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!

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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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.

Plant of the Week

As I was writing yesterday’s post, I happened across a few photos of a plant that I had been very eager to see while on my trip. It’s an iconic outback plant, and you really have to see it for yourself to experience it. It’s a truly remarkable sight:

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Sturt’s Desert Pea – Swainsona formosa

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The Swainsona genus is an iconic and ubiquitous Australian taxon, comprising >40 species spread throughout the dry arid zone, and along the wetter margins of the east and west coast. Swainsona is in the Fabaceae or pea family, which is one of the most widespread and diverse in Australia – particularly because of the Acacia genus (the wattles) of which there are approximately 800 species in Australia.Sturt’s Desert Pea, like much in the Outback, is named after the (in)famous 19th Century Explorer, Charles Sturt, who led an expedition into the centre of Australia in search of the ‘Great Inland Sea’. Needless to say, it didn’t end too well. It is an ephemeral plant, which means that it’s growth and reproduction occurs in response, or is timed to occur, after the seasonal rains that provide temporary relief to this harsh environment. It grows at an amazing rate, and is a sight to behold as it spreads across ephemeral creek beds, usually close to the ground in a way reminiscent of the The Red Weed

The flowers themselves are just exquisite, and so different to other members of the Swainsona genus. They are about 8-9cm long, arranged usually in a group of six in a circular arrangement. The blood red petals are long and pointed, and in the centre of the flower is a deep black spot that lends an even more surreal quality to the plants. The specific name formosa is a derivative of the latin formosus for beautiful. The pictures below show just how beautiful these flowers are, taken in Dead Horse Gully in Sturt National Park, just 5 minutes from Tibooburra.

S. formosa growing across an ephemeral creek bed
at Dead Horse Gully, Sturt National Park.
[Click Image to Enlarge]

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Close up
[Click Image to Enlarge]

Outback Australia NSW

In August and September last year I spent two weeks in the outback, around the area of Broken Hill, Fowlers Gap, and right up in the north-western corner at Sturt National Park, collecting plants for my Masters. I travelled with Tony and Viv Whitaker, who provided the most amazing field support. Tony, as I mentioned in my last post, is a herpetologist who travels all over the world doing field work for varied individuals and organisations. It was an absolute pleasure to travel with Tony and Viv, who were invariably optimistic and motivated in the face of the law of diminishing return.We flew into Sydney and then straight to Broken Hill, where we spent one night before heading onto the road up to Fowler’s Gap, a research station of the University of New South Wales. We stayed in a little single room cottage running solely of solar and wind power, of which there are plenty in the outback.

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The Ochre Cottage

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The Barrier Ranges around Broken Hill

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The landscapes are just phenomenal; they really have to be seen to be believed. Gibber plains – the eroded remnants of billion year old mountain ranges represented today by the low lying Barrier Ranges – stretch on for hundreds of kilometres. The roads are criss-crossed dry creek beds that flood during the rains in winter, but remain dry for 90% of the year, bordered by Red River Gum (Eucalyptus camaldulensis) which dominates the land along with Belah (Casuarina pauper), Mulga (Acacia aneura), Dead Finish (A. tetragonophylla) and millions of saltbushes, daisies and peas.

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A common sight

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A not so common sight – Swainsona fissimontana after rain

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Probably the hardest thing to grasp about the area is that every square metre, except for those in the National Parks, is farming land. Where you see the ground covered in nothing more than rock and sand, you will see fences. It is incredibly unproductive and extremely damaging on an already vulnerable environment. Communities essentially collapse there because the slow growing vegetation simply can’t withstand the herbivore pressure from cows, sheep, goats and kangaroos. Of course with the vegetation gone, the invertebrate and invertebrate communities also suffer. Not to mention the pressure on the Murray-Darling water system that farming here places. But of course, no one would dream of suggesting that farming ought not to be undertaken in the deep deep Outback because, well ‘it’s a way of life’. One that probably won’t last too much longer.

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Grazed Land at Fowler’s Gap

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Non-Grazed Land at Fowler’s Gap – The Mulga Reserve

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The land to the left of the fence is grazing land.
The land to the right has been fenced off for 30 years (the Emu Pen).

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After Fowler’s Gap, we stayed in Sturt National Park, a protected area in the topmost corner of New South Wales. We stayed at the Mount Wood Historic Homestead, administered by the NSW National Parks and Wildlife Services and run by the amazing head ranger, Ingrid. Ingrid was a German PhD student studying kangaroos at Fowlers Gap who fell in love with the Outback and its kangaroos, and now nurses orphaned joeys back to health – with the help of pillowcases as surrogate pouches. She has an incredible amount of energy and passion for her job, which was inspiring. We should all hope to love our jobs with that much passion. The lack of grazing in SNP has allowed for a fantastic regeneration of the vegetation – where in Fowler’s Gap the land was barren and rocky, the plains of SNP are covered with beautiful herbs and shrubs.

