Glass Eels are Arriving in our Creeks

On 6 March 2016, it was a dark still night (~8 pm) and the tide had just peaked when I took a look in a tiny creek at the northern end of Palm Cove, Cairns, Queensland Australia.  The small fish that leap when a torch is shone on the water where not to be seen today and I had to look for creatures.  After a few minutes, it became apparent that every few seconds a tiny, clear living thread would zoom past. They were hard to catch and it took a while to get the first one.

Glass eel or elvers of longfin eel (Anguilla reinhardtii) - click to enlarge

Most of them were following the thin film of freshwater that lay at the surface of the tidal creek. They were mostly moving through the thin film of the very margins of the creek, where the creek cut across the sandy beach.  In all the photos that follow, the gravel that is visible is actually some of the finest whitest sand in Cairns and it is just the small size of the eels that makes the sand look coarse.

Glass eel moving up the very boundary of the water - probably following a salinity gradient

Three glass eels are present in this photo

The glass eels rested momentarily in the mangrove detritus before striking out again.  It proved to be easier to capture the resting eels.  A highly venomous box jellyfish was also bumping its way along the bank.

Box jellyfish with 2 cm bell

It was so hard to photograph these small creatures in the surging water, I made a video.  The clarity is not great as fresh and saltwater are mixing near surface creating haze.

I captured a few glass eels to photograph and later placed them in an established freshwater fish tank with a few neon tetras.  The elvers seemed to handle an instant transition from saltwater to freshwater well and were alive in the morning.  Instant transitions kill most fish as their gills have to switch from excluding salt to absorbing it and kidneys from excreting salt to recovering it.  I guess that animals which are desperately seeking freshwater can handle sudden transitions.

Glass eels become large freshwater longfin eels when they grow up.  The creek at Palm Cove is very small and it is a wonder that glass eels were attracted to it.  There was a noticeable salinity gradient with relatively fresh water present at the very surface.  Upstream there is only 100 m of mangrove creek before the vegetation transitions into a paperbark/rainforest swamp forest.  These areas tend dry out in the dry season so how do the eels survive?  Back in April 2014, I was looking around in this area for interesting biodiversity when I found a mature eel half out of the water in the mangrove roots. I thought the eel was dead but when I got close, it took off.  Perhaps the eel was surviving by taking refuge in a thin film of freshwater floating above the seawater.

Mature longfin eel using mangrove roots to lift its body to/above the surface.

Place where I found the eel

Postscript
I took a few eels and let them go in my fish tank.  Two weeks later, most seem to be still alive.  After about 4 days they started to develop a dark skin, but their flesh is still clear.  During the day they hide under objects but at night they swim frenetically, perhaps 40 cm per second.  So they are not just trying to reach freshwater, they want to penetrate upstream as fast as possible.

Beach Recovery at Yorkeys Knob

In the 1950's the sea was threatening to eat the houses on esplanade at Yorkeys Knob.  The original cause of this crisis took place in 1927, when the Barron River had carved a new channel through the cane fields to connect Thomatis Creek which flowed to the Barron with Richters Creek that went to the sea.  This new route was seven kilometres shorter than the old course of the Barron River.  Some years later, the mouth of the Barron also moved north by nearly 2 km after breaking through the beach during a flood.  Rivers pump sand out into the sea, yet only when the near shore waters near river mouths become almost choked with sand, do waves to return some of this sand to the beach.  It has taken nearly eighty years for the flow of sand back to the beach to be restored and beach to grow to its maximum width.

Changes in Yorkeys Knob Beach 1952-2015 (click here to enlarge)

Sand mining from the bed of the Barron River continued until the 1990's and intercepted both the 20 000 tonnes of sand coming down the river each year and consumed an additional 70 000 tonnes per annum of previously deposited bed load.  This consumption of the sand supply had a terrible effect on the beaches particularly Machans Beach and Holloways Beach, which lie between the old mouth of the Barron River and the new mouth at Richters Creek.  The fight to protect Holloways Beach and Machans Beach are covered in previous posts (see Coastal Protection in the subject index).  In contrast, Yorkeys Knob Beach is positioned to receive the high volume of sand that takes the shortcut to the new mouth and as soon as sand mining stopped began to grow quickly.

