New paper: ‘Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region’

My first PhD paper has been published in Royal Society Open Science on the conservation genetics of the Growling Grass Frog around Melbourne, Australia. Remnant populations of the species around the city of Melbourne are threatened by urban expansion and I found generally low levels of genetic diversity. However, one of the regions studied, the Cardinia Shire, did exhibit unique genetic types and relatively high diversity and should therefore be recognised as a separate Management Unit.

The paper’s publication is particularly exciting for me, as it involved countless hours standing in the middle of urban wetlands catching frogs, learning how to do genetics lab work to process hundreds of samples, and I had a baby the week it was submitted.

One of my Growling Grass Frog photos on the cover of the journal

Herping in Amherst, Massachusetts

While visiting Amherst, Massachusetts, recently, I had the opportunity to go out herping (looking for reptiles and amphibians), with a few local ecologists. As I mentioned in my previous blog post, I was unfortunately not in Amherst at the right time of year to see the Spotted Salamander, Ambystoma maculatum, migration. I also just missed the Marbled Salamander, Ambystoma opacum. Two very large and impressive salamander species. However, all was not lost, as I still got to see some amazing amphibians.

My favourite was the Red spotted newt, Notophthalmus viridescens, in the terrestrial red eft (juvenile) stage. While aquatic larvae, they have olive coloured skin, and while aquatic adults, they are an olive to brown-green. In between their larval and adult phases, however, the juvenile red or orange efts spend 1-3 years on land. Their bright colour warns of their toxicity, and as such, they are commonly seen out in the open in the woodlands they inhabit. When we ventured up into the nearby mountains, these little guys were everywhere! An almost fluoro orange and breathtakingly beautiful.

Another highlight was holding a large American Bullfrog, Lithobates catesbieanus. I thought my PhD study species, the Growling Grass Frog, Litoria raniformis, was big, but they are dwarfed by the American Bullfrog.

The state of Massachusetts has 10 salamander species and 10 frog/toad species. I was fortunate to find quite a few of these in Amherst, and have included photos of some of the amphibians we saw and habitats we explored.

Red spotted newt, Notophthalmus viridescens, terrestrial red eft stage

Three Red spotted newts!

An older Red spotted newt eft

Eastern Red-backed Salamander, Plethodon cinereus (lead colour morph)

Eastern Red-backed Salamander, Plethodon cinereus (red colour morph)

Eastern Red-backed Salamander, Plethodon cinereus (red colour morph)

Northern Two-lined salamander, Eurycea bislineata

American Bullfrog, Lithobates catesbieanus

American Bullfrog

Spring Peeper, Pseudacris crucifer

Gray Treefrog, Hyla versicolor

Green Frog, Lithobates clamitans

Wood Frog, Lithobates sylvaticus, metamorph

Wood Frog

American Toad, Anaxyrus americanus, metamorph

American Toad

Salamander road crossings

I’m currently spending some time in the USA. A few weeks ago I attended the International Congress of Conservation Biology (ICCB), held in Baltimore, Maryland. I spoke on ‘Comparing the efficacy and impact of genetic sampling techniques for amphibians’. I also attended a great introduction to landscape genetics short course prior to the conference.

I’ve just left Amherst, Massachusetts, where I was visiting an urban ecology lab, in the Department of Environment and Conservation, at the University of Massachusetts for three weeks. Amherst is a really beautiful, small college town and I loved riding my bike around and enjoying the sunshine (a good excuse to escape the cold of winter back home in Melbourne, Australia).

When I chose to visit Amherst, I had no idea I was visiting the first place in North America to build salamander tunnels under the road! The salamander underpasses were created in 1987, for the yearly mass migration of the Spotted Salamander, Ambystoma maculatum. Every year, after the first rain of spring, most of the salamanders migrate during one night, to the nearby vernal pools to mate and lay their eggs. Drift fences along the road guide the salamanders to the two tunnels, which have holes above them, to let in light and moisture. Noah Charney took me to see the tunnels and look for amphibians while I was there. He narrates a video on the salamanders making their annual trek through the Henry st tunnels.

Unfortunately, I wasn’t in Amherst the right time of year to see the Spotted Salamander migration. Looks like I’ll just have to go back.

Spotted Salamander, Ambystoma maculatum.
Image: Leo Kenney

The salamander tunnel from above

My natural history note

I have a natural history note in the latest issue of Herpetological Review 44(2) 2013. It details the leucistic Growling Grass Frog we found in Melbourne in 2012, which I wrote about in a previous blog entry, titled ‘The most remarkable frog‘.

Litoria raniformis (Growling Grass Frog). Leucism.

