BLASTing my way to a Thesis…

Its been a while, apologies for the lack of posting…I haven’t been doing much writing on my thesis, I’ve just been in the lab, trying to get some sequences for my plants and in some cases failing miserably. I’m at the stage where I’m having to alter the PCR protocols and primers in order to get something from the most intractable samples. Nonetheless I have some sequences to work with, so it’s not entirely miserable, I guess!

My supervisor’s funding dried up very rapidly so I have had to basically halve my intended sample set – it’s still enough to write a Masters, but it’s going to be difficult to publish straight from my thesis without doing some extra work expanding my data set, although my supervisor also just got an article accepted for PNAS so it’s possible that some funding may forthcoming from the University some time in the near future…

At the moment I’m running a whole lot of phylogenetic analyses on my sequences producing trees, and hopefully, estimating relative branch lengths for my ingroups. Unfortunately methodological constraints have prevented me from getting sister taxa as my ingroup, so I am not able to run robust Relative Rates Tests, and have to rely solely on the estimated parameters that come out of Maximum Likelihood phylograms. At the moment I don’t have PAUP* on my computer, for which I first need to get the Mac OS9 Classic environment which for some reason I don’t have automatically…so I’m using the PHYML plugin of Geneious, to run some preliminary ML analyses just to sort out topology. Geneious is quite an impressive programme with a whole bunch of bioinformatic and computational biology tools, developed by BioMatters, a commercial group from the University of Auckland. I would seriously suggest downloading a demo version if you don’t have one just have a play around. It has a Bayesian analysis plugin – MrBayes – but my poor laptop crashed while running it!

Anyway more to come later – I have to run and do some work!

MIA

So busy doing stuff! Quickly: Doing lab work, not writing Masters chapters, no more funding for the project so no more trips, down to a third of the intended data set…but I’m doing lots of photography of plants and flowers more updates soon…

Coastal New South Wales, or: An Exercise in the Law of Diminishing Returns

Ok so I’ve actually been back a week two weeks, and I’ve been somewhat tied up in the lab working on my DNA extractions so I have only just had the chance, nay, the motivation to blog. And it’s an excellent form of procrastination! I don’t really want to start writing my thesis; yesterday I spent a good two hours working on the template for my chapters, but didn’t actually write anything…needless to say I will attempt to get onto that tonight…
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I’m still in two minds about the trip; on the one hand it was an incredible experience and I saw some pretty amazing things (from a geeky scientist’s point of view, anyway), but it was also much more stressful than I remember my Arid NSW trip being, especially the inevitable cabin fever. The problem with covering such a big area (2600kms total, from Coolangatta to Sydney and everywhere in between) is that most of the time you’re just driving along at 100kms an hour, stopping at random to look at plants that seem a little different – a practice I have dubbed Drive By Botany. The whole experience wasn’t helped by the fact that I got molested by MAF on the way back in because it was my supervisor’s name on the permit, and not mine.
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Anyway, there are some amazing sights in that part of the world; most people spend their time in NSW either in Sydney, or on the Pacific Highway travelling up to Brisbane, without having a look at the landscapes that exist only 100km or so westwards. These areas have some incredible subtropical and temperate rainforests, with the last remnants of ‘Gondwanan’ plants, including the Podocarpaceae (eg. rimu, kahikatea, miro etc in New Zealand) and Nothofagaceae (i.e. southern beeches) which dominate New Zealand’s flora and some amazing Araucariaceae such as the hoop pines, the same family as our kauri. In most other parts of Australia, these once dominant families have been marginalised by the sclerophyllic plants that have evolved in situ in response to changing climatic and soil conditions – genera such as Eucalyptus, Grevillea and Acacia. The Eucalypts in particular have come to dominate many of the wetter and dryer environments to produce wet and dry sclerophyllic communities, which are quite different in terms of their composition from the rainforests. Nonetheless, both are quite striking, and hugely different from the arid landscapes we encountered in the Far Western Plains.

