RAD-seq for Next-Generation Phylogenetics

Following decades of using mitochondrial DNA or universal multi-copy ribosomal DNA regions for taxonomy, phylogeny and phylogeography in plant and animal taxa, here comes the turn of nuclear genes. In recent years, single-copy or low-copy genes have been increasingly employed to resolve species-level or even deeper relationships. Some genes (or portions of them) were chosen because of their rapid evolutionary rate, some because of their capacity in revealing hybridization, introgression, allopolyploidization or adaptation. In the process of developing these markers, there is a need to identify genes with an evolutionary speed suitable for that phylogenetic level and a need to compare the nuclear phylogeny with the phylogeny inferred from the uniparentally inherited mitochondrial DNA.


Today, I needed this hung on

the wall next to my lab bench
(from www.sugarscientist.com)

Negative issues are: a) the development of low-copy or single-copy nuclear markers relies heavily on the availability of genomic resources for the group in question, b) nuclear genes may not be suitable in cases of recent speciation therefore the concatenation of multiple loci is required to resolve among species, c) in the process of marker selection, it is necessary to eliminate from the formula the “paralogous” (i.e. duplicated genes, gene families) to avoid confusion between gene genealogies and species phylogenies. Several protocols have been proposed for the selection of single copy nuclear markers from genomic data.  The process however is a pain in the neck. This is becasue the development of the markers is almost always based on genomic data from a limited – nearly insignificant - number of taxa when compared to the real number of the species in the group…. Hence the rounds of failed PCR, the redesigned, degenerated primers, the years of postdoc effort into a single project, hence the missing data….

Natural and Artificial Selection at work

This is a set of morphological variants corresponding to the common cauliflower, slowly selected by early farmers during domestication, to create modified inflorescence structures corresponding to multiple varieties, characterized by distinct shapes, colors, geometries, dimensions and even tastes.

Well, this is Pocillopora damicornis sensu Linnaeus, 1758. Each ecomorph is the result of local natural selection forces dictated by environmental variables, bathymetric gradients, symbiotic bacteria or any other type of cue capable of apparently manipulating epigenetic mechanisms in this coral.  Everybody knows Pocillopora damicornis as the experimental “guinea pig”, the “poster child”, the “reef builder” or simply in Aquariology, the “cauliflower coral”!

Ranging morphologically from a filiform, pointed, branching colony to a compact and stunted posture, depending on whether it is growing in wave-exposed or protected environments, this species is unquestionably an important component of the reef.

The Torres Strait: Phylogeography Made Easy (but not always)

Torres Strait represents a major biogeographical barrier between the Indian and Pacific Oceans and is well known for acting as an intermittent land bridge in line with periodic ice age glaciations over the past 250,000 years. The periodic closing and opening of the Strait, which now connects the Arafura and Coral Seas, promoted the fragmentation and secondary contact of several marine populations including sponges, the less famous residents of the Great Barrier Reef. The same events favored more than once the selection of lucky genetic variants capable of persisting in refugia zones east and west of the Strait.

To put everything into a context: as of today, the distance across the Torres Strait from Cape York to New Guinea is approximately 150 km (93 mi) with its northwestern region reported to be really shallow (10-5 meters). During the last glacial maximum, the Gulf of Carpentaria and the Strait were part of a large highway between Australia and New Guinea.  Humans were one of the many species to make (successfully) use of the connection with the Australian continent!

Genetic variants hidden in the deep seas

In a recent paper with Gary Poore, we used a good dose of humour to describe two new species by means of genetics and morphometrics, from within a mysterious genus of squat lobsters known from more than 400 m down. The originally described bloke is known as Uroptychus naso due to his prominent rostrum. The new mates names were chosen following their equally noticeable rostra: one is Uroptychus pinocchio after the famous Italian marionette; the other, Uroptychus cyrano after the legendary French writer and duelist. In our new paper with Gary, we have used again morphology and genetics to sort out the same issue from within another mysterious genus of squat lobsters: Agononida. This time we fished out four new species, distinct from the originally described Agononida incerta and, one previously confused with the latter. They summed up to a total of six valid taxonomic units. The new ones are: A. africerta, A. auscerta, A. indocerta and A. norfocerta; the confused one: A. rubrizonata. But checkout their distribution! How does that fit with large scale geological events and big biogeographical barriers, responsible for the present’s day diversification and distribution of deep sea species? Wallace’s line, Huxley’s line, Indo-Pacific break or Wallace line marine equivalent?

The names of the new entries: too serious this time: after Australia, Africa, Indian Ocean and the Norfolk Ridge. You can tell them apart only on the basis of the shape of the anterolateral lobe of the telson and the shape and setation of the dactyli of pereopods 2–4, unless you wish to use molecules. Give it a try!

 

Relevant literature

• The Agononida incerta species complex unravelled (Crustacea: Decapoda: Anomura: Munididae). GCB Poore and N Andreakis. Zootaxa. 3492: 1-29.
• Morphological, molecular and biogeographic evidence support two new species in the Uroptychus naso complex (Crustacea: Decapoda: Chirostylidae). GCB Poore and N Andreakis. Molecular Phylogenetics and Evolution. 60: 152-169.