Celebrating milestones

A few days ago marked the 3 year anniversary of the commencement of my PhD. It felt a bit like a mini-birthday; I was in a great mood, received lots of kind words from friends and even received a present (although admittedly, from myself). I’m not sure if this is exactly how you’re meant to act when you hit the 3 year mark in your PhD and you’re not yet finished (especially in Australia, where a PhD is technically meant to only go for 3 years). I think it helps that I’ve spent a large proportion of my PhD chasing frogs in the field and working in the genetics lab. These were activities I always knew would take up a lot of my time, so I never expected to finish in 3 years.

I choose to view my 3 year milestone as a celebration. A time to recognise that I’ve worked really hard for 3 years now, learnt so much, made amazing friends, and am starting to see the light at the end of the tunnel (although it’s still quite a long tunnel). A few months ago I wrote about finishing my field work and now, as of a few weeks ago, I’ve finished my genetics lab work (I think). It’s starting to feel like this PhD is getting somewhere, and not going to go on forever (something I was genuinely concerned about and earnestly asked one of my supervisors a few months ago).

A wise post-doc mentioned to me the other day that this is often how it feels when doing a PhD. For most of  it you can feel like you’re not getting anywhere and then suddenly everything starts falling into place. This is how I feel at the moment. Who knows how long it will last, but for the time being, I’m really happy with all I’ve achieved and feel like celebrating!

I’ve included photos of some of my favourite PhD memories so far…

My first day of PhD field work

Celebrating friends’ PhD graduations

Dinosaur t-shirt day

International Congress for Conservation Biology 2011 in NZ

Making dinosaurs in the lab

More dinosaurs…

Writing workshop In Queenscliff, Victoria

My PhD 3 year present to myself (mini swing tennis)

Data entry while staying with my in-laws at their home in the WA bush

Camping in Olympic National Park, USA, on my way to the 2012 World Congress of Herpetology in Vancouver

Jumping with friends on the blow up castle at the Australian Society of Herpetologists Conference 2013

Finding my leucistic Growling Grass Frog!

The end of field work

Almost as soon as it began, my ‘mini’ third field season is over. Field work has been a large part of my PhD so far, with considerable time and effort spent finding and catching Growling Grass Frogs over the past three summers. My field season actually finished last week, but I was too tired to post a blog entry marking the occasion. I feel like I shouldn’t just let the moment pass though, because it’s actually a big deal to me. The ‘mini’ third season was quite underwhelming for the most part. Many sites lacked Growling Grass Frogs and some were no longer even ‘sites’, long since dry and overgrown, due to the extremely low spring/summer rainfall Melbourne has had.

When I reflect on my time in the field during my PhD, I have a mixture of emotions. The overwhelming emotion is concern. I really worry about the future of this species. Already considered endangered in Victoria, so many of the sites you find Growlers are pretty awful. Many of the sites are characterised by rubbish, polluted water, overgrown weeds, encroaching development and introduced predators. This season, fire and a lack of rain also played their parts.

However, I also feel optimism when I visit the good sites. Some of the waterbodies I visited were on private property, or in fenced areas, and these were beautiful. Some sites (although far too few) were just covered in Growling Grass Frogs. This is a species that was once abundant throughout most of its distribution, so the sites with high densities always put a smile on my face. This is what they’re meant to be like. As my field work included not only locating these frogs, but also catching them, the sites with abundant Growlers were also extremely fun. It seems fitting that surprisingly, my very last night of field work was one of these sites. Not pretty or clean and definitely not one of the safest sites I’ve visited (one night last season involved police and search helicopters), this site was unremarkable last summer. This season it was completely different. We went there on a perfect night for frogging, it had rained heavily during the day, so everything was wet and the night was extremely hot and humid. There were frogs everywhere. It was a great reminder to me that things can change. Sure, some of my previous sites have disappeared, but there are still sites with Growlers and still time to make a difference for this species. Ending my very last night of field work surrounded by so many frogs was both a blessing and a curse. It feels really good to end on such a productive and fun night… but now I want to get back out there for more.

The very first Growling Grass Frog I caught for my PhD (in 2010)

My last Growling Grass Frog (in 2013)

My third (mini) field season

Last night marked the beginning of the third and final field season for my PhD research. This will just be a ‘mini’ season however, as I plan on spending only 1-2 weeks out collecting samples from sites I found low numbers of Growling Grass Frogs last summer. This is in contrast to the past two seasons, which saw me spending months in the field, out until about 4am each night. Although perfect conditions last night (very warm, it was still 29ºC at midnight), we unfortunately found no frogs at the two sites we visited, and were unable to access our third site, due to bushfires in the area. We did visit an additional site however, a small waterbody with a very large number of Growling Grass Frogs, to take some photos. Last season, this was my site of choice for taking field assistants learning to find and catch Growling Grass Frogs and thankfully this year, it did not disappoint. Numbers are still extremely high there, and when I analyse my genetic data from the site, I’ll be interested to see whether this is also a genetically fit population. Here are some photos of last night’s cuties….

