Amy Whitehead's Research

the ecological musings of a conservation biologist

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Wildlife Wednesday: Tomtit

The tomtit (Petroica macrocephala) is a small passerine bird in the Australasian robin family (Petroicidae). Also known as miromiro, or historically the great-headed titmouse, tomtits are endemic to New Zealand. Weighing in at only 11 grams, tomtits are one of the smaller species of New Zealand birds (the lightweight record goes to the rifleman at a mere 6 grams). But what they lack in size they make up for in character. They are common throughout New Zealand and live in shrubby and forested areas, where they typically perch on a branch or tree trunk to watch for flying insects. Once spotted, they will flit out and snatch up the target before resting on the next perching spot. You can often attract a tomtit into photographing range by imitating their call and then stirring up the leaf litter to disturb insects into the air. As kids we used to imitate bird calls by rubbing a piece of polystyrene on a wet glass jar and would be rewarded with tomtits perching on our packs or boots while they scanned the air for insects.

Tomtits have played a special role in one of New Zealand’s conservation success stories, acting as surrogate parents for a number of critically endangered Chatham Island black robin chicks. Black robin numbers dropped to just five individuals in 1980 due to predation by introduced mammals. With only one female (Old Blue) remaining, a dedicated team of conservationists devised a cunning plan to rescue the species by eliciting the help of the humble tomtit. Each year the team would remove the first clutch of eggs from Old Blue’s nest and place them in a tomtit nest. The unsuspecting tomtits raised the chicks and Old Blue would lay a second clutch of eggs. This cross-fostering was so successful that some of the first fostered chicks grew up thinking they were tomtits! Some careful tinkering with the techniques produced robins that thought they were robins and there are now ~250 black robins on two islands in the Chatham Islands.  All thanks to Don Merton and his team of dedicated conservationists and tomtits!


Wildlife Wednesday: Feral Pigeon

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Rock pigeon

So it’s been quite a while since my last “weekly” Wildlife Wednesday post.  I’m blaming it on the excessive amount of travelling I’ve been doing (16 flights in 2.5 months!) but really it’s mostly laziness (with a dash of busy-ness and general craziness).  But on my travels about the place, I’ve been taking pictures of some of the things I’ve been seeing along the way. One thing that struck me was how often I was seeing the same species over and over again in completely different parts of the world.  Some of them have been moved around by people, some have made the journey by themselves.

Feral pigeons (Columba livia) are one of those cosmopolitan species that seem to be in every city you visit.  Descended from domesticated rock doves, pigeons have become well established in cities where the ledges of buildings and bridges make great substitutes for their natural roosting habitat on cliffs.  Pigeons generally get a pretty bad wrap, with “avian rats” and charming monikers used to describe them. And to be fair, some pigeons are pretty nasty looking – lice-infested, missing toes and feathers or some weird motley hybrid. But they can also be quite pretty birds, with a beautiful iridescent green sheen around the back of the neck.

In some parts of the world, feral pigeons are doing their bit for threatened species conservation by offering themselves up as prey (although probably not knowingly or willingly).  Peregrine falcons are making a comeback in some urban centres, where tall buildings provide cliff-like nesting habitat and flocks of feral pigeons provide dinner.  It was pretty cool to be able to watch a pair of peregrine falcons going about their business next to the London Eye thanks to the RSPB (& someone dressed as a hedgehog!).  Urban ecology at its best.

RSPB hedgehog

Wildlife Wednesday: Dobsonfly


DobsonflyGo swimming in a stony bottomed stream in New Zealand and you might just find yourself toe to face with a toebiter or dobsonfly larvae (Archichauliodes diversus).  Looking like they have stepped straight from a B-grade horror movie, dobsonfly larvae are New Zealand’s largest freshwater insect reaching up to 5cm.  They have strong jaws, capable of giving you a good nip, but they prefer to dine on other stream invertebrates.  The “legs” that give them a centipede-like appearance are actually large gills. They can survive periods of time out of the water and are often found in small cavities dug into the mud.

However, just like the ugly duckling and the swan, this story has a pretty ending.  The adults, like the one above,  have a wingspan of up to 8cm and are pretty spectacular insects.

Wildlife Wednesday: Kōwhai


Kowhai flower

The kōwhai (Sophora spp.) is a New Zealand tree legume that typically grows in open areas and along the edge of streams and lakes.   The name kōwhai comes from the Māori word for yellow – a reference to their prolific flowers and small pea-like seeds.  One of NZ’s most iconic plants, they flower from July to November and are an important source of nectar for native birds, particularly tui and bellbirds.  They are a common garden plant and most children I know spent time trying to get the seeds to grow by throwing them in boiling water or attacking them with sandpaper (okay I may have grown up in a strange neighbourhood but these are actually the best techniques for breaking the tough outer coating of the seed to get them to grow).   However, almost all parts of the tree are poisonous to humans, so don’t be tempted to take a nibble!

While New Zealand doesn’t have an official national flower, kōwhai would do pretty well in a floral showdown.  Indeed, kōwhai flowers are one of only two plants to make it onto New Zealand coins, featuring on the New Zealand 2c coin from 1967 to 1990 (the other being the silver fern on the 1c and $1 coins).  They also featured on a 3D (as in threepence, not three-dimensional) stamp released in 1960 and the 2.5c stamp when NZ converted to decimal currency in 1967.  Apparently they have also been immortalised in folksong, although I think this may have been popular a little before my time.


