Banded Phlogius

A couple of weeks ago I mentioned a new species of Australian tarantula, the Banded Phlogius, a picture of which appears below courtesy of Brendan Stent.



White banding can be seen at the ends of the leg segments.

Selenotholus sp. Queensland

Well it looks like I summarised the main new species announced in 2008 (see last weeks post) way too early! Greg Finch advised that he is obtaining a new species that Steve Nunn has called Selenotholus Queensland which may turn out to be the only true Selenotholus in Queensland after reclassification of the genus is completed. I have obtained permission from Steve Nunn to post the picture below that he took of this species.

Selenotholus sp. Queensland - Photograph by Steve Nunn

This species grows to 18 cm (males 16 cm) and its closest relative is Selenotholus sp. Black. Thanks to Greg Finch and Steve Nunn for this information.

New species 2008 - Australian Tarantulas

I preface this post by advising that Dr Rob Raven is currently revising Australian tarantulas and we believe that a major work is about to be released. I do not have a date but am advised it will be soon. This work will contain many surprises and will probably turn most of our current classifications on their head (pers. comm. S. Nunn). The information here is therefore based on our knowledge at the present time and it is almost certain to become outdated upon release of Rob Raven's forthcoming work.

Until then it is worth noting the very exciting discoveries or rediscoveries of tarantula species that have been made in the last 12 months.

Brendan Stent of Tropical Tarantulas found a possible new genus named tentatively the Rattlesnake Tarantula in February 2008. This amazing species makes a sound simlar to a rattle snake when aggravated. Apparently Rob Raven knew of this species but Brendan was the person that first brought this species to the public which makes it one very exciting discovery by Brendan. Brendan also found another species which appears to be somewhere between Selenotypus plumipes and Selenotypus sp. "Nebo" and has been given the placeholder name Selenotypus sp. "plumebo". The video shows the Rattlesnake Tarantula using its unique stridulating organ to produce its characteristic rattler sound.

YouTube video of Rattlesnake Tarantula filmed by Brendan Stent

Another interesting species that surfaced in 2008 is the Ghost Tarantula announced by Steve Nunn in June 2008. This species has a unique pale colour with white setae which is very unusual for Australian tarantulas. In addition it was found in swamp habitat. Unfortunately the single specimen that was collected moulted out to a male so at present an active captive breeding program has not been commenced. It will take another collecting mission to get this species breeding in captivity but it will certainly be a very highly sought after species due to its colour.

Ghost Tarantula - Photo by Steve Nunn

In a year of big discoveries and new species perhaps the biggest impact on Australian enthusiasts was made by Steve Nunn’s announcement of the discovery by a collector of Phlogius sp. "Goliath" or the Australian Goliath Tarantula. This species is possibly the largest species discovered to date and reaches at least 20cm as a mature adult. I managed to acquire a couple of specimens of the Goliath that were not required for the breeding program that was immediately established and they are truly a fascinating species. Steve advises that this was actually a rediscovery of a species not seen for 103 years despite attempts to locate it and that there is only a single specimen in the Queensland Museum (Australia) incorrectly labelled as Phlogius crassipes. Several matings have been reported by those involved in the breeding program led by Steve and we are waiting impatiently for the first spiderlings to appear. Greg Bylund, of the Green Scorpion, produced the first captive bred eggsac in July 2008 but unfortunately the female ate the eggs before he had a chance to remove the sac for incubation. Greg and Steve have other gravid females and spiderlings are expected by December 2008. This was the first time that a captive breeding program was established at the outset and is a model that will hopefully be reproduced in the future.

Phlogius sp. "Goliath" - photo by Steve Nunn

Phlogius strenuus is another giant that is rare in collections but has been bred in 2008 by Greg Bylund and Grant Miller. No doubt other individuals will also be breeding this species in 2008. Its captive breeding status is secure for now. This species although not a new discovery is highly sought after and thus the successful captive breeding program has been an initiative of tremendous importance. There have been other giants found this year but as they have not been publicly announced I will hold fire on making an announcement on this site.

The tentatively named Phlogius sp. "Rubiseta" (yes I know that doesn't quite work but its only a placeholder name) was announced by Greg Bylund in March 2008. There has been some discussion to date as to whether this is a new species or whether it is synonymous with the previously discovered Stents Tarantula however we will know soon enough the eventual outcome. The redish colouration makes this a very attractive tarantula.

