Duncan Golicher’s weblog

The Little Blue heron (Egreta caeurulea) is, as its scientific name suggests, a form of egret. Like other egrets it tends to walk when feeding rather than standing patiently in one spot as would a typical heron. Juveniles are white and easily confused with the Snowy Egret. This individual is feeding on small carp in a rapidly shrinking artificial pond close to the house. Permanent water bodies are rare in the highlands of Chiapas thus there are comparatively few specialist water birds even in the wetlands (humedales) of the valley.

There are four groups of the Northern Flicker (Colaptes auratus). This is the southernmost sub species, Colaptes auratus mexicanoides (sometimes known as the Guatemalan Flicker). It is a typical woodpecker in many ways and uses old, decaying trees for food and nesting sites. However the species also spends a surprising amount of time on the ground, often picking insects out of hard dried cow pats. This sort of complex habitat use is very common among “forest” birds. Conservation initiatives in the tropics thus need to take a quite sophisticated view of landscape connectivity and habitat diversity. It is not a simple case of planting more trees. Incidentally as I have been asked to provide georeferences and dates, all photos unless otherwise stated have been taken within 1 km of my house ( 16°42′14.62″N,  92°36′32.71″W) and on the same day that they are posted to the weblog. This was on an alder tree along the side of a small stream.

A constant frustration when working in tropical regions is the shortage of really high quality data. The quantitative knowledge that applied conservation needs in order to prevent the extinction of the world’s endangered species of plants and animals is still surprisingly hard to come by. At best the available hard data is fragmented, of variable quality, difficult to organize and thus hard to analyze in a formal manner. At worst it is either missing or positively misleading

Information used for conservation planning also forms the central subject matter of the scientific discipline of ecology. In other words, it concerns the abundance and distribution of organisms. Our ignorance of this most basic characteristic of the planet we live on is remarkable. Astronomers (arguably) provide estimates of the number of stars in our galaxy with narrower proportional margins of error than we have for the number of species in a Mexican forest. For example, Wikipedia cites three sources in stating that of 2006, the Milky Way is thought to be comprised of between 200 to 400 billion stars. A defensible estimate of the number of tree species in Chiapas could still range from 500 to 2500 depending on how data of dubious quality is interpreted. This is not good enough for such highly visible and important elements of ecological communities. The hard data is just not there to improve on this.

Although in recent years considerable advances have been made in systematics (Linnean shortfalls), these so called “Wallacean” shortfall remains. The large scale, systematic, planned, coordinated field work needed to redress our ignorance is simply not being funded.

In recent years I have been working with techniques for producing automated distribution maps of tropical tree species using R. Even using comparatively good data for areas that we know at first hand, it is a remarkably difficult task. Modelling species distributions can involve more pragmatism than theoretical insight. At a regional scale the task becomes yet more challenging.

This is not because R is too limited in the number of useful tools it provides. A very broad range of models are available. They range from rule based classification and regression trees through AI “black boxes” such as neural networks, to generalised additive models and simple logistic regression. All can be fit within R in a common framework. The models can be used to produce predicted distributions based on either presence-absence data or known occurrences alone (with the addition of “pseudo absences”). It is also possible to automate linkages between R and other popular software such as maxent or GARP. Increasingly accurate layers for many key predictor variables are now available.

However at least fifty well distributed occurrence points are needed to provide credibly well validated distribution maps for a single species using a fully automated procedure. If fewer data points are available some sort of input from “expert judgement” is inevitably required in order to evaluate which of the potentially infinite outputs from species distribution models are most credible. Well documented, repeatable automation of the fitting process using R is very useful in this process, as many maps can be produced in a short space of time based on different assumptions. However resorting to visual pattern matching is frustratingly informal and breaks a standard rule of data analysis, i.e. ensuring perfectly reproducible results.

The code example below is one possible very simple implementation of GAMs with pseudo absences. It is is applied here to modelling the potential distribution of tree species using data points provided mainly from MOBOT. The code (deliberately in this case) does not take into account spatial trends or autocorrelation, thus potential matching climates will often be suggested outside a “known” species range. This can be corrected by adding in coordinates as predictors to the model, but at the cost of potential loss of insight into the distribution of species that may not yet have been collected from their entire range. Any modelling technique has to find a balance between too many false positives and too many false negatives. A common technique is to look at the ROC curve, but this is not particularly useful if the number of known occurrences is very low and restricted to a small part of the suspected range.

I have come to the conclusion that we should not be overly defensive regarding the failings of automated species distribution mapping algorithms when these are inevitably attributable to the poor quality of the underlying data. There is an unavoidable “garbage in, garbage out” syndrome that is difficult to avoid without extremely time consuming data cleaning. This is best undertaken at the point of origin, i.e. in the herbaria and museums where the data is collated.

