How to: create nexus input files for Network (www.fluxus-engineering.com)

It is a bit of time I was thinking that this post may be of help to people intersted in genealogical network reconstruction under the median joining algorihtm. www.Fluxus-engineering.com provides, free of charge, the phylogenetic Network software in its as of today version 4.611. Network makes use of the median joining algorithm to generate genealogical trees from DNA, aminoacid, linguistic and other data but can also provide age estimates for the ancestral nodes in the tree topology. I have used several times this software in the past and I was impresed for its versatility, the graphics (compared to TCS or Splitstree) and its friendly interface. However, contrary to TCS and Splitstree, the Network team suggests the use of “recommended” add-ons such as DNA Alignment, Network Publisher and pibase for importing data without errors, create publication quality graphics and generating network input files (.rdf) from next generation sequencing files respectively. Despite Network is freely distributed, the add-ons are not.

FÜR ALICIA - Pocillopora aliciae

A new coral species has been recently discovered by Sebastian Schmidt-Roach and the new taxon, genetically delineated in a previous publication, is now in great detail  morphologically described in this new paper. And the name of the new species? Well guess what? Of course, after Sebastian’s wife, Alicia! Pocillopora aliciae! Is this great or not?

Abstract: Lack of morphological features of diagnostic value and high levels of environmental phenotypic plasticity obscure species boundaries for most taxa in the genus Pocillopora Lamarck, 1816 and complicate the definition of taxonomically distinct units. Species of the genus are colonial, generally ramose, rarely massive or encrusting and mostly hermatypic; corallite arrangement is plocoid, septa are generally poorly developed and usually arranged in two cycles; the columella is mostly poorly developed (Veron & Pichon 1976). Verrucae are common, although reduced in some species. Currently 17 species are formally acknowledged within the genus (Veron 2000). Using a molecular phylogenetic approach, recent studies were able to identify genetically distinct lineages in Pocillopora, indicating that Pocillopora damicornis (Linnaeus, 1751) consists of a cryptic species complex (Souter 2010; Schmidt-Roach et al. 2012a). One of these species, previously considered a temperate ecomorph of P. damicornis, is here described as a novel species, based on its distinct morphology, unique mitochondrial haplotype and incongruity with previously described taxa in P. damicornis. Pocillopora aliciae sp. nov. exhibits a flat, plate-like growth (usually displayed by deep-water morphs of pocilloporids) at all depths, which clearly differentiates it from P. damicornis colonies at subtropical Lord Howe Island or Rottnest Island. Furthermore, Stylophora pistillata Esper, 1797, which is equally known to exhibit flat deep-water morphs, maintains its common gross morphology at equal depth to P. alicae sp. nov..The new species is described below. Types are deposited in the Museum of Tropical Queensland (MTQ), in Townsville Australia

 

Relevant literature

·         Schmidt-Roach, S., K. Miller and NAndreakis (2913) "Pocillopora aliciae: a new species of scleractiniancoral (Scleractinia, Pocilloporidae) from subtropical Eastern Australia." Zootaxa 3626: 576-582.

Phylogeography of Stylophora pistillata

Pink, brownish or yellowish, this is Stylophora pistillata (Esper 1797), another coral species characterised by a “cauliflower-like” morphology, commonly used in ecological, physiological and evolutionary studies ranging from reading morphogenesis, exploring apoptosis, symbiosis and coral bleaching to understanding circadian rhythmicity, thermal stress and calcification.

Stylophora ecomorphs

Stefani and co-workers (2011) and Flot and co-authors (2011) have recently questioned the validity of ecomorphs and genetic lineages within Stylophora using morphology and molecules. The studies were independently performed on specimens collected globally (north-western Gulf of Aden and Taiwan, Madagascar, Okinawa, the Philippines and New Caledonia) and multiple cryptic species have been identified.

Quantitative Cladistics and the Use of TNT

Interesting workshop in Quantitative Cladistics organized by Pablo  Goloboff and Claudia Szumik at Els Hostalets de Pierola, Barcelona (Spain). The workshop will cover the basics of parsimony analysis and character optimization, tree-searches, diagnosing and summarizing results efficiently, and measuring group supports.

The course will be informal, with extensive hands-on exercises which will help students get familiar with the main aspects of phylogenetic analysis using TNT. For each of the units in the workshop, there will be a lecture (one to two hours, depending on the topics), then switching to exercises illustrating the points just seen in the lecture. Switches between "lecture" and "hands-on" mode will be dynamic, depending on how students advance on the exercises.The workshop will make extensive use of TNT. There will also be a demonstration and some practice withGB->TNT, a program to create TNT matrices from GenBank data (in turn, GB->TNT requires installation of some alignment program, ideally Mafft or Muscle and possibly BioEdit to inspect alignments). ENJOY!

 

Polyploidy and the rise of invasiveness in marine seaweeds

A good part of research suggests that only a limited number of species within algal orders or just a single genetically distinct lineage from within the same morpho-species complex, becomes suddenly invasive. In plants, the switch to invasiveness has been recently related with differences in ploidy levels, meaning that genetic attributes such as polyploidy and high chromosome counts may be the drivers for the phenomenon (Pandit et al. 2011).

 

In their elegant study, Pandit and co-authors (2011) prove that endangered plants exhibit disproportionally low levels of ploidy and chromosome numbers compared to invasive plant species. Similar to hybridization therefore, polyploidy may lead to the production of novel and greater numbers of genetic variants, which increases the probability of a successful invasion. But what is happening in invasive marine seaweeds?

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.