Phlogius sp. "rubiseta" - photo by Grant Miller

Greg Bylund announced the discovery of an entirely new genus in September 2008 in the form of the tentatively named JT Tarantula. A new genus is certainly big news. This species lives in very harsh dry conditions and is an incredible discovery. Early reports from keepers are that this is a very docile species which should make it very popular indeed.

JT Tarantula and burrow - photo by Greg Bylund

Just this month Brendan announced another species he discovered which has been named the Banded Phlogius. This is another very fine looking species with fine bands of white setae at the end of leg segments which are especially noticeable on legs I and II.

Two persistent rumours continue to circulate. One relates to a nearly pure white form of tarantula, whiter than the Ghost Tarantula, and another relates to a metallic blue tarantula. It would not surprise me if one or both of these rumours turn out to be correct as most of Australia is unexplored for tarantulas and new species are being found at an amazing rate. Given Australia’s geological history I would not even be surprised to hear the Selenosmia dichromata turned up somewhere in the northern tropics of Australia.

Day 5 in the blogosphere

Well it has been a whole 5 days since I made the first post on this blog and we have just cracked 40 visitors. It is a lot of fun seeing the visitors light up on the maps in the sidebar! A big thanks to everyone who took the time to visit and especially to the people posting the two comments so far. My first overseas visitor was Azoreano Náufrago from Santa Maria, Portugal which I think is in the Atlantic Ocean somewhere and my second visitor was from the US. Woohoo!

I'll be adding some more human interest posts relating specifically to my tarantulas as well as the usual mix of reports on scientific advances and technology relating to biology. I wish you all well!

Ecological software: Ecopath with Ecosim (EwE)

EwE is windows based ecological simulation software with development centred on the University of British Columbia’s Fishery Centre. EwE has three main components: Ecopath – a static, mass-balanced snapshot of the system; Ecosim – a time dynamic simulation module for policy exploration; and Ecospace – a spatial and temporal dynamic module primarily designed for exploring impact and placement of protected areas. The Ecopath software package can be used to:

• Address ecological questions;


• Evaluate ecosystem effects of fishing;


• Explore management policy options;


• Evaluate impact and placement of marine protected areas;


• Evaluate effect of environmental changes.

EwE together with papers and published models are available at the EwE website.

The foundation of the EwE suite is an Ecopath model (Christensen and Pauly 1992, Pauly et al. 2000), which creates a static mass-balanced snapshot of the resources in an ecosystem and their interactions, represented by trophically linked biomass ‘pools’. The biomass pools consist of a single species, or species groups representing ecological guilds. Pools may be further split into ontogenetic (juvenile/adult) groups that can then be linked together in Ecosim.

Initial impressions – beginning the journey

For the non-expert user I recommend starting with the default models installed with EwE. Note that EwE is now available in version 6.x.x. Although most of the features available in the previous version 5.x.x some elements have not been able to be carried forward (notably Ecoranger) so it may be worthwile downloading and using both versions in order to explore the full functionality of the software suite. It is likely that over time the later version will totally supercede V5 and earlier and personally I prefer the latest version of Ewe 6. The models should be thoroughly explored before advancing to other data sets.

Predator/prey niche overlap screen in EwE 6.04

Data requirements for the model are not overly onerous and can be obtained from stock assessment, ecological studies, or the literature: biomass estimates, total mortality estimates, consumption estimates, diet compositions, and fishery catches. As an enthusiast user it did take me a little time to track down data sources relevant to certain Australian marine environments however the fact that I could do this without too much effort shows how readily available the data can be if a little effort is expended.

I am exploring published models available on the Ewe website and online at other sources. I am also completing models for which a published paper exists but the model itself is not available for download. I am using two models by Gribble (Gribble, N. A. (2003) GBR-prawn: modelling ecosystem impacts of changes in fisheries management of the commercial prawn (shrimp) trawl fishery in the far northern Great Barrier Reef and Gribble, N. A. (2005) Ecosystem Modelling Of The Great Barrier Reef: A Balanced Trophic Biomass Approach) as a base to fill in the gaps to complete a model based on a masters thesis by Paul Tudman (Tudman, P. D. (2001) Modelling the trophic effects of fishing on a mid-shelf coral reef of the central Great Barrier Reef ) for which limited data was available. The results have been useful and interesting to date although more work fine tuning and getting the relationships between clades correct needs to be done by me before my modelling of the Rib Reef ecology is “completed”.

Biomass screen in EwE 6.0.4

Habitat base map of Rib Reef (GBR) in EwE 6.0.4

The most important conclusion from running my adapted Rib Reef model thus far is that maximum yield fishery (MYF) management is not the way to proceed as it is not a sound scientific basis for management of the entire fishery. Fisheries management of a species based on MYF does not allow for the often dramatic consequences for other clades that either feed upon, directly or indirectly, or are preyed upon, again directly or indirectly, the species which is being managed. This is fascinating stuff for the enthusiast and no doubt even more so for the cutting edge expert scientists!

I advise reviewing the literature and modifying already well documented habitat and ecological data where prime sourced empirical data of your own is not available. I have used Gribble who in the Australian Great Barrier Reef context is an authority. Where Gribble’s data is not sufficient I have utilised data from similar reef habitats located elsewhere in other ecosystems. Obviously empirical data from the actual locality of interest is preferable although for a non funded party costly, time consuming and let’s face it almost impossible to obtain. Even the scientists have difficulties obtaining the data so do not let this discourage you. With careful data selection and analysis important relationships can be analysed and explored and the need for exact data is not required. Basic knowledge of modelling in any context after all tells us the utility of a model is not dependant upon its realism but rather its value lies in its predictive ability and in this context I am referring to realism or exactness of data specific to a particular locality. Generalised data fine tuned to specific systems can be used as the basis for later field research to obtain specific data for the system and focus further research required. Validation through empirical research is another topic for more research by scientists.

Ecosim plot of Rib Reef (GBR)

From the EwE authors

This section of the about file (quoted below) on the EwE site gives an excellent snapshot overview of the software and how it works. The literature (available on the site) gives much deeper insight and analysis.

“The parameterization of an Ecopath model is based on satisfying two ‘master’ equations. The first equation describes the how the production term for each group can be divided:

Production = catch + predation + net migration + biomass accumulation + other mortality

It is the aim with the Ecopath model to describe all mortality factors; hence the ‘other mortality’ should only include generally minor factors as mortality due to old age, diseases, etc. The second ‘master’ equation is based on the principle of conservation of matter within a group:

Consumption = production + respiration + unassimilated food

In general, an Ecopath model requires input of three of the following four parameters: biomass, production/biomass ratio (or total mortality), consumption/biomass ratio, and ecotrophic efficiency for each of the functional groups in a model. Here, the ecotrophic efficiency expresses the proportion of the production that is used in the system, (i.e. it incorporates all production terms apart from the ‘other mortality’). If all four basic parameters are available for a group the program can instead estimate either biomass accumulation or net migration. Ecopath sets up a series of linear equations to solve for unknown values establishing mass-balance in the same operation. The approach, its methods, capabilities and pitfalls are described in detail by Christensen and Walters (2000).

The process of constructing an Ecopath model provides a valuable end product in itself through explicit synthesis of work from many researchers. Several EwE models illustrate this, e.g., for the Prince William Sound (Okey and Pauly 1999), the Strait of Georgia (Pauly et al. 1998), the Hecate Strait (Haggan and Beattie 1999) and several North Atlantic models being created by the Sea Around Us project at the UBC Fisheries Centre. The model construction process has brought together scientists, researchers and data from state and federal levels of government, international research organizations, universities, public interest groups and private contractors. Key results include the identification of data gaps as well as common goals between collaborating parties that previously were hidden or less obvious. We find the process especially important for enabling the interest groups to take ownership of the model that is derived; this is especially required when operating at the ecosystem level, where multi-faceted policy goals have to be discussed widely as part of the management process. This is facilitated by the policy exploration methods included in the Ecosim model discussed further…”.

Although EwE has a primary focus on modelling marine systems it is possible to develop other models. In the future I will be exploring this functionality. I will be posting more on the software (after all it is the namesake of this blog) including details of my modelling so check back and see where it is taking me.

Baboon and Trapdoor Spiders of Southern Africa: An Identification Manual (2002)

A visually appealing text which I found available as a pdf this book is a great read for fans of Mygalomorphae. The book contains:

· illustrated keys to identify families, subfamilies, genera and where possible species
· diagnostic and descriptive characters for each family, subfamily and genus
· taxonomic and natural history notes for each genus
· a complete species list with maps to illustrate their distribution· notes on conservation and toxicity
· and an extensive bibliography.

