Pattern in the geographical orientation of diversification

In 'Guns, Germs and Steel' Jared Diamond argued that European technological advance was enhanced by the East-West orientation of Eurasia which allowed domesticated animals and plants to easily migrate, as ecological conditions are generally more similar to the east and west than to the north and south. I wondered if this increased motility would lead to more or less diversification? Increased motility may result in larger ranges and hence a greater probability of vicariance (splitting and diversification). Alternatively, mobility may prevent divergence through increased admixture. Perhaps the relative importance of these factors changes through time?

To investigate this question, I calculated the bearing between the geographical centroid of the ranges of terrestrial mammal sister clades. I classified the lines connecting range centroids as north-south or east-west and plotted them on a map and as a temporal histogram.

North-South diversification is most common in South America (except the Atlantic coast), Western North America, Sub-Saharan Africa, S.E. Asia and Western Australia - New Guinea, but much rarer in Eurasia and the majority of North America. East-West diversification occurs everywhere, except polar regions. Glaciations will have severely eroded pattern in northern latitudes, but why is north-south diversification uncommon in western South America and Eastern Australia?

Interestingly, over the last 50 million years the frequency of east-west diversification has been consistently 2.5-3 times more frequent than north-south diversification. Temporal slicing of the map (not shown, but see) shows that pattern does vary though time with east-west connections between southern continents being more common further back it time - traces of the breakup of Gondwana.

So, these data seem to show that, yes, diversification is more 2-3 time more common east-west than north south, and that this pattern has been consistent in mammals for the last 50 million years. It also shows there is considerable geographical variation in north-south diversification, possibly related to recent environmental change destroying pattern.

GeoPhyloBuilder for ArcGIS 10

The labs here at the Silwood Park campus of Imperial College are still running ArcGIS 9.3, but with our recent license renewal I finally decided it was time for me to personally upgrade to v10 and recompile GeoPhyloBuilder.

Following the instructions from ESRI upgrading turned out to be pretty straight-forward. I just had to remove and re-add the ESRI.ArcGIS references (they are now in C:\Program Files\ArcGIS\DeveloperKit10.0\DotNet\), change the platform CPU target and change runtime binding from using the ESRI.ArcGIS.esriSystem.IAoInitialize class to the code generated by the ArcGIS License Initializer wizard. Amazingly it all worked.

The new version can be downloaded from SourceForge, I just need to work out how to make it the default download from the project page and sort the ssh key problem out that is preventing posting the code to the repository.

The Scope of Evolution

Here is another old visualisation from the soon be history EvoViz wiki.

A very crude attempt to show how far evolutionary thinking permeates science from the evolution of organisms themselves, their effect on the environment, it's use in medicine (e.g. understanding the origins of disease), genetic algorithms, evolutionary psychology and politial thinking.

Terrestrial Mammal Geophylogeny - another view

A third visualization of the terrestrial mammal geophlylogeny. Here it is displayed in ArcScene with nodes elevated and coloured by age. I particularly like how it shows differentiation in node age between the southern and northern hemispheres, both within continents and across ocean basins.

Mammal Geophylogeny from David Kidd on Vimeo.

Terrestrial Mammal Geophylogeny

I have been intending to build a geophylogeny from the Bininda-Emonds et al. mammal supertree and range maps (Sechrest "World Wide Global Diversity, Endemism, and Conservation of Mammals". PhD Thesis, Univ. Virginia 2003) but have only got round to doing it. The delay was primarily due to the need to prune the mammal tree to species for which there are range maps. This I have now implemented in the Entangled Bank.

The geophylogney was built in GeophyloBuilder using the range centroids with an envelope model. I have put together two quick visualizations, a map with nodes coloured by age and a movie in ArcGlobe. The map shows a clustering of old nodes toward the center of continents and in ocean basins. The former represent continental endemicity, the latter transcontinental vicariance or dispersal.

In ArcGlobe something strange is going on with branches the cross the inverse-prime meridian, looks like an ESRI bug to me.