A metamorph sitting on rubbish. Unfortunately a common sight…

3 frogs found on 1 rock! An unusual sight for an endangered species.

Museum Victoria Grampians Bioscan

I recently returned from The Grampians, Victoria, where I was helping Museum Victoria conduct a large biological survey of the area. Sixty-two Museum staff and twenty Parks Victoria rangers surveyed the flora and fauna of the Grampians National Park for 12 days. I spent most of my time there conducting nocturnal amphibian surveys and we found 9 frog species, including the Growling Grass Frog. This is my PhD study species, listed as vulnerable to extinction nationally and endangered in Victoria. My study field sites are located around the urban fringes of Melbourne and are often very polluted and degraded, so it was really exciting to find the frog in beautiful, clean, healthy waterbodies in the Grampians. Another highlight was the discovery of Common Spadefoot toad metamorphs! The species spends most of its time burrowed underground and uses little black ‘spades’ on its back feet to dig. Velvet worms were another incredible find. After being a little obsessed with these gorgeous creatures for awhile now, I finally saw them for the first time and they didn’t disappoint.

Lots of cute animals were found, I’ve included photos of some of my favourites below.

The Growling Grass Frog, Litoria raniformis

Me holding a large female and a small male Growling Grass Frog

Common Spadefoot Toad metamorph, Neobatrachus sudelli

Common Spadefoot Toad displaying it’s little digging ‘spades’

Velvet worms!

An Eastern Long-necked Turtle, Chelodina longicollis, attempting to lay eggs on the road

A baby Jacky Dragon, Amphibolurus muricatus

A young Stumpy-tail Lizard, Tiliqua rugosa

Tailed frogs, Salamanders and the World Congress of Herpetology

I’ve just returned from The 7th World Congress of Herpetology in Vancouver, Canada. The conference was lots of fun and it was great to see presenters with so many amazing study species and beautiful field sites from around the world. The conference was held at The University of British Colombia, and I presented my work on the genetic structure of the Growling Grass frog in an urbanising landscape.

I also spent a few days before the conference camping in Olympic National Park, Washington, USA and Vancouver Island, Canada. Olympic National Park was incredible, with beautiful remnant forest, wildflowers and snow-capped mountains. However, the most exciting attraction the park had to offer (well, to a herpetologist anyway) were its adorable amphibians. We found Olympic Torrent Salamanders and Tailed Frogs! My entire reason for going to Olympic NP was to search for Tailed Frogs and they did not disappoint. There are two species of Tailed Frogs; the Rocky Mountain Tailed Frog, Ascaphus montanus and the Coastal Tailed Frog, Ascaphus truei. The species we encountered in Olympic NP was Ascaphus truei. Unlike other frog species, which have external fertilisation, Tailed Frogs actually use their little tail (an extension of their cloaca) for internal fertilisation. This is a helpful adaptation for life in fast-flowing streams and additionally means that females can store sperm and delay oviposition. Tailed frogs are an ancient frog lineage that also lack the ability to vocalise.

I’ve included some photos of gorgeous Tailed Frogs, as well as some of the other amphibians we encountered on the trip.

Male Coastal Tailed Frog, Ascaphus truei, Olympic National Park

Ventral surface of male Coastal Tailed Frog, Ascaphus truei

Female Coastal Tailed Frog, Ascaphus truei, Olympic National Park

Olympic Torrent Salamander, Rhyacotriton olympicus, Olympic National Park

Rough-skinned Newt, Taricha granulosa, Vancouver Island

Western Toad, Anaxyrus boreas, Vancouver Island

Northern Red-legged Frog, Rana aurora, Vancouver Island

Pacific Tree Frog metamorph, Hyla regilla, The University of British Columbia

Amphibian adventures in the northern hemisphere

Recently I’ve been spending time in the genetics lab, where I’ve been optimising both nuclear primers for sequencing and microsatellite markers. I’ve also been preparing my presentation for the World Congress of Herpetology at the University of British Columbia, Vancouver, Canada. I’m really excited about this conference and had an amazing time when I attended the previous WCH, four years ago in Manaus, Brazil.

I’m spending a few days in Olympic National Park, Washington, USA on my way to the conference, in search of salamanders and tailed frogs. As Australia has no native salamanders, I’m looking forward to hopefully finding some in Olympic NP.

If all goes to plan, my next blog entry will be filled with amphibians and amphibian stories from the northern hemisphere!