The author, Dr Ansie Dippenaar-Schoeman, is a professional arachnologist and head of the Spider Research Centre in the Biosystematics Division of the Plant Protection Research Institute, Agricultural Research Council, Pretoria, South Africa. She has devoted her entire career, spanning more than 30 years, to the study of Afrotropical spiders, both from a biological and a taxonomic perspective. This pdf will be of interest to Australian tarantula enthusiasts and of course to those located elsewhere that actually have access to these very interesting species.

Modelling of Life History Changes

A study published on 10 November 2008 (Kuparinen A, O'Hara RB, Merilä J (2008) Probabilistic Models for Continuous Ontogenetic Transition Processes. PLoS ONE 3(11): e3677. doi:10.1371/journal.pone.0003677) by PLuS One introduces probabilistic reaction norm models of continuous ontogenetic transitions such as animal life history changes or invertebrate metamorphosis.

Reaction norms have traditionally been formulated deterministically, so as an organism's developmental status is assumed to change exactly at the time it hits the reaction norm.

Two alternative survival analyses based modeling approaches for describing ontogenetic transition processes in continuous time are proposed by the authors. The models are simplified compared to previous models but are easier to use in terms of modelling effort and data requirements. Therefore, they provide user-friendly and broadly applicable tools for continuous time analyses for typical ontogenic transition data sets, as well as for predicting transitions at very fine time scales. The authors examine performance of the models using empirical data on timing of metamorphosis in the common frog, Rana temporaria.

All equations reproduced here have the same reference numbers as in the original article for ease of use. A brief summary of the models is presented below and taken largely from the paper the original of which is provided in a link at the end of this post. Any errors in the summary are mine and the orignal should be referred to by those interested in this topic.

Survival analysis based approaches for ontogenetic life-history transitions

Ontogenetic transition processes are of a type where an individual ages, and at some point in time experiences an event that can only occur once for each individual. In medicine, this kind of process is investigated using survival analyses, the name deriving from the fact that the considered event is often death. The starting point for survival analysis is to assume that the probability that an event will occur is governed by a rate h(t), which is usually called the hazard. If the mathematical form for how this changes with t is known, then the probability that the event (e.g. maturation or death) will not occur before time t, denoted as S(t) and called the survivor function, can be calculated by

(2)

Or, if time is discrete, the probability that nothing happens before time t is the product of the probabilities of nothing happening in each time step before t. Typically, survival analyses use data on the times to events (T) to ask how the hazard function or, equivalently, the survivor function is affected by different covariates.

The paper proposes two alternative modelling approaches that relax the effort of composing the exact analytical form of the hazard, by directly making assumptions about the survivor function, and how it is affected by the covariates.

1. A Parametric Survival Analysis

The model used in the paper reduces modelling effort to a parametric survival regression in which the distribution of an individual's survival time T (i.e. the time it takes until an individual faces the transition event) is modelled directly by

(3)

where α is an intercept parameter, β is a vector of free model parameters, x is a vector of optional covariates, σ is a scale parameter (also a free model parameter) describing variance in the data, ε is a random variable, following some distribution, and f is a link function appropriate for the distribution of given ε.

The estimated parameters of eqn (2) can be used directly for assessing how much variation is induced to the timing of the transition event by the covariates.

Once the parameters of the survivor function have been estimated, the paper explains how model can be used to predict the occurrence of transitions.



Figure 1. Timing of metamorphoses of common frog (Rana temporaria) reared in a common garden experiment.

Individuals are exposed to three temperature and two food level (ad libitum or restricted) treatments. In both panels, growth temperatures are indicated with colours (see colour legend), and restricted food is indicated with open circles/dashed line, and ad libitum feeding with filled bullets/solid line. Individual observations of ages and weights at metamorphosis are shown in panel A. Cumulative probabilities for the timing of metamorphoses calculated from the raw data are shown in panel B.