Terrestrial Mammal Geophylogey from David Kidd on Vimeo.

Consistent tree drawing

In his VizBi 2011 presentation, Rod Page discussed how the same tree can be drawn in different ways. This is a problem as tree may display differently between viewers, and following the addition or removal of leaves.

Image extracted from Rod's VizBi 2011 presentation

He showed how leaves can be ordered using sequential ids, for example from the NCBI taxonomy. This ordering is then used to specify how leaves are be displayed in the Y dimension leading to consistent display between viewers. In addition, this ordering is not affected by the addition of new, or deletion of existing, leaves.

Image extracted from Rod's VizBi 2011 presentation

Ordering from an arbitrarily ordered list, such as the sequence of names added to the NCBI taxonomy, results in an arbitrarily node ordering. Yet leaves are often names, not numbers, and we are used to viewing text in alphabetical order (a-z).

Leaves may, however, be ordered alphabetically when a tree is first built. To prevent restructuring of a tree, following the addition of new groups of leaves, new groups can be appended to the initial list in alphabetical order. Such ordering maintains consistency in tree rendering while supporting partial alphabetical ordering of tips.

Image edited from Rod's VizBi 2011 presentation

When desired the sequential alphabetically ordered groups can be sorted to create a new fully ordered list.

Image edited from Rod's VizBi 2011 presentation

Whether such partial alphabetical ordering improves tree comprehension requires evaluation, but it is likely to be most beneficial for trees with many polytomies, e.g. taxonomies. There are also overheads associated with maintaining the ordered list(s) with trees to be considered.

Areas of Endemism and Event-Based Methods

In a recent Journal of Biogeography editorial, Ontology of areas of endemism, Brian Crother and Christopher Murray argue that areas of endemism should be the preferred unit in historical biogeography, including event-based methods such as Dispersal Vicariance Analysis and La Grange. I disagree.

Event-based methods reconstruct the history of a clade from an observed distribution of taxa and their evolutionary relationships, given a biogeographic model that defines three things.

1. How geographical space is divided into units
2. How those units relate through time
3. How organisms respond to different configurations of units.

Crother and Murray state that the geographic units should be areas of endemism. Like the 'niche', an 'area of endemism' is a simple concept that most biogeographers' recognise, yet are unable to agree on a clear simple definition. It is, however, essentially an area occupied by a group of species that share similar ranges. It is argued that sharing ranges implies a shared history of the taxa, and, by inference, a history of place. Common phylogenetic pattern confirms hypotheses of shared taxa history. Areas of endemism are further believed to be hierarchical as they are (usually) created by vicariance, and they are geographical units which can be nested within other such units, e.g Jamaica can be nested within North America.

I am interested in reconstructing the spatial and temporal history of a family of freshwater fish species as they diversified with the rise of the Trans-Mexican Volcanic Belt. I know where the fish live now, their evolutionary relationships, and I have a partial hydrological history inferred from geological evidence. The fish cannot disperse between drainage basins and the configuration of the drainage basins changes through time. Basins split, coalesce, or part of one may be exchanged with an adjacent basin in a river capture event. While identifying areas of endemism occupied by sister taxa may help identify past splitting and exchange events, the units that determine the history of the clade are the basins themeselves, and to a lesser extent environmental variation within basins. Basins which change in extent and connectivity through time, and are not in any way hierarchical.

Areas of endemism may exist, they may be correlated with shared history, but they are only one of many artifacts left by history. To reconstruct taxon histories fragmented information must be integrated from many sources to build scenarios consistent with all the available information. Areas of endemism are just one source of information.

GeoPhyloBuilder for ArcGIS v1.2 released

GeoPhyloBuilder for ArcGIS v1.2 introduced two new tip-fan options, 'Internal+' and 'Drop' which with 'Internal' and 'Tip' makes four tip-fan options.

The release also fixes bugs in the positioning of nodes and branches when placed using overlap and disjunction between sister clades.

GeoPhyloBuilder for ArcGIS v1.2 can be download from SourceForge.