The models can however provide some useful heuristic input to the evaluation of the potential range of a species. In my opinion, any assessment of the area actually occupied should not be attempted using regional scale models alone. Even obvious techniques such as using forest cover maps as masks to remove non-forested pixels will have mixed results. Some tree and shrub species are still common in areas classified as pasture at a regional scale. Urban areas also can have many trees. Unpublished studies have suggested that tree diversity is higher in urban Managua than in surrounding agricultural areas. Other species have very specific requirements for non mappable habitat characteristics.

These concerns led our group to the conclusion that given the current data the best that can be achieved at a regional scale is to map the distribution of “climatically associated species pools” (CASPS). The “CASP” approach suffers the serious weakness of rather devaluing individualistic species responses, but may be the best that can be achieved until new initiatives begin to provide contemporary, accurately georeferenced and correctly determined occurrence (and absence) data from across the tropics. Data sharing and pooling between currently active research groups will be a vital first step in this process.

simple-gam-models.doc

The output from the R code above is overlain on the 3d Blue Marble image from code in the previous posts to give a visual impression at a very broad regional level. Green points are the input to the model (recorded occurrences) and red points are grid squares with similar combinations of regionally important climatic variables mapped at an approximately 5 km x 5 km scale. Further details of this and similar procedures including mapping of species pools are available in this document.mnp-workshop3.pdf

This model could provide some heuristic input to expert evaluation of the potential distribution and threats to some species currently being assessed for IUCN red list status. 450 maps produced through an automated procedure are included as low resolution jpg files within pdf archives in alphabetical order here.

A B C D E F G H I J L M N O P Q R S T V W Y Z

Acer. negundo is a familiar tree to North Americans who know it as Box Elder” or “Box Elder Maple”. This is apparently due to the fact that its its whitish wood resembles boxwood and the similarity of its pinnately compound leaves with those of some species of elder (Sambucus). Other common names are based upon this maple’s similarity to ash as it is the only North American maple with compound leaves. There are many varieties or sub-species across its range and the species is a good candidate for more work on its genetics.

The species is fully dioecious and these are clearly male flowers. They are very attractive to bees. This individual is in flower this week close to Ecosur.

A colleague contacted me yesterday with some interesting modelling work based on the neutral community model of Stephen Hubbell.

Hubbell’s work fascinated me when it was first published. I have always assumed that it is easily misunderstood. If Hubbell is taken to imply that all species are equal, then the work appears to be eroding the basic subject matter of ecology. Ecologists tend to look for informative differences between species. However this is not exactly what the theory is based on. It is rather more subtle. The theory concerns the equality of individuals (in this sense it almost has political implications). Hubbell writes.

“The theory treats organisms in a community as essentially identical in their per capita probabilities of giving birth, dying, migrating, and speciating. This neutrality is defined at the individual level, not the species level. All that is required is that all individuals of every species obey exactly the same rules of ecological engagement. So, for example, if all individuals and species enjoy a frequency-dependent advantage in per capita birth rate when rare, and if this per capita advantage is exactly the same for each and every individual of a species of equivalent abundance then such a theory would qualify as a bona fide neutral theory by the present definition.”

I have illustrated this idea for students with a very small simulation in R . R code, like matlab or octave, is very terse and efficient so a couple of lines can do a fair amount of work. Lets assume a very simple reproductive rule applies to all individuals. The rule is that all have the same discrete generation time, in other words they all survive one time step of a simulation. At the end of the time step each individual produces two offspring. The lottery then applies. The offspring are randomly mixed and placed back on the finite space occupied by the previous generation. So half find a home and half “die”. The process is then repeated. This was exactly how I first implemented the model. I then re-implemented the idea in fewer lines by making the probability of selection depend on the proportion of individuals in each species, which amounts to the same thing.

This is all the code needed to run the model. (Try this if the quotation marks are not right lottery.doc)

nspecies<-8
gridsize<-20
time<-100

RUN<-function(){
X<<-matrix(0,nspecies,time)
palette(rainbow(nspecies))

mat<-sample(1:nspecies,gridsize*gridsize,replace=T)
X[,1]<-table(mat)
image(matrix(mat,gridsize,gridsize),col=sort(unique(mat)))

for (i in 2:time){
a<-X[,i-1]
mat<-sample(1:nspecies,gridsize*gridsize,prob=a,replace=T)
X[,i]<-table(factor(mat,levels=1:nspecies))
image(matrix(mat,gridsize,gridsize),col=sort(unique(mat)))
gc()
}

matplot(t(X),type=”l”,lwd=2,col=rainbow(nspecies))
}

#However to get a little tcltk interface add this

############################################

library(tcltk)