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Dry Littoral Rainforest
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Wet Sclerophyll Forest
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Dorrigo National Park – one of the last remnants of Podocarp Rainforest in Australia

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The fauna was also quite different – huge golden orb web spiders (Nephila edulis) that just hang there, only to be noticed the second before you plough head long into their webs. For an arachnophobe, not the best experience. But there were some amazing thorny spiders (not sure of their taxonomic affiliation?)

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Golden Orb Web Spider Nephila edulis
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Thorny Spider Cudman Reserve Dry Littoral Rainforest
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Thorny Spider Wollemi National Park

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Of course there were the usual reptiles such as the skinks and snakes. Sadly, no photos of the snakes that we saw – a juvenile Eastern Brown Snake (Pseudonaja textilis) which hightailed as soon as it heard us coming and a Red Bellied Black Snake (Pseudechis porphyriacus) that was dozing on a track on the Watagans National Park before dashing off quickly just after I missed stepping on it!
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The highlight of the trip, of course, was my first run in with the the hirudineans – leeches! New Zealand has a few native leeches, but they aren’t really known to parasitise humans. Their Australian counterparts, however, are another story…I ran into my first one in the wet sclerophyll forests of Kyogle and the Richmond Range, and ran into them consistently all the way down to Sydney. They either ‘walk’ along the ground and then up your leg, or stand on leaves and wait for movement, before falling onto you and attaching for a bit of blood sucking. The annoying thing is that they bite with an anaesthetic, so you usually can’t feel them attach. then when they finally do drop off, or you rip them off, or burn them off with toothpaste, you continue to bleed due the fact they they also inject you with an anticoagulent. They grossed me out at first, but you tend to get used to them!

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A leech after my leg
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My leg after a leech

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There were some other awesome sights – huge beautiful moths, Hibiscus plants that look like Cannabis sativa at first glance, impressive epiphytic ferns and the beautiful chaotic flowers of the mistletoe Amyema congener. The sad thing is that these areas are under huge threat from introduced weeds, specifically Lantana and Madeira vine which form massive inpenetrable thickets that prevent forest regeneration. Considerable effort is being made to remove these and other weeds, which is vital to prevent the final loss of some of these ancient systems.

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Random Beautiful Huge Moth
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Young Hibiscus heterophyllus plant…hmmmm…suspicious looking
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Hibiscus heterophyllus flower
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Epiphytic ferns – Richmond Range National Park
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Amyema congener flowers
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Me

Bloody Malarchy!

So I’m five hours away from having to get up and fly out of Auckland to Coolangatta, driving down the Pacific Highway of New South Wales picking plant specimens for my masters – what a drama getting the export permit! Anyway, light(er) blogging over that time period, but lots of pictures when I get back!!! Exciting!!!

Plant of the Week

It’s quiet here today as I realized the journal article I brought from home is actually largely irrelevant, loaded with theoretical mathmatics and ergo, ripe for the recycling bin. I’m also flat out preparing for my trip to Coastal NSW on the 20th (flying out at 6.40am ^^..^^) so it’s nice to take a break from arranging permits and getting identification books sorted out.
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So, this week’s plant of the week is another member of the pea family (Fabaceae), one of the few native peas found in New Zealand, apart from the kowhai (Sophora spp.) and native brooms (Carmichaelia spp.).

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Kowhai-ngutu-kaka – Clianthus puniceus – Kakabeak

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This plant is really striking, with beautiful red flowers that apparently look something like the beak of the native Kaka (Nestor meridionalis), hence the common name.

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Kakabeak flowers look remarkably similar to the other pea that I have profiled Sturt’s Desert Pea, that the latter was originally classified in the Clianthus genus before being reassigned to Swainsona. Kakabeak is now the only remaining species within the Clianthus genus.

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Despite being a popular garden cultivar, Kakabeak is actually a threatened native species. It occurs naturally in the East Cape/Hawkes Bay area, where only about 200 wild individuals survive. Most of the garden varieties that people have are clones or cultivars, which means that the genetic diversity of the species is actually far smaller than what would be expected from the number of individuals alive. In the wild, Kakabeak is threatened by goat, deer, pig and possum browsing.

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Rapid molecular evolution in a living fossil

Much of the work I’m doing for my Masters focuses on rates of molecular evolution in plants, specifically neutral; molecular evolution, that is, areas of the genome that are not under any strong selection and are ‘free’ to gather mutations without constraint.

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I’m specifically looking at the effect of environmental conditions on those rates, and without giving too much away, rainfall.

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Anyway, a recent article by some New Zealand researchers, including Dr. Craig Millar from my department at the Univeristy of Auckland, presents some very interesting data within the field that I’m working in, and it’s seriously cool…

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Tuataras are ancient animals, in that they are the only living representative of a lineage of reptiles (the Sphenodontia) that emerged early during the age of the dinosaurs, some 220 million years ago. Since then, they have undergone very little morphological evolution, hence their designation as a ‘living fossil’. They are poikilothermic (cold blooded), they have very low metabolic rates, they grow very slowly, and they reproduce even slower. As a result, and in line with their minimal morphological change, it could be expected that they have a relatively low rate of neutral molecular evolution.

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Well, apparently not. Using ancient and modern Tuatara bones, the authors were able to show that the rate of tuatara mitochondrial DNA change isn’t even similar to warm blooded, rapidly breeding animals which have changed their appearance and body structures relatively rapidly over time, but much much faster. Amazing!

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This has two important consequences. Firstly, it shows that rates of change to DNA aren’t necessarily matched by rates in morphology or appearance – an animal like the tuatara has changed very little in appearance over the last 220 million years, compared to say a Moa, or a Horse or Cave Lion, which have, relatively speaking, changed very rapidly in the intervening years. Moreover, and more importantly for me: the rate of molecular evolution isn’t necessarily bound to environmental conditions such as temperature, or to life history characteristics like generation time, or even endogenous factors such as metabolic rate.

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This field just gets more and more interesting every day! O.o

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Article:

Rapid Molecular Evolution in a living fossil

Jennifer M. Hay, Sankar Subramanian, Craig D. Millar, Elmira Mohandesan and David M. Lambert

Trends in Genetics 24(3):106-109

He’s got a face like a dropped pie…

So early on and I’ve already lost so much motivation to write here! Well…only for a little while. I’m finishing one job, starting a new one, preparing for my trip to Coastal NSW on the 20th (including trying to deal with the Australian Department of Environment Arts and Heritage to get my permit to export plant material…enough said) and trying to get the energy to work on my thesis…

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You’ll have to excuse the silence…but a plant of the week will be posted shortly! Not that many people actually read this thing anyway

I’d rather not be accountable, thanks…

What a surprise – Condoleeza Rice has confirmed that she wouldn’t run for Vice President with McCain:

“I have always said that the one thing that I have not seen myself doing is running for elected office,” Rice said at a news conference. “I didn’t even run for high school president. It’s sort of not in my genes.”

Read: I’m happy to make the decisions, but I’m sure as hell not happy to be held electorally accountable for them…

Plant of the Week

This week’s plant of the week is a New Zealand native that many people do not recognise as such. It’s really really common and has been planted as an ornamental all over the place, especially on some of the newer streets where they have finally realised that planting exotics is not that good when you have so many beautiful natives to put in.

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Titoki – Alectryon excelsus – New Zealand Oak/New Zealand Ash

The Alectryon genus is widespread, extending from the Asian Palaeotropics, through New Guinea and Australia and out into the Western Pacific. Classicists among you will realise that Alectryon is ancient Greek for rooster, which refers to the shape of the fruit, which apparently look like they have a rooster’s comb, but I’m yet to be convinced. One of my samples in Western NSW was also of the Alectryon genus, but looks nothing like Titoki save its fruit, so obviously a very morphologically diverse genus!

Anyway, I just love this species – its so big and grand when it’s fully grown, and it can live for hundreds of years. I think the New Zealand Oak descriptor is very apt.

I think it’s a joke

Did anyone else think that maybe Howard Morrison was taking the piss when he suggested that Owen Glenn offered $1million to stand for Parliament as an independent?

I get the impression that a number of people are the butt of a joke, but maybe not.