DOI: 10.5061/dryad.4m281
title: Data from: Anatomy of a neotropical insect radiation

description: Background: Much evolutionary theory predicts that diversity arises via
 both adaptive radiation (diversification driven by selection against
 niche-overlap within communities) and divergence of geographically
 isolated populations. We focus on tropical fruit flies (Blepharoneura,
 Tephritidae) that reveal unexpected patterns of niche-overlap within local
 communities. Throughout the Neotropics, multiple sympatric
 non-interbreeding populations often share the same highly specialized
 patterns of host use (e.g., flies are specialists on flowers of a single
 gender of a single species of host plants). Lineage through time (LTT)
 plots can help distinguish patterns of diversification consistent with
 ecologically limited adaptive radiation from those predicted by
 ecologically neutral theories. Here, we use a time-calibrated phylogeny of
 Blepharoneura to test the hypothesis that patterns of Blepharoneura
 diversification are consistent with an “ecologically neutral” model of
 diversification that predicts that diversification is primarily a function
 of time and space. Results: The Blepharoneura phylogeny showed more
 cladogenic divergence associated with geography than with shifts in
 host-use. Shifts in host-use were associated with ~20% of recent splits
 (&lt;3 Ma), but &gt;60% of older splits (&gt;3 Ma). In the
 overall tree, gamma statistic and maximum likelihood model fitting showed
 no evidence of diversification rate changes though there was a weak
 signature of slowing diversification rate in one of the component clades.
 Conclusions: Overall patterns of Blepharoneura diversity are inconsistent
 with a traditional explanation of adaptive radiation involving decreases
 in diversification rates associated with niche-overlap. Sister lineages
 usually use the same host-species and host-parts, and multiple
 non-interbreeding sympatric populations regularly co-occur on the same
 hosts. We suggest that most lineage origins (phylogenetic splits) occur in
 allopatry, usually without shifts in host-use, and that subsequent
 dispersal results in assembly of communities composed of multiple
 sympatric non-interbreeding populations of flies that share the same
 hosts.
description: Bleph lineages R data
 filecontains data on host
 and distribution for all barcoded specimens, the DNA distance matrix for
 specimens included, and the phylogeny used in data
 analysesBleph
 lineages.RDatadiversification tests R
 data filecontains input and
 output for diversification tests reported, using fitdAICrc function of the
 R package laserdiversification
 tests.RDatagamma simulations R
 scriptR script that calculates
 gamma statistic on set of simulated trees with specified percentage of
 tips removed to determine significance level for gamma
 statisticgamma
 simulations.Rlaser simulations R
 scriptscript that calculated
 deltaAIC statistic in laser on set of simulated trees with specified
 percentage of tips removed to determine significance level for deltaAIC
 statistic after fitting Yule, birth-death, DDX, and DDL models of
 diversificationlaser
 simulations.Rcharacter mapping R data
 filecontains input and some
 output for character mapping and character evolution tests
 reportedcharacter
 mapping.RDatatabulate_parsimony_shift_counts R scriptscript that uses pars.shift.counts (in character mapping R data file) to tabulate proportion of old vs. young splits associated with host shift or regional dispersal, and draw barchart as in Fig. 4A; can also tabulate by cladetabulate_parsimony_shift_counts.Rmpr_shuffle R scriptscript that performs permutation to test whether observed difference between proportion of old vs. young splits associated with host shifts or regional dispersal is greater than expected under a null distribution of shuffled character statesmpr_shuffle.Rsummarize_simmap_results R scriptscript that summarizes host shift information from set of simmap reconstructions (used to create fig. