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.

Morphometrics or DNA for species identification?

Exact species identification underpins accurate biodiversity estimates, effective management of sustainably exploited, protected or endangered species up to assisting in bio-discovery and elucidating biological introductions and symbiosis relationships.  Melody in her recently accepted paper makes use of COI barcoding to identify 65 taxa of flatheads across the Indo-West Pacific out of 48 currently accepted morpho-species. During this exercise we had the opportunity to appreciate the performance of the Automatic Barcode Gap Discovery species delineation tool (ABGD) developed by Puillandre and co-authors and implemented at the online ABGD species delineation tool: http://wwwabi.snv.jussieu.fr/public/abgd.

M. Puckridge, N. Andreakis, S.A. Appleyard & R.D. Ward (2012) Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding. Molecular Ecology Resources (in press)

abstract: Identification of taxonomical units underpins most biological endeavours ranging from accurate biodiversity estimates to the effective management of sustainably harvested, protected or endangered species. Successful species identification is now frequently based on a combination of approaches including morphometrics and DNA markers. Sequencing of the mitochondrial COI gene is an established methodology with an international campaign directed at barcoding all fishes. We employed COI sequencing alongside traditional taxonomic identification methods and uncovered instances of deep intraspecific genetic divergences among flathead species. Sixty-five operational taxonomic units (OTUs) were observed across the Indo-West Pacific from just 48 currently recognized species. The most comprehensively sampled taxon, Platycephalus indicus, exhibited the highest levels of genetic diversity with eight lineages separated by up to 16.37% genetic distance. Our results clearly indicate a thorough reappraisal of the current taxonomy of P. indicus (and its three junior synonyms) is warranted in conjunction with detailed taxonomic work on the other additional Platycephalidae OTUs detected by DNA barcoding.

Relevant literature

DNA barcoding Australia's fish species (2005) by Bob D Ward, Tyler S Zemlak, Bronwyn H Innes, Peter R Last and Paul D.N Hebert. Phil. Trans. R. Soc. B 360, 1847-1857.

ABGD, automatic barcode gap discovery for primary species delimitation (2012) by Puillandre N, Lambert A, Brouillet S, Achaz G. Mol. Ecol. 21, 1864–1877.

Photos by Phil Mercurio

Book Chapter

The increasing number of marine seaweed invasions is mainly due to intensified shipping and global environmental changes. However, many invasive seaweeds are commercially used, despite the risks are high and the strategies are not always in place to control unintentional and accidental releases. Check out chapter 12 contributed by me and Britta Schaffelke (AIMS) in the newly released book: Seaweed Biology: Novel Insights into Ecophysiology, Ecology and Utilization, edited by C. Wiencke and K Bischof.

Invasive Marine Seaweeds: Pest or Prize? - Abstract

Seaweeds were among the first harvested human food supplies in several parts of the world and are today valuable natural resources. They are, however, part of one of the most pressing conservation issues of our time: biological invasions. Global patterns of biodiversity are changing by relocations of organisms at the species and sub-species levels, with the latter often remaining cryptic. The increasing occurrence of marine invasions is mainly due to intensifying maritime traffic and global environmental changes. Following introduction, if suitable conditions for survival occur in the “recipient” environment, seaweeds will establish and spread. Many high profile invasive seaweeds are commercially used in their native range and have biological traits similar to high-yield terrestrial crops, e.g. high growth rates. The incentives to introduce potentially invasive taxa for commercial use are significant. However, the associated environmental risks are high and robust strategies to prevent and control intentional and accidental seaweed introductions remain essential. For industrial and commercial use, preference should be given to the harvesting and culture of native seaweeds.

AMSA-NZMSS 2012

The Australian Marine Sciences Association - New Zealand Marine Sciences Society conference approaches quickly! The theme of the conference this year is: Marine Extremes - And Everything In Between. The words suggest a creative reflection of the environmental events of the past year and cover extreme events such as cyclones, floods, tsunamis, dust storms, thermally-induced bleaching, hypoxia, ocean acidification, biological invasions or ecosystem shifts, which can periodically dominate the marine realm. Amongst the proposed symposia, me (AIMS) and Daniel Gledhill (CSIRO – Hobart) will run symposium SS01 “Hidden species in the Oceans: environmental extremes, rapid cladogenesis and morphological stasis”. We expect to have constructive discussions and our five selected presentations to point the finger towards biogeographical barriers and large scale geological or climatic events responsible for past population fragmentation and genetic differentiation associated with morphological stasis and instances of cryptic speciation. We hope to emphasize the challenges related to biodiversity estimates, conservation and evolutionary consequences.



http://www.geographia-and-genesis.com/3/post/2012/06/amsa-nzmss-2012.html