Footnotes for A Web of Evidence
¹ That is, weighing traits by expert intuition, calculating overall physical similarity numerically, and strictly grouping organisms by shared derived characteristics — these were the methods used by the three primary schools of taxonomy in the 1960s.
² In her book, Naming Nature: The Clash Between Instinct and Science, Carol Kaesuk Yoon’s description of a genetics lab she worked at illustrates how dramatically molecular techniques changed taxonomy:
“In the laboratory at any given time people were studying not just fruit flies but naked mole rats, colonies of ants, Australian birds that built nests the size of a minivan, flocks of red-winged blackbirds, and schools of lake trout, to mention just a few. You might imagine that meant the lab was zoolike, with aquaria and cages full of squawking, skittering animals, but it certainly was not. You might think that, at the very least, it had the look of a natural history museum, with specimens, tagged and labeled, around the room. But it was nothing like that, either. It was a high-tech lab, thoroughly devoid of any sign of life. What you saw instead were rows of glass vials and bottles, tiny plastic tubes and machinery with lights flickering on and off, the room laced with stark black laboratory benches. There were no living things to be seen, because we had, all of us, essentially no need of actual animals to do our work. All we needed was a bit of the organism, or a small clump of them if they were as small as fruit flies, from which to extract the DNA that we were studying.”
³ Because mitochondrial DNA (mtDNA) is present in hundreds to thousands of copies per cell — compared to just two copies of nuclear DNA (nDNA) — it is significantly easier to recover from degraded, ancient, or small tissue samples.
⁴ DNA sequencing has been extremely important in a lot of quote-unquote high-profile taxonomic cases.
For instance, genome sequencing proved that the African elephant actually comprises two completely distinct species: the savanna elephant (Loxodonta africana) and the forest elephant (Loxodonta cyclotis). The genetic divergence between these two was found to be nearly as deep as the divergence between Asian elephants and woolly mammoths. (Vogel, 2001)
⁵ MSH1 is considered ancestral to animals — meaning it was present in the common ancestor of all animals — and it functions primarily in DNA mismatch repair, maintaining mitochondrial genome stability. While hexacorals retained the nuclear MSH1 gene, octocorals completely lost it, acquiring mtMutS instead.
⁶ The ghost-white, “spiderweb-strewn” Fiordland coral seen in the beams of the ROV had transformed once at the surface, displaying a faint orange-brown to ocher pigmentation.
For centuries, this kind of physical variability — where an animal's color or shape shifts based on its environment or whether it is expanded or contracted — has plagued taxonomists, especially those relying on damaged specimens dredged up by trawls. Even observed in its environment, morphological traits like the shape of a coral colony or its colour can vary significantly based on local environmental conditions or the state of the coral.
⁷ To isolate the sclerites, researchers dissolved small pieces of coral flesh in a solution of bleach. All of the organic tissue was dissolved, leaving behind only the tiny, mineralized structures that form the coral's internal frame. Cleaned with hydrogen peroxide and water, the microscopic sclerites were mounted on metal stubs and coated in an ultra-thin layer of gold, allowing a scanning electron microscope (SEM) to bounce electrons off their surface and render high-resolution 3D images.
Under the SEM, the sclerites of Aquaumbra klapferi looked like uniformly slender, rod-like needles covered in only sparse micro-bumps. In contrast, the Fiordland specimen possessed a varied array of sclerite shapes, including curved spindles in its polyps and chunky “irregular bodies” in its stem and base that were densely studded with prominent, cone-shaped bumps.
⁸ ddRAD-seq is short for ‘Double Digest Restriction-Site Associated DNA Sequencing.’
⁹ While the nuclear data (ddRAD-seq) for the first ten lineages showed they were all interbreeding and exchanging genes, the data for S07 and S09 remained distinct. Instead of the twelve species initially suggested by the COI barcode, there are likely three species in this complex:
The main E. sicilianus species (incorporating 10 of the COI lineages).
Cryptic Species 2 (lineage S07).
Cryptic Species 3 (lineage S09).
¹⁰ Full genome-wide sweeps aren't always feasible or necessary for routine field surveys. But when isolated markers like COI and mtMutS fail, taxonomists can build extended barcodes.
By stacking multiple regions together — such as combining COI with an intergenic region and the MSH1 gene — they create a composite barcode that is significantly more effective at discriminating between stubborn sister taxa than any single marker is on its own.
¹¹ One of the types of genes most widely used is called ultraconserved elements (UCEs) — genomic regions that have remained virtually unchanged across millions of years of evolution.
“It is really the regions that flank these highly conserved genes that contain the variation necessary to infer relationships,” says McFadden.
Because an UCE remains remarkably stable — virtually identical across species separated by hundreds of millions of years — scientists can easily locate it. The volatile flanking regions surrounding that core, meanwhile, mutate rapidly enough to resolve relationships at both deep and incredibly shallow evolutionary levels. For a molecular taxonomist, UCEs are the anchor and the surrounding regions the clock.