The growing width of Yorkeys Knob Beach provides more than a happy story of how a beach was saved, it is a chance to answer a swag of questions about how coastal features form as they have literally been forming in front our photographic eyes.  These questions are important to land management as well as being scientifically interesting.  Developers like to claim that dense coastal vegetation is just regrowth and that they should be able to remove some of it to create views.  Dense vegetation developing where previously there was open sea could affect the public by blocking cooling sea breezes and possibly by allowing increased mosquito activity.  Conversely, a wider beach with dense vegetation provides a much better buffer against storms.  Scientifically interesting aspects include the development of landscape features such as chenier ridges form and how and why some areas become impoverished grassland yet metres away a ferny rainforest is created.  Topics of scientific interest will be covered in future posts.

In overview, it appears that between 2002 and 2008, the beach got wider by approximately 5 metres  per year.  From 2008 to 2016, the position of the beach has been stable as sand is now able to escape around the rocks at the northern end of the beach.  Recently the beach has been getting higher rather than wider, with the foredune growing about one metre in height.  As the beach grew, a series of small ridges and swales were created that are now stabilised by dense grass and herb cover.  In places trees colonised, mostly in lines that were probably created by high tides washing seeds up onto the foredune.  Many of these seedlings have grown to become trees that are approaching maturity.  In places the dense wall of regenerating trees is lifting off the ground and an open understorey is developing where is breezy and open but shady.

2010 (left) and similar 2016 views (right).  The foredune has become much higher and has continuous vegetation

Another important observation is the resurgence of native plants.  In my first intensive survey of this area, much of the vegetation on the low dunes was composed of introduced species.  There was para grass, guinea grass, Tridax daisy, Hyptis, Singapore daisy, Chinese violets and Mossman River grass, which has nasty burrs that penetrate our skin.  Most of theses exotics have waned and been replaced by a vigorous sward of native grasses and herbs.  Healthy natural vegetation looks better than weed infested areas.  Native plants seem to fit together, each providing a different visual texture and each occupying a defined area.  In contrast exotic species tend to run rampant and form smothering tangled masses which 'lack natural design'.  The exotics are still present but have only a minor presence.  The photos below show how they were.

Top: Tridax daisy and Mossman River Grass (the nasty one)| Bottom: Singapore daisy and Hyptis

For me, seeing these changes is not a matter of good memory.  Since approximately 2004, I have been photographing a very wide range of subjects using geotagged photos.  I am possibly one of the leading practitioners in the world when it comes to using photos to track ecological change, yet after more than fifteen years of development, I am still working hard to make a system that makes it easy monitor the environment with photos.  If anybody thinks that they can do time series research without having developed or acquired powerful tools for this purpose, they will have a very hard time matching photos in future.  In another post I will describe how to use photos for monitoring.  Most of the hard work is done by a database application that I have been developing for many years.  The information in this post comes mainly from my personal photo collection, aerial imagery from Google Earth (thanks Google) and some really old aerial imagery that I have scanned in.  To make the beach fit better on the page. the aerial photography has been rotated.

Coverage of geotagged photos - you can never have enough

Leatherback Turtle near Cairns

I get cheeky and go out to the Great Barrier Reef in my open boat on calm days.  Today, I was in deep dark blue waters about 5 km from the reef when I passed by a giant turtle basking just below the surface.  It did not seem to be worried by a 40 horsepower outboard passing by at full throttle only 20 m away.  However when I turned and can back for a closer look the turtle lifted its head up for a look, saw me and departed to the depths.  I don't think there was anything wrong with the turtle.

