized before.

I reviewed this issue among coral reef fishes in a chapter in 2015 in the book "Ecology of Fishes on Coral Reefs", since then many interesting cases have been studied.

Combined, we have barcodes for perhaps 3/4 of the roughly 1200 shorefish species in the tropical western Atlantic and about 2/3 of the roughly 2,000 total fish species in the tropical eastern Pacific. The Indo-pacific, with its astonishing shorefish diversity, is much less covered.

As a result of this DNA "prospecting", I have discovered and described about 60 reef-fish species in the past twenty or so years- they can be seen on my publications page.

Here i am old-fashioned diving on my foray to Dominica, a volcanic island in the Windward chain of the Lesser Antilles. I am on the hunt for tiny fish with my trusty green aquarium net! note the scarcity of live corals- that is typical of many sites in the Lesser Antilles these days.