Defining biogeographic regions
To define a practical biogeographical categorization of regions, we
balanced capturing the complexity of our focal regions (i.e. the islands
between Australia and continental south-east Asia), with limiting
biogeographic model complexity (i.e. minimising states for which there
is insufficient data to estimate parameters). We also structured regions
to a) allow comparisons between the major continents and islands with
long histories of isolation from continental landmasses, and b) to allow
some investigation of biogeographic patterns within the islands of the
geologically complex IAA.
To begin with, we used 21 sub-regions or areas to describe insular and
continental region pigeon diversity (Table S3). Geographic range data
was initially summarised from the Handbook of the Birds of the World
(Baptista et al. , 1997) and then cross-referenced and updated
based on two online databases (https://www.iucnredlist.org/ and
https://www.worldbirdnames.org/new/). Grouping of areas was initially
explored using turnover of phylogenetic diversity (phylobeta: Graham &
Fine 2008; Leprieur et al. 2012). Phylogenetic beta-diversity was
estimated using Simpson’s phylobeta index (pβsim) using the BEAST MCC
tree (after removing outgroups), and compiled into a pairwise pβsim
distance matrix (using custom script GTREER5) (see Dryad repository).
Using this distance matrix we visualised differences between regions
using both hierarchical clustering (average = UPGMA) and Multi
Dimensional Scaling (MDS) 2-D plot (hclust and cmdscale, ’stats’ R
package; R Core Team 2016)). Five taxa that occur in >8
sub-regions were removed from estimation of pβsim to limit emphasis on
recent connections at the expense of underlying older endemicity, which
is the focus of this study.
We then assigned taxa to broad regional categories (hereafter referred
to as regions) based on modifying the pre-existing historical
regionalizations (e.g. Jønsson et al. 2010, and also including the
IOC9.2 breeding range zones) with information from both phylogenetic
turnover (Fig. S1) and geological models for the history and formation
of islands around the Indo-west Pacific (see above and Zahirovic et al.
2016). This resulted in an eight region scheme: 1) New World – North,
South and Middle America: 2) – Old World (Europe, Africa and mainland
Asia combined); 3) – Philippines; 4) Wallacea – Sulawesi and the
Lesser Sundas; 5) West Melanesia - New Guinea plus the islands of
Maluku; 6) Indian Ocean Islands – especially the Mascarenes and
Madagascar; 7) Australia (not including New Guinea) and; 8) Pacific
Ocean – the islands of the south-west Pacific including East Melanesia,
New Caledonia and New Zealand. Assignment of phylogenetically sampled
species to these eight regions is listed in Table S4. We note that our
configuration of Wallacea does not include Maluku. This is because our
phylogenetic turnover analyses indicate that much of Maluku is more
closely allied to New Guinea (Fig. S1A). Geological (Hill & Hall 2003)
and biological (Oliver et al. , 2022) data also indicate a close
relationship between islands of Maluku and New Guinea. We separated
Australia from West Melanesia in our analyses because: a) phylobeta
analyses indicate the dominant pigeon faunas of the two regions are
relatively discrete and b) geological models indicate that the New
Guinea has been separated from the main Australian landmass by at least
a shallow sea for most the late Cenozoic (see geological context above).
Species that occur across regions were scored as such and allowed to
have multiple states in analyses.
To investigate the role of islands in pigeon diversification and
dispersal, we collated regions into broader categories of islands (a
composite of the Wallacea, West Melanesia, Philippines and Pacific Ocean
regions) versus continents (Americas, Old World and Australia). This was
done by post hoc combining states and state changes inferred in the full
eight region analyses into summary results (see below).