Leatherback Turtle near Green Island-Cairns North Queensland

The special thing is that there are no published records that I can find for leatherback turtles (Dermochelys coriacea) near Cairns.  The nearest record in the Atlas of Living Australia is from Mackay and dates from 1985.  Another record shows on the map near Cooktown, however this record is for a fossil!  Leatherback turtles are endangered, so this sighting is significant.

The water was clear and there were some small clumps of floating yellow-brown algae, probably sargassum and occasional lines of widely dispersed mangrove detritus.  However there were no major collections of floating materials which would indicate a downwelling zone and there was no other wildlife activity in the area.  In the water, transparent jellyfish with fine filaments at the edge of the bell were visible (Aurelia?) on the reef.  I even photographed one strange jellyfish then realized that the bell had been eaten by something, probably a turtle.  Leatherback turtles eat jellyfish as do green turtles.

Checkout the teeth a Leatherback has for dealing with jellyfish in this blog

Around the Rocks at Island Point – Port Douglas

Sometimes you can't get to the Great Barrier Reef because there is not enough time, the sea is too rough or you can't afford it. It is always good to know a few areas that are easy to get to and that can provide a little adventure.  Today, I walked around the sea coast of Island Point which is at the end of the famous Four Mile Beach at Port Douglas.

View from near near Port Dickson (click photos to enlarge)

View from near Four Mile Beach

This time instead of clambering over the cliffs at the Four Mile Beach side of the headland, I walked in from the Dickson Inlet side, which proved far easier.  On rounding the first corner, all of the bustle of the busy tourist port was left behind and it was like being on a deserted tropical island.  It is the kind of place Bear Grylls uses to challenge modern humans.  It was 37 degrees Celsius, and despite a sea breeze in the Port, the rocky coast was almost airless and 100% humid, right in the danger zone for the unacclimatised.  Visiting this area requires the crossing of almost a kilometre of large round boulders.  These boulders have a layer of ancient blue green bacteria (Nostoc) which is natures first attempt at a non-stick coating.  Finally, with the mangroves being close there is a low but credible risk of crocodiles, there are nasty oyster reefs and the rocky coast is where the toxic jellyfish breed so swimming around the headland is not recommended.  If you are are fit and take care then you will be rewarded with a rugged coastline featuring dozens of rock pools full of darting fish.

A rock pool with a black sea sausage

Juvenile diamond-scale mullet and two sergeant majors

Most of the fish present are specialised for living in rock pools and include a variety of gobies, pipefish, dart fish and juvenile reef fish which use rocky coasts as a nursery.  If it is high tide or if our seasonal 15-20 knot trade wind is pumping large waves onto the coast, very little of this marine life will be visible.

Higher up are smaller pools in the black rock.  These have grazing snails and sometimes even have live coral! It seems that under the right conditions, coral is even tougher than algae.  The rocks were so hot that the limpets were almost being cooked alive.

Most of the bottom of this tiny pool is covered by colony of hard coral.  It has a touch of bleaching on one edge.

Nerita costata snails feed on the thin layer of algae

Heat-stressed limpets were holding their shells as high as they could to cool down

The sub-tidal zone is dominated by brown macro-algae and black sea urchins (Diadema).  I do not know if this community is a recent community that has developed due to climate change and loss of coral.  Until recently it was incredibly hard to make an environmental record, there were no GPS, no cheap underwater cameras and each photo cost a dollar which is probably 1000 times the cost of a digital photo.  I only have fading memories of what places used to be like twenty years ago and these often do not include vital information such as which season it was.

The coast that I observed a few days ago is not that different to temperate coasts where algae dominate the swash zone.  Under the water, algae cover the rocks and a few metres further out the rocks give way to sand flats.  In this underwater rock garden, sea urchins are the gardeners.

