University of Glasgow

Roderic Page

We all have a \"past\" that we might not advertise widely, and my past
includes flirting with panbiogeography. Indeed my PhD thesis
[hdl:2292/1999](http://hdl.handle.net/2292/1999) is entitled
\"Panbiogeography: a cladistic approach.\" Shortly after graduating I
moved on to host-parasite cospeciation and the gene tree/species tree
problem (\"reconciled trees\", see Katz et al.
<http://dx.doi.org/10.1093/sysbio/sys026> for a recent example of this
approach), but part of me misses the glory days of vicariance,
dispersal, and panbiogeography.  
  
One thing which strikes me is how little use large-scale historical
biogeography makes of [GBIF](http://data.gbif.org) data. One of the
things that made Croizat\'s panbiogeography so interesting was the way
he exposed similar distribution patterns in unrelated groups of
organisms. He did this by hand, producing map after map, some
embellished with all manner of annotations (\"gates\", \"nodes\",
\"massings\", etc.). In some ways, Croizat as an early data miner. Now
we are awash in distributional data, where are the people revisiting
global scale historical patterns? In particular, wouldn\'t it be cool to
have a biogeographic search engine that could pull out taxa with
particular distribution patterns that we could then analyse.  
  
For example, while working on a project to map taxonomic names to
literature and genomics data, I embedded a widget to display GBIF maps.
Every so often I come across taxa have the classic \"Gondwana\"
distribution pattern. For example, below is a map for stoneflies of the
family the [Notonemouridae](http://data.gbif.org/species/7225/) from
GBIF.  
  
![](http://ogc.gbif.org/wms?request=GetMap&bgcolor=0x666698&styles=,,&layers=gbif:country_fill,gbif:tabDensityLayer,gbif:country_borders&srs=EPSG:4326&filter=()(%3CFilter%3E%3CPropertyIsEqualTo%3E%3CPropertyName%3Eurl%3C/PropertyName%3E%3CLiteral%3E%3C!%5BCDATA%5Bhttp%3A%2F%2Fdata.gbif.org%2Fmaplayer%2Ftaxon%2F7225%5D%5D%3E%3C/Literal%3E%3C/PropertyIsEqualTo%3E%3C/Filter%3E)()&width=721&height=362&Format=image/png&bbox=-180,-90,180,90){width="360"}  
  
Below is a map for the Notonemouridae using an orthographic projection
(see [earlier post for
details](http://iphylo.blogspot.com/2012/07/using-orthographic-projections-to-map.html)):  
  
![Notonemouridae](http://lh3.ggpht.com/-hYVjqmTNoZ8/UGA7m7GXkTI/AAAAAAAAB_g/CUJjJI0qD4c/Notonemouridae.png?imgmax=800 "Notonemouridae.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="210" height="194"}  
Another family of stone flies, the
[Gripopterygidae](http://data.gbif.org/species/2999/), show a similar
pattern:  
  
![Gripopterygidae](http://lh4.ggpht.com/-5vUMpAmgc4k/UGA7mBXvBMI/AAAAAAAAB_Y/US8pgeljVTc/Gripopterygidae.png?imgmax=800 "Gripopterygidae.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="201" height="193"}  
  
What I\'d like is to be able to query a database like GBIF for patterns
such as these Gondwanic distributions, then be able to pull out
associated phylogenetic information (e.g., via sequences in GenBank) so
that we could determine the antiquity of these patterns, and whether
they are consistent with geological models. We could begin to do
large-scale testing of biogeographic hypotheses in a (semi-)automated
way. At present we generally rely on a few well-studied examples that
are either broadly consistent with  