Wildlife Wednesday: Monarch butterfly

Monarch butterfly

Monday was a public holiday in Victoria in honour of the Queen.  I’ve often been intrigued by how many birthdays the Queen has in a year, given the numerous dates on which it is celebrated throughout the commonwealth.  But it turns out that we were really celebrating the (approximate) birthday of King George III, with the first Monarch’s Birthday celebration held in Australia in 1788.  So it seems appropriate to celebrate with a monarch butterfly (Danaus plexippus).

The monarch butterfly is a pretty amazing beast.  Native to North America, they migrate from Mexico to southern Canada and back every year, a journey which can take up to four generations.  They are following seasonal changes in the abundance of their main food source,  milkweed. Typically, it takes three generations to get from Mexico to Canada, with the adults in each generation living for about two months.  The fourth “super” generation can live for up to seven months and is capable of making the entire return journey back to Mexico.  That’s about 4,000 km – not a bad effort for an insect with a wingspan of ~ 10 cm!  Monarchs overwinter in a small area of forest in the Mexican mountains at the Mariposa Monarca Biosphere Reserve, with up to one billion individuals occupying  sites that cover less than five hectares within the reserve.

Not much was known about the monarch migration until Fred and Nora Urquhart began researching the monarch butterfly in 1937, recruiting an army of citizen scientists across North America to help them in their quest to find the wintering sites.  Individual butterflies were marked with small stickers on their wings and released to continue their journey.  Sightings of tagged butterflies were recorded and plotted on a map but it took 38 years before the mysteries of the monarch migration and the location of the wintering sites in Mexico were revealed.

The video below has a nice summary of both the migration and the citizen science movement (and fun things you can do with google earth).

Monarchs are also found in New Zealand (where this photo was taken), Australia and the UK.  However, they don’t make the same large-scale migrations (partly because they would totally run out of land, at least in NZ and the UK!).

Wildlife Wednesday: Ants



Last week a few qaecologists and I went on a gum tree (Eucalyptus spp.) identifying expedition up to the mallee in north-west Victoria.  It turns out that identifying Eucalytpus is actually quite difficult – they all pretty much look the same and the species we were looking for differ only by subtle changes in the shape of the buds or fruit.  I am glad I  work on virtual plants!

But we did see lots of  interesting things, including these large ants on a shrub that had recently been burnt in a bushfire.


Creating a presence-absence raster from point data

I’m working on generating species distribution models at the moment for a few hundred species. Which means that I’m trying to automate as many steps as possible in R to avoid having to click buttons hundreds of times in ArcView.

One of the tasks that I need to do is to convert presence-only latitude and longitude data into a presence-absence raster for each species. It seems like this would be something that relatively simple but it took me longer than it should have to figure it out. So I’m posting my code here so 1) I don’t forget how I did it; and 2) because I had someone ask me how to exactly this thing this afternoon and it took me ages to hunt through my poorly organised files to find this piece of code! So here it is:

Because I’m a function kinda girl, I wrote this as a function. It basically goes through three steps:

1. Take an existing raster of the area you are interested in mask.raster and set the background cells to zero (absences).

2. rasterize the presence points for your species and set those cells to one (presences).

3. Label the new raster by your species names raster.label and save it as a new raster.

presence.absence.raster <- function (mask.raster,,raster.label="") {

# set the background cells in the raster to 0
mask.raster[!] <- 0

#set the cells that contain points to 1
speciesRaster <- rasterize(,mask.raster,field=1)
speciesRaster <- merge(speciesRaster,mask.raster)

#label the raster
names(speciesRaster) <- raster.label

Below is an example of how the function works using data on the global distribution of foxes data from the biomod2 package.


# read in species point data and extract data for foxes
mySpecies <- read.csv(system.file("external/species/mammals_table.csv", package="biomod2"), row.names = 1)
species <- "VulpesVulpes"

# extract fox data from larger dataset and keep only the x and y coordinates <- mySpecies[,c("X_WGS84", "Y_WGS84",species)] <-[$VulpesVulpes==1,c("X_WGS84", "Y_WGS84")]

# read in a raster of the world
myRaster <- raster(system.file( "external/bioclim/current/bio3.grd",package="biomod2"))

# create presence absence raster for foxes
pa.raster <- presence.absence.raster(mask.raster=myRaster,, raster.label=species)
plot(pa.raster, main=names(pa.raster))


In this plot, the presences (1) are shown in green and the absences (0) in light grey.

Helpful things to remember (or things I learnt the hard way)

  1. Make sure your species point data and raster are in the same projection and that they actually overlap!
  2. Set your desired raster extent and resolution in the mask.raster before you get started.
  3. The species point data that you feed into the function should just be a list of x and y co-ordinates – no species names or abundances or you’ll confuse the poor beast and it won’t work!

And yes, foxes are also present in Australia where they are a pest. I guess this map shows their natural range before people started doing silly things.

Bought to you by the powers of knitr & RWordpress 

(Well it was and then things went a little awry, so I had to do some tinkering!)