Boulders quickly give way to a sandy seabed 

Diadema sea urchin

Close to then end of the headland, rainforest gives way to patches of natural grassland with pandanus trees due to the constant blasting of wind and salt spray. Up the top, parts of the hill belong to very rich people so avoid the temptation of bush bashing up the slope.  To get to the top, find the path at the end of the headland.

As with any posts on this blog, original photos and data are available to anyone doing biodiversity studies.

Introducing the Subject Index

Please start with the Subject Index if you are looking for something.  It is in the panel on the right of the page.

Humans still do a much better job of indexing books and websites than computers. So I have indexed all of the posts on this blog manually and the result is the subject index. Compared with search features that come with Blogger, an index made by a human is like a magic map of the blog that lets you find things instantly.

If you have a great blog where old posts are getting buried in archives, read on.

Making a back-of-book index

At first, I just tried to create an index directly as a word document.  This was very painful as it is very hard to be consistent and it is so much hard work to scan posts for items that should be indexed.  So I wrote a program to help me index the posts.  The type of index I created is called a back-of-book index and can only be made by people.

At first the program scans all of the posts and makes a list of words that it contains.  The list of words
is called a Concordance.  There are a lot of words that no one is interested in within the Concordance such as [the] or [a].  More than 95% of the words in the Concordance tell us nothing about the subject of a post.  These words just help make sentences.  The trick is to display only the 'subject' words and hide the rest.  So after each post is scanned, the program displays the new words it has found so that I can flag the subject words.

To create an index, I view each post and the list of subject words found in the post.  I cannot make an index directly from the subject words as there are many issues.  For example scientific names get broken up into two separate words when they should be treated as one word.  Most of the words in the list are also marginal to the main subject.  Putting too many words in an index creates information pollution.

This is the process for indexing a page using a program I wrote in ms-access which is a very easy place to write small programs.  It is good to have a switchboard which opens the forms you need in work flow order.

Next, I have to paste in text from the blog (see below). The post that I am indexing is the one on Popeye Mullet.   One day I will automate this step.

Then I scan for new words and flag the words that have subject relevance.

Next, I scan the new post for subject words.  The list is not bad but there are many words that are peripheral to the subject of the post.

I type the items I want in the index into the box below.  A category can be added in front of any item by using a back slash.  I have also decided that common names will be followed by scientific names and that scientific names will not be followed by common names.  Making cross-references like this is a key skill of human indexers.

Next I generate the index for all posts as a table and there I can edit entries to make the formatting more consistent and to add information that points to the differences between similar posts.  The edits are saved so I only have to make them once.

Finally I preview the index in a browser.  Here I can see errors such as the fiddler crab entry being displayed without a category.

It is quite easy to generate html from a database table.  Here is the actual code that generates the code for the index from the database table.

The code above makes the html text, which is then placed in a text box so I can just copy and paste  into blogger to create the site index. Clicking on the label beside the text box selects the text, then I press Ctrl-C to copy it (including all the lines that do not fit in the box).

I wrote my own indexing program because I could not find any on the net other than old programs that no longer work or very expensive professional programs.  The entire program took about 8 hours to develop.  In its current form the program is basic but it works.  Let me know if you are interested.

Fauna on Floating Mangrove Debris

A few days ago, I was cruising along a rock coastline near Cairns when I realised that many of the floating objects had a passenger. Photographing these passengers is ridiculously hard as they hide on the other side of the object when you approach and everything is vigorously bobbing up and down. In smooth weather, one also has to consider that Irukandji jellyfish are likely to be present. These small jellyfish which are as clear as ice are occasionally lethal. Irukandji and their relatives hunt for copepods at the water surface in glassy weather. Irukandji jellyfish kill by inducing so much pain that people can and do die. That would not be a nice experience on a remote coastline and I fear these creatures more than sharks and crocodiles.  Tourists should go on organised tours to minimise the risk of jellyfish sting.

Rocky coastline near Cairns

I did manage to photograph a couple of creatures that one would not expect to be floating around the sea on bits of mangrove. The first creature was a sea hare and the second a crab.