Run<-function(…){
nspecies<<-as.numeric(tclvalue(”nspecies”))
gridsize<<-as.numeric(tclvalue(”gridsize”))
time<<-as.numeric(tclvalue(”time”))
RUN()}

tt <-tktoplevel()
d1<-tklabel(tt,text=”Numero de species”)
d2<-tklabel(tt,text=”Tamaño del grid”)
d3<-tklabel(tt,text=”Tiempo”)

s1 <- tkscale(tt,from=0, to=20, variable=”nspecies”,
showvalue=TRUE, resolution=1, orient=”horiz”)
s2 <- tkscale(tt, from=2, to=100, variable=”gridsize”,
showvalue=TRUE, resolution=1, orient=”horiz”)
s3 <- tkscale(tt, from=10, to=500, variable=”time”,
showvalue=TRUE, resolution=10, orient=”horiz”)

but <- tkbutton(tt, text=”Run”,command=Run)

tkgrid(d1,s1)
tkgrid(d2,s2)
tkgrid(d3,s3)
tkgrid(but)

The model is to be played with (just download R from CRAN and paste all the code into the console), rather than watched but here are some example runs on You Tube,

The moral of the story is that under a neutral model some species start a random walk to extinction if co-existing in a small space with other species. However we cannot tell which will dominate and which become extinct from their characteristics, because all individuals, regardless of species are governed by exactly the same rules. The fate of species is determined by the cumulative luck or misfortune of the individuals that have been given the label. The larger the grid the more species that can be supported for a longer time, but extinction risk is always present if a long losing streak hits. The element of Hubbell’s theory that this model does not reproduce well is the log-normal (-ish) relative abundance distribution of the surviving species, although come to think of it I have not tried running the model with a really large number of species and a really large grid. R runs out of colours for the illustration, but this is not important.

Many interesting questions remain. Could a simulation model based on this sort of idea be used to predict extinction over a real landscape? Models of this sort seem far too abstract to provide real insight into the real world. But in some sense the process that Hubbell describes in a more formal mathematical way in his book probably does apply. But, how can these sort of ideas be communicated accurately to prevent them from provoking the sort of unproductive SLOSS debate that has often resulted from theory being pushed too far?

This small woodpecker (Sphyrapicus varius) is a common winter migrant to the region. As its name suggests it does feed on sap and is often found on exuding trees. This was on a pine in the Ecosur grounds and seemed to be picking insects out of the resin. The bird can remain still for long periods of time, but this unfortunately makes it a prime target for young children with catapults. I have found several dead individuals, obviously hit by stones during my time here.

Vireos are quite difficult to photograph and identify and this is not a great photo. They are small, active birds that don’t remain in one place for long. This individual seems to be the plumbeous form of the solitary viero Vireo solitarius plumbeus, sometimes assumed to be a distinct species Vireo plumbeus. The photograph was taken in the grounds of Ecosur. The species is a winter migrant

The similar Cassin’s vireo is a resident of Baja California but winters north of the Isthmus. The identity of the birds in San Cristobal requires checking.

This sadly injured painted bunting (Passerina ciris) flew into the window of our library building around an hour ago and was brought to me for identification. I doubt if the bird will survive. Despite its very bright colours this is the first time I have seen an individual of the species. It is apparently secretive and shy. Unlike most finches and buntings it spends most of the time in dense woody vegetation.

The eastern bluebird (Sialia sialis) is a resident here and is usually seen in small family groups of two to five birds. Although it is a thrush it feeds in a rather similar way to a flycatcher by flying from the perch to the ground to pick up insects, which are sometimes caught in mid air.

The mockingbirds in our garden are relatively silent at this time of year, but are very active seeking food in the dry grassland.

I grew up in Lincolnshire which is rarely in the news, so I was quite proud to hear that it was at the epicentre of an earthquake that measured 4.8. To put this into perspective the earthquake I reported at 6:52 am on the 12 February in San Cristobal measured 5.2. However to be fair an earthquake in England is a rare event, while in Mexico we have several every year. I imagine that tomorrow’s news will be full of eye witness reports of the event. Much of the reporting will no doubt be quite light hearted. British residents don’t appreciate the sheer terror that people experience when an earthquake is felt in regions where they are destructive. Even though San Cristobal itself has had few major earthquakes, every time we feel the earth move we are very unsure how bad it could turn out to be. But this time we have been stirred rather than shaken.

As an aside I made the small illustration above using a Nasa satelite image and the excellent open source software QGIS. QGIS stands for Quantum GIS. It took less than a minute to connect to the Nasa site, download the image and find the rough epicentre. I am a great fan of Google Earth but at the moment the fact that GE has a mess of overlays at different scales is a barrier to it being used for illustration at a regional scale. Also the 3d terrain in Google Earth is great for Chiapas, but rather irrelevant in Lincolnshire.

I have just registered with the Encyclopedia of Life. The idea behind the project is outlined in this BBC article.

