DOI: 10.5061/dryad.bnzs7h4c3
title: Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards

description: How biotic and abiotic factors act together to shape biological diversity
 is a major question in evolutionary biology. The recent availability of
 large datasets and development of new methodological approaches provide
 new tools to evaluate the predicted effects of ecological interactions and
 geography on lineage diversification and phenotypic evolution. Here, we
 use a near complete phylogenomic-scale phylogeny and a comprehensive
 morphological dataset comprising more than a thousand specimens to assess
 the role of biotic and abiotic processes in the diversification of monitor
 lizards (Varanidae). This charismatic group of lizards shows striking
 variation in species richness among its clades and multiple instances of
 endemic radiation in Indo-Australasia (i.e., the Indo-Australian
 Archipelago and Australia), one of Earth’s most biogeographically complex
 regions. We found heterogeneity in diversification dynamics across the
 family. Idiosyncratic biotic and geographic conditions appear to have
 driven diversification and morphological evolution in three endemic
 Indo-Australasian radiations. Furthermore, incumbency effects partially
 explain patterns in the biotic exchange between Australia and New Guinea.
 Our results offer insight into the dynamic history of Indo-Australasia,
 the evolutionary significance of competition, and the long-term
 consequences of incumbency effects.
description: <strong>Code.zip:</strong> Contains the scripts and
 files used to run the analyses of diversification, morphological
 evolution, and incumbency effects. The .zip file contains individual R
 scripts used to run each group of analyses and two folders. The folder
 AuxiliaryFiles contains: a matrix with the maximum snout-vent length (SVL)
 per species and the mean of each other morphological trait
 (AllPhenoTraits.csv), a matrix used to replace placeholder names of DAISIE
 (https://doi.org/10.1111/ele.12461) models with the names used in the
 manuscript (model_names.csv), results of simulations under the DREaD model
 (https://doi.org/10.1086/701125) used to infer the geographic mode of
 speciation (simulation_results.csv), a shapefile with polygons
 representing the distributions of living varanids and auxiliary files
 (distrib.*), the main phylogenetic tree used in downstream analyses
 (Tree.tre), the anagenetic and cladogenetic events tables obtained from 50
 stochastic maps obtained with BioGeoBEARS
 (https://doi.org/10.21425/F5FBG19694) (RES_ana_events_tables.Rdata and
 RES_clado_events_tables.Rdata), a sample of 100 phylogenetic trees
 (sample_of_trees.rdata), and a raster with polygons representing the
 distributions of living varanids (spp_rasters.rda). The folder called
 AuxiliaryScripts contains: scripts needed for the DREaD analyses
 (see https://doi.org/10.5061/dryad.d9j09bm for details) (DREaD.R,
 environmentalChange.R, findSisters.R, generateSummaryStatistics.R,
 helperFunctions.R, nicheEvolution.R, nicheRecenter.R, rangeDispersal.R,
 seedSpecies.R, speciateAllopatric.R, speciateDispersal.R,
 speciateParapatric.R, speciateSympatric.R, and
 summary_statsitics_functions.R), a function to run DAISIE in parallel
 (search.surface.DAISIE.R), and a function to calculate support for DAISIE
 models (Calculate_AICs.R).
 <strong>Head_shape_dorsal.csv:</strong> Unaligned
 coordinates of landmarks and semi-landmarks used to describe head shape in
 dorsal view. The landmarks/semi-landmarks were digitized from photographs
 using 'geomoprh 3.0.3'
 (https://doi.org/10.1111/2041-210X.12035). For each individual, the
 following is indicated: taxon (the operational taxonomic unit to which the
 individual belongs), voucher (the collection and unique identifier of each
 individual; acronyms follow Sabaj 2019, available at
 http://www.asih.org/), sex (male or female), and whether the individual is
 sexually mature or not (inferred from size and/or gonad inspection). The
 remaining columns indicate the location of landmarks/semi-landmarks in the
 horizontal and vertical axes (e.g., 1x, 1y; numbering follows top panel in
 Fig. S2 of the article). The matrix includes some specimens that were
 excluded from the final analyses due to sexual dimorphism (see article for
 details). Some data could not be recorded for all specimens due to their
 poor condition. Missing data is indicated by "n/a" and was
 imputed using random forest training.
 <strong>Head_shape_lateral.csv:</strong> Unaligned
 coordinates of landmarks used to describe head shape in lateral view. The
 landmarks were digitized from photographs using 'geomoprh 3.0.3'
 (https://doi.org/10.1111/2041-210X.12035). For each individual, the
 following is indicated: taxon (the operational taxonomic unit to which the
 individual belongs), voucher (the collection and unique identifier of each
 individual; acronyms follow Sabaj 2019, available at
 http://www.asih.org/), sex (male or female), and whether the individual is
 sexually mature or not (inferred from size and/or gonad inspection). The
 remaining columns indicate the location of landmarks in the horizontal and
 vertical axes (e.g., 1x, 1y; numbering follows bottom panel in Fig. S2 of
 the article). The matrix includes some specimens that were excluded from
 the final analyses due to sexual dimorphism (see article for details).
 Some data could not be recorded for all specimens due to their poor
 condition. Missing data is indicated by "n/a" and was imputed
 using random forest training.
 <strong>Linear_measurements.csv:</strong> Linear
 measurements. For each individual, the following is indicated: taxon (the
 operational taxonomic unit to which the individual belongs), voucher (the
 collection and unique identifier of each individual; acronyms follow Sabaj
 2019, available at http://www.asih.org/), sex (male or female), and
 whether the individual is sexually mature or not (inferred from size
 and/or gonad inspection). The remaining columns indicate the following
 unprocessed measurements in mm: snout-vent length (SVL; along dorsal
 midline, between tip of snout and vent), head length (along dorsal
 midline, between tip of snout and anterior edge of tympanum), head width
 (at level of anterior edge of tympanum), head depth (at level of middle of
 eyes), neck length (between anterior edge of tympanum and gular fold),
 body length (between gular fold and vent), arm length (between base of
 forelimb and proximal edge of claw on finger IV), hand width
 (perpendicular to base of finger V), hip width (width of pelvic gridle
 measured at level of middle of hindlimbs), leg length (between base of
 hindlimb and proximal edge of claw on toe IV), foot width (perpendicular
 to base of toe V), tail length (between vent and tip of tail), tail width
 (measured at level of one third of tail length from vent), and tail depth
 (measured at level of one third of tail length from vent) The matrix
 includes some specimens that were excluded from the final analyses due to
 sexual dimorphism (see article for details). Some data could not be
 recorded for all specimens due to their poor condition. Missing data is
 indicated by "n/a" and was imputed using random forest
 training. <strong>Ranges.zip:</strong>
 Contains a shapefile (Ranges.shp) and auxiliary files. The shapefile
 contains polygons representing the distributions of living varanid species
 and two closely related taxa in the families Lanthanotidae and
 Shinisauridae (modified from Roll et al. 2017
 https://doi.org/10.1038/s41559-017-0332-2). The "Binomial"
 attribute indicates the taxon.
 <strong>Tree.tre:</strong> Main tree used in
 downstream analyses. The phylogeny is a time-calibrated tree in Newick
 format that is primarily based on the phylogenomic analyses presented by
 Brenan et al. 2021 (https://doi.org/10.1093/sysbio/syaa046). We added tips
 based on previous studies or our own analyses of publicly available
 molecular data (see article for details). Units are millions of
 years.