2 Semi-parametric Survival Analysis.

A method developed by Cox performed an analysis of survival data by splitting the model into two parts: 1) the survival function, which only depends on time, and 2) a term for the ratio of the hazards (i.e. rates of the events) for different classes (the proportional hazards model). This modelling approach is particularly convenient if interest lies on the proportional effects of the covariates on T, rather than the distribution of T itself. The Cox proportional hazards model assumes that the effects of the covariates are multiplicative, so that the survival probability S(t) = P(T>t) is given by

(4)

where β and x are as above, t is any freely chosen time point, and P0 (t) is a baseline hazard function that gives the probability P(T≤t x = 0). The authors state that the Cox regression is very convenient in the sense that no underlying distribution for the transition time needs to be assumed. Similarly, when assessing the proportional effects of the explanatory variables on S(t), P0 does not have to be known either. It is only required for estimating the actual survival probability S(t) = P(T>t). From these, predictions for transition probabilities can be derived for any time interval similarly as above.



Figure 2. Cumulative probabilities for the timing of metamorphoses predicted by the parametric survival model (eqn. 3).

Different growth temperatures are indicated with different colours, and different food level treatments with different line types (solid line = ad libitum, dashed line = restricted food). Gray lines beneath the estimated cumulative probabilities are the observed cumulative distributions for the timing of metamorphosis.

The models presented in the paper make the concept of probabilistic modelling of ontogenetic life-history transitions in continuous time more easily accessible. Transition data can be analysed which is typically available from the wild with little prior knowledge of mechanisms underlying transitions. As random effects can be incorporated into the model survival based models can be used to estimate genetic variability in transition probabilities by using data obtained from breeding under controlled conditions or through the use of genetic markers. The aquaculture industry is an obvious possible user of these models.

Of particular interest to me is that survival based models would be useful in studies investigating and predicting patterns of metamorphosis in insects and amphibians. The authors conclude that more generally, the models should aid the concept of probabilistic reaction norm becoming as general and applicable tool in the studies of life-history variation as the deterministic reaction norms are today.

The article can be found here at PloS One.

Australian Invertebrate Forum Journal

I am the editor of the Australian Invertebrate Forum Journal. We released our first issue in June 2008. If you would like a good read on Australian invertebrates you can get Issue 1 here. We are currently working on our second issue for release in late December 2008 so stay tuned. The AIF forum is owned by Greg Bylund who set up The Green Scorpion website which sells tarantulas, scorpions, and other invertebrates and accessories. Greg, who is a builder in real life, is an absolute gold mine of information on invertebrates and has given freely of his time to me to assist in my little research projects. Members of the Australian Invertebrate Forum can access the journal and many other articles written by members and non-members alike.



Greg Bylund taking a picture of his awesome Phlogius crassipes.



Phlogius crassipes close up with Greg Bylund

Thanks to Grant Miller for kind access to the above pictures taken on a visit to Greg's house in August 2008.

Open Acess Scientific Journals

It is very exciting to see the development of open access online taxonomy and related scientific journals. A great barrier to the dissemination of scientific information both amongst scientists and the general public is the old paradigm of very expensive journal subscriptions. One very new journal showing great promise is ZooKeys and I have placed it in an rss feed on this site. An additional rss feed on this site is for First Monday which was one of the very first open source peer reviewed journals avilable online.

Another great open access journal is PLoS One which should not be missed. You can even add comments and engage in discussions on papers which evolves the whole publishing concept even further.

Of course some traditional Zootaxa articles are available online for free which makes it a hybrid of sorts however few writers pay for the right to have their article appear in that journal free of charge to readers. I hope that scientists will adopt the new completely open access format with enthusiasm as I strongly believe it will increase our rate of scientific development by making access to data quicker and easier. For a detailed examination of the hybrid journal format and the limitations of this approach by an academic check out Peter Suber's newsletter and related blog.

I have a deep interest in Arachnology and am a keen keeper of approximately 30 tarantulas. My interest extends to all aspects of tarantula biology, ecology, habitat, breeding habits, distribution, and especially taxonomy with a particular interest in Australian species. I know from experience how hard it is to gain access to peer reviewed work as an outsider who does not have easy access to paid subscriptions through a university science department. Access for a private researcher is too expensive to be of use even for a well off individual unless he or she is only interested in a limited number of articles. There are workarounds such as requesting papers direct from authors however this is a very time consuming process. By way of note I have never had a scientist knock back a request from me for a paper and for that I am grateful. I am keeping my fingers crossed that open access journals will simply become the defacto model and will have an effect on peer reviewed paper publishing much like the net and mp3's have had for the music industry where the old paradigm users are simply bypassed to the point of irrelevancy. See links on Peter’s article referred to above and read his blog for ways to encourage the uptake of the open access paradigm especially if you are writing and publishing peer reviewed work.