Complex Life Cycles and their contribution in species relocation, adaptation, survival: lessons from Rhopaloeides odorabile, a common sponge of the GBR

Like other sessile invertebrates (such as corals), sponges represent important components of the Great Barrier Reef in terms of biomass production, diversity levels and pelagic processes. Like corals however, sponges have specific eco-physiological windows for survival, characterized by rigorous temperature optima. In other words, sponge populations suffer seriously thermal stress associated with increases in sea surface temperature, a consequence of climate change.

Larvae of the sponge Rhopaloeides odorabile in the GBR show a remarkable thermal tolerance compared to adults. Rhopaloeides larvae are capable of surviving and metamorphosing in seawater temperatures even 9 ^oC above the annual maxima. This suggests that the chances for Rhopaloeides to survive global warming are great given the capacity of the species to relocate towards more suitable habitats via larval dispersal. But the question is, how?

Neotrygon Maskrays, a Complex Chondrichthyan Radiation in the Cenozoic: How and When!

Neotrygon maskrays are distinguished by a dark mask-like band over the eyes and represent an ideal group for understanding how evolutionary forces, geography and environmental dynamics may have shaped marine populations in the Indo-Australian archipelago. This is because, they are confined to the Indo-West Pacific and four of the five nominal species exist as narrow-ranging endemics along the interface between the Australian and Eurasian tectonic plates. Further, they inhabit shallow coastal and continental shelf waters. This habitat makes them easy targets to population fragmentation due to environmental pressure, such as cycles of glaciations responsible for the formation of phylogeographic breaks and/or contact zones.
In this paper, Melody assesses the partitioning of the genetic diversity within the genus, the taxonomic validity of some morphs and the timing of species divergence. The results are interpreted in the light of large scale paleo-climatic and geological events. Finally, conclusions are discussed given the formation of biogeographic barriers, responsible for vicariance and population contraction/expansion or secondary contact mechanisms across the Indo-Pacific.

 

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….