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Ingrid and her ’son’  

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You can see why she fell in love with them…

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The outback is a harsh but beautiful place. It can kill you easily if you’re not careful or prepared. But if you look closely enough you can see a world of colour and life, animals and plants that are so beautifully adapted to their environment, unique in their evolutionary histories. I hope that more Australians get the chance to experience it, and learn to treasure it.

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Me

View my slideshow here

Plant of the Week

This week’s plant of the week isn’t actually a single species, but rather a group of plants that have become endangered in New Zealand – the representatives of the Loranthaceae family, or mistletoes.

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Mistletoes are found throughout the world, and it often comes as a surprise that we have a number (8) of native species here, so absent as they are from public consciousness. Granted, they are certainly more well known in the South Island, where they are more common, but they are generally so rare nowadays, that they are almost unknown by most Kiwis. During my field trip last year to Australia, I couldn’t help but notice the huge amounts of mistletoes there, both in terms of sheer numbers and the number of species, even in the driest regions of the Outback: In any given area, at least one tree had a mistletoe growing into it; in some areas, every tree had one, often more massive than the tree itself.

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Like all mistletoes, the New Zealand species are hemi-parasitic. Mistletoe seeds are generally spread by birds, and germinate on host tree branches, often with their own complete portion of fertiliser. From there the seed grows into the branch of the host plant, tapping into the host’s vascular system to get access to sugars, nutrients and water. Over time, the mistletoe will grow and begin to photosynthesise on its own, relying less on the host plant for sugars, and more for its water and nutrient requirements. Like all parasites, mistletoes have negative effects on their hosts, and can severely restrict growth and reproduction. However, they are also recognised as a keystone species in most ecosystems, providing food and nesting sites for a number of animals, particularly birds.

New Zealand has Beech-, Green- Dwarf-Mistletoes. The Beech Mistletoes, as their name suggests, comprise three species (Peraxilla tetrapetala, P. colensoi and Alepis flavida that predominantly parasitise the native southern beech species (Nothofagus spp.), although they are also found on other native species including Tawheowheo (Quintinia serrata) The two Peraxilla species have bright red flowers in Summer, which in older times would turn entire mountain ranges red at Christmas. The Green Mistletoes are perhaps less charismatic but far more generalised than the Beech Mistletoes, and one species, Ileostylus micranthus has been recorded on over 200 host species, including totara and the Pittosporum species.

The main threat to our native mistletoes are possums, which is not unsurprising given the damage that the barstards have done to many of our plants and ecosystems. Mistletoes have declined hugely in range over the last 100 years, and are now entirely absent in many areas where they were previously common. Possums browse the flowers, leaves and shoots of mistletoes, removing vital food source for native birds such as tuis and bellbirds, which in turn act as pollinators for the mistletoes. As a result, not only do the mistletoes disappear, but bird populations also begin to suffer. Many areas that have effective long term possum population control (through 1080 drops) have had remarkable restoration of their mistletoe populations.

Peraxilla tetrapetala
Peraxilla colensoi
Peraxilla tetrapetala on Beech in the Southern Alps.

Plant of the Week :)

Well! Yesterday’s rant put me in a bit of a foul mood, so what better to clear the air than perusing through another botanical treasure! This week I thought I would include something non-native (despite my assurances I would mostly stick to natives! Ha!), but an absolute delight nonetheless:Leopardwood – Flindersia maculosa

In August and September of last year I made my first field trip to Australia for my Masters. My project involves comparisons between arid and wet-coastal plants, so my first trip was to the arid regions of New South Wales, in the area in and around Broken Hill. I’ll probably post some photos later, but it was such an experience! For those of us from New Zealand, it’s simply an alien landscape: so dry, so dusty and so so red. More on that later…

Anyway, my absolute favourite plant from that area is Leopardwood, a member of the Rutaceae family – the family most well known for the Citrus genus. The joy of Leopardwood is revealed when you get up close -it has this fantastic spotty bark that gives the tree it’s common name. After seeing boring Casuarina and Acacia for hundreds of kilometres, its a treat to see something a little different!

Plant of the Week!!! Yay!!!11

So one semi-regular thing that I thought I would do is write about some plants that I like or come across that are interesting…can’t promise I’ll do one every week, but what they hell. You probably don’t even read this regularly. I’ll mainly do natives, but an exotic every now and then won’t hurt…This week…

Nihinihi – Shore bindweed – Calystegia soldanella

Like all bindweeds, nihinihi belongs to the Convolvulaceae family. Most of the Convolvulaceae, including the Convolvulus genus after which the family is named, are creeping herbaceous vines or prostrate shrubs. Nihinihi is no exception, forming large mats in sandy and rocky coastal areas and lakes.

Nihinihi is native to our shores, and is found throughout most of the country, especially in the northern regions of the North Island. It really is a neat little plant with lovely curved leaves and beautiful pale pink or mauve flowers. I found it recently growing on Te Haupa, an uninhabitated island in the Hauraki Gulf, during some field work there, but I have spotted it elsewhere.

Anyway, it’s nice to say some positive things about the Convolvulaceae, given that several species, particularly from the Convolvulus genus, are invasive in New Zealand, forming inpenetrable mats over everything.What a treat