Overlap-Disjunction Analysis Geophylogeny

In overlap-disjunction analysis tree nodes are placed at the centroid of the region of disjunction or overlap between sister clade ranges.

An ODA geophylogeny ofthe Goodeidae is displayed against four palaeohydrological models for Central Mexico. Five clades are identified by colour and observations treated as polytomies of their first internal node. The direction circle has a radius of 100km. Box divisions are every 5 million years from present (bottom).

A Macroscope of Evolution

Microscopes allow us to see very small things, similarly macroscopes help us see very big things.

The evolution of life on earth is a very large thing indeed. It has existed more than 2 billion years and extends over 500 million square kilometers. It is currently composed of at least 4 million species, believed to be a small fraction of the total number that have ever lived. Each species is composed of many individuals that vary in morphology, genetics and behaviour. All these individuals are linked through an often tree-like space-time network of common descent, which formed by interacting with the planet, and with itself.

That's pretty big and complicated!

One way of understanding entities that extend over wide ranges of spatial and temporal scales is to plot information against logarithmic axes of space and time. In my macroscope of evolution objects of study, biological processes, scientific disciples and structures generated are shown.

Choosing between alternative biological names with uBio

Background

The format and organisation of taxonomic information in the GPDD leaves a lot to be desired.

Queries on compound name entries require the extensive use of wildcards that increase query complexity and reduces efficiency. If I want fields with unambiguous single names I must decide between alternative names.

I am going to use some the biological names services to answer my questions and in doing so I hope to learn more about what each does and how they interconnect, or not, as the case may be.

I began with Phyla in theTaxonomicPhylum field. Three of which have compound names; Chromophyta (Heterokontophyta), Cnidaria (Coelenterata), and Dinophyta (Pyrrophyta).

Universal Biological Indexer and Organizer (uBio)

UBio is collated from a wide range of sources complied by taxonomists and other scientists so data quality should be good. It is a Taxonomic Name Server (TNS) composed of two parts. NameBank stores the names and facts that link names while ClassificationBank stores classifications and taxon concepts. I type the first name, "Chromophyta" into the box and press search. One match, but does it help?

NamebankID is the unique ID of the name in NameBank, the LSID is its resolvable Life Science Identifier. A clickable list of common names given, one of which is "heterokonts", and some information on record insertion. Clicking "view metadata" returns the string,

urn:lsid:ubio.org:namebank:10129547 Vernacular

This tells me it is a common name. "Heterokontophyta" also returns a single record.

A record with the metadata string,

urn:lsid:ubio.org:namebank:1560200 Heterokontophyta Heterokontophyta 5 Heterokontophyta Heterokontophyta Scientific Name Canonical form Phylum

Therefore, according to NameBank, "Heterikontophyta" is the correct scientific name for the Phylum, but what is the metadata string format and why are Heterikontophyta and Chromophyta not cross-linked if they refer to the same taxon? These questions must remain for another day.

What of the other two name pairs?

Both Cnidaria and Coelenterata appear to be valid scientific names, but the returned metadata does not seem to help me to make an informed decision between the two names. Wikipedia searches provides an answer,

"Cnidarians were for a long time grouped with Ctenophores in the phylum Coelenterata, but increasing awareness of their differences caused them to be placed in separate phyla."

"Coelenterata is an obsolete long term encompassing two animal phyla, the Ctenophora (comb jellies) and the Cnidaria (coral animals, true jellies, sea anemones, sea pens, and their allies)"

A search of ZooBank, the official registry of Zoological Nomenclature, returns no acts for either name. So, Cnidaria it is.

NameBank searches for Dinophyta and Pyrrophyta reveal the latter to be a vernacular name. Again, Wikipedia provides a quick and easily understood resolution to why both names exist. They were classified as both plants and animals! So Dinophyta they are, although on both Wikipedia and the University of California Museum of Palaeotology the phylum is "Dinoflagellata". So, it looks like neither name is correct.

Will other taxonomic name services provide more information than uBio? We shall see.