> Bocxlaer, I. V., Roelants, K., Biju, S. D., Nagaraju, J., & Bossuyt,
> F. (2006). Late Cretaceous Vicariance in Gondwanan Amphibians. (M.
> Hofreiter, Ed.)PLoS ONE, 1(1), e74.
> [doi:10.1371/journal.pone.0000074.t002](http://dx.doi.org/10.1371/journal.pone.0000074.t002)

  
or contradict  

> Cook, L. G., & Crisp, M. D. (2005). Not so ancient: the extant crown
> group of Nothofagus represents a post-Gondwanan radiation. Proceedings
> of the Royal Society B: Biological Sciences, 272(1580), 2535--2544.
> [doi:10.1098/rspb.2005.3219](http://dx.doi.org/10.1098/rspb.2005.3219)

  
the hypothesis that the history of biota of the southern hemisphere has
been largely structured by the break-up of Gondwana.  
  
A first step might be to index distributions at, say, family level and
above, and provide a series of polygons representing different
distribution patterns. We then search for distributions that are largely
concordant with those patterns, and query GenBank (or TreeBASE) for
sequences (or phylogenies) for those taxa. We then ask the questions
\"how old are these taxa?\" and \"what biogeographic histories do they
have?\"  
  


We all have a "past" that we might not advertise widely, and my past includes flirting with panbiogeography.

Towards a biogeographic search engine

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-vTLJwvJFrnv95hnhcSFfaKuI5X5MObgzHyp7mv9q0WBWqusYJwtlA8D3_lcnE1v9Ex-fZfcdk0SGQVYLoHkhtf9qSntS4tYuflOKu_C2t8gywtmza7ZS38NCSGvCoN0BZw-r/s200/small_Snapshot+2007-11-16+06-13-00.png){#BLOGGER_PHOTO_ID_5133319276681937570
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-vTLJwvJFrnv95hnhcSFfaKuI5X5MObgzHyp7mv9q0WBWqusYJwtlA8D3_lcnE1v9Ex-fZfcdk0SGQVYLoHkhtf9qSntS4tYuflOKu_C2t8gywtmza7ZS38NCSGvCoN0BZw-r/s1600-h/small_Snapshot+2007-11-16+06-13-00.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
One side effect of the trend towards digitising everything is that stuff
one forgot about (or, perhaps, would like to forget about) comes back to
haunt you. My *alma mater*, the [University of
Auckland](http://www.auckland.ac.nz/) is digitising theses, and my PhD
thesis \"Panbiogeography: a cladistic approach\" is now online
([hdl:2292/1999](http://hdl.handle.net/2292/1999)). Here\'s the
abstract:  
  

> This thesis develops a quantitative cladistic approach to
> panbiogeography. Algorithms for constructing and comparing area
> cladograms are developed and implemented in a computer program.
> Examples of the use of this software are described. The principle
> results of this thesis are: (1) The description of algorithms for
> implementing Nelson and Platnick\'s (1981) methods for constructing
> area cladograms. These algorithms have been incorporated into a
> computer program. (2) Zandee and Roos\' (1987) methods based on
> \"component-compatibility\" are shown to be flawed. (3) Recent
> criticisms of Nelson and Platnick\'s methods by E. O. Wiley are
> rebutted. (4) A quantitative reanalysis of Hafner and Nadler\'s (1988)
> allozyme data for gophers and their parasitic lice illustrates the
> utility of information on timing of speciation events in interpreting
> apparent incongruence between host and parasite cladograms. In
> addition the thesis contains a survey of some current themes in
> biogeography, a reply to criticisms of my earlier work on track
> analysis, and an application of bootstrap and consensus methods to
> place confidence limits on estimates of cladograms.

  
1990. Ah, happy days\...


One side effect of the trend towards digitising everything is that stuff one forgot about (or, perhaps, would like to forget about) comes back to haunt you. My
<em>
 alma mater
</em>
, the University of Auckland is digitising theses, and my PhD thesis "Panbiogeography: a cladistic approach" is now online (hdl:2292/1999). Here's the abstract: Ah, happy days...

Messaggi di Rogue Scholar

Towards a biogeographic search engine

Thesis online