Sea hare on a stilt mangrove propagule

Crab on a floating branch about 1 km from land

I really do not know why animals ride on floating objects. It would seem that the risk of being taken out to sea or getting washed up on a beach would be so high that it would almost suicidal. It obviously takes these animals some deliberate effort to find a floating object. For example, I have never found a sea hare any near a mangrove swamp, they are an animal of the sub-tidal zone. Likewise the crab has chosen to ride the branch. It is unlikely that the crab just happened to be on the branch when it started floating.  Most of the animals that associate with floating mangrove material also have planktonic larval stages so they do not need mangrove help to disperse.

One day I would like to do a proper job of photographing mangrove hitchhikers because there are so many of them. Many actually mimic common floating mangrove debris including orange leaves, specks of bark and even thin green eel grass leaves. The only thing that is not mimicked to my knowledge are mangrove flowers.   

Giant Semi-terrestrial Crabs

Some of the subjects I would like to write about take years to track down. Finding out about them was like solving a mystery where I get one clue at a time. Nocturnal animals in particular fit into this category as finding them and learning about their habits can be very difficult. Sometimes I do not know which animal makes the signs that I am observing so it is very hard to organise the clues I am observing into records. For this reason, special attention needs to be be given to recording animals which are rarely directly observed. I am writing my own software to make the task of piecing such information together easier. It was actually the creature described below that gave me the idea to do so.

The mystery burrow

Not far from home and close to the path to the beach, I found two large burrows that were much larger than usual and I had no idea what creature made them. Each time on my way past, I would watch the holes for signs of life. Just once, I saw a stilt mangrove dropper slowly disappearing down the hole, so now I new what it ate. One day the hole was closed over and remained so for all of the cooler months, reopening only quite late in the year. A second year passed without laying sight on the creature. The hole closed over again. I bought an inspection camera with a 7 m cable and eased it down the hole. Without the ability to steer the camera, it quickly buries into the sandy side of the twisting tunnel and no images were forthcoming. I resisted the urge to just dig the creature up. In late 2015, I caught my first glimpse of the creature, a huge black boxy crab about 15 m from me-too far to see any detail. Gradually, I eased out of the crab's view and ran to grab a camera but the crab was gone when I returned. A few months passed and I was just walking to the beach and cast a glance in the direction of the holes and there it was. This time, I stood frozen, which induced the crab to freeze and I asked someone else to run for the camera. In the weak light of late afternoon and with a superzoom camera at full length, I finally got enough detail to find out what this creature was. It was a giant oceanic land crab (Cardisoma carnifex), which can be 125 mm across the carapace – making it the second largest crab in the mangroves after the mud crab.

Repairing burrow after heavy rain. (Click to enlarge)

Same crab - close up.

There was no record of this species on the Australian mainland in the Atlas of Living Australia, although there is a brief description of the species being present in a book on crabs by by Peter Davie at Queensland Museum so they are known from the mainland. It is certainly not common. Despite searching similar habitats through the area, I found no other similar holes although I did have some near misses with some very large feral pigs whilst exploring some remote backswamps. Apparently these crabs are present in select places around the Cairns/Port Douglas area. I had privilege of claiming the first mainland entry into the Atlas of Living Australia!

The species is one of the dominant life forms on many Pacific and Indian Ocean Islands, where they are an important source of food for local peoples (Lairo seems to be the recognised common name). Yet despite its importance, very little accessible information is available about its ecology. Some additional information is available from the following link. http://www.oocities.org/ericdemuylder/gecarcin.htm

Update February 2016
Two years ago, there was single crab hole, last year there were two holes becoming three by the end of the year.  Now there are twelve holes in the colony.  I am pretty sure that the crabs have only a single hole as sometimes I see the crab above at its nearest neighbour as the same time.  I have not found any other colonies, even in places where the crabs have been reported by others.