The project aims to be the equivalent of Wikipedia in the field of systematics and ecology. If successful detailed descriptions of all the world’s known organisms could be available to anyone with an internet connection. This is a very exciting prospect, especially if the success of the project coincides with advances in the barcode of life. One of the barriers to greater understanding of the distribution and abundance of organisms remains difficulty in identification and ignorance of their characteristics. This initiative should help to democratise this knowledge and place it in the hands of field researchers. It is also a collaborative project in which we too have an obligation to contribute.

This is another picture of a wild bird taken in Tuxtla Zoo, the Great Egret (Ardea albus). I include it mainly as a comparative reference with the cattle egret, as the white herons can be confusing. I have yet to see the white morph of the great blue heron (Ardea herodias)  although they are apparently found in Chiapas and can be easily mistaken for the Great Egret.

I took this rather poor picture in Tuxtla Zoo yesterday (Sunday 24 Feb 2008). Obviously taking pictures of birds in zoos would be cheating, but this is in fact a wild bird outside the cages. The zapote trees in the zoo attract a lot of native wildlife. The reason I have uploaded a low quality picture is to provide proof of observation. The rather coarse scale distribution map for the Squirrel Cuckoo (Piaya cayana) in Howell and Webb suggests that the species is not present in the central depression of Chiapas. In fact it is common in most of the more mature dry forest of the region. It is a rather tame, easily spotted and unmistakable bird. In spite of the poor light the darker characteristics of the southern thermophila form of the species can be made out here.

The cattle egret (Bubulculis ibis) is an immigrant from Africa, this species arrived in the USA in the 1940’s although it apparently first colonized the Americas in Surinam in 1877. It spread through the interior of Mexico in the 1960s and 70s. I photographed this individual when I was on the way to work, feeding around the legs of cattle near my house.

The open fields around my house with many perches form prime habitat for highland flycatchers. However I have not see this particularly large (18 cm) species (Contopus pertinax pertinax) very often. The bird appears much darker grey than the illustration in Howell and Webb, but its Id is confirmed by the bright orange lower mandible.

One of the most attractive resident birds in my garden is the vermilion flycatcher (Pyrocephalus rubinus). It is a widespread and rather common species, being found from the South Western United States to Nicaragua. It has been reported locally in South America and even the Galapagos islands.

Like most flycatchers the bird favours open or semi open areas, providing there are shrubs, small trees or fence posts available as perches. The female is much paler than the bright red male, but is still an attractive bird. The photographs were taken on Sunday 10 Feb 2008. Some earlier pictures of the same species are available here 

Male vermilion flycatcher (Pyrocephalus rubinus)

Female

The Golden Cheeked Warbler (Dendroica chrysoparia) is a migratory species of particular conservation concern. In 1990 only an estimated 2,200 to 4,600 birds remained in their Texas breeding sites. There are many internet sites with information regarding the species. A quick google provides ..

http://www.tpwd.state.tx.us/huntwild/wild/species/endang/animals/birds/gcw.phtml

http://animaldiversity.ummz.umich.edu/site/accounts/information/Dendroica_chrysoparia.html

http://www.tpwd.state.tx.us/huntwild/wild/species/gcw/

Some particularly good photographs of the bird are available from

http://www.greglasley.net/gcwarblr.html

The decline in the golden-cheeked warbler is due primarily to loss of mature Ashe juniper habitat in Texas. The expansion of the cities of Austin, San Antonio, and Waco has been reported as having an impact, which might suggest that unlike many warblers the species does not use the habitat provided by domestic gardens. This preference may also be shown in its overwintering areas. This could partially explain my frustrating failure to have ever seen this species.

I live surrounded by pine oak woodland that should be suitable over wintering habitat for the species. Both my garden and the trees and shrubs around my workplace are visited by flocks of warblers daily from September through to late March. There are two common species that are somewhat similar to the Dendroica chrysoparia. They are Townsend’s warbler, D. townsendii, an extremely common bird in the winter months, and the black throated green warbler, D. virens. The second species tends to overwinter at slightly lower altitudes and is more common in the dry forests of the central depression. The Blackburnian warbler (Dendroica fusca) is also fairly frequently seen in San Cristóbal and also has a superficial similarity to the Golden cheeked.

I have developed the habit of very carefully observing every bird I see in the hope of a definite sighting of D. chrysoparia in San Cristóbal. To date I have still not observed a single individual of D. chrysoparia after having checked many hundreds of similar looking birds. Below are some illustrations taken from Edwards’ field guide of the three species.

I am placing pictures taken in my garden on this site in order to show the difficulties involved in obtaining a clear, definitive ID of this species. All the photographs below are of D. townsendii.

(Click on the thumbnails to see a full size picture. THESE ARE CLEARLY NOT GOLDEN CHEEKED!)

Pastures now are very green, although the new seasons growth has not yet covered up the dry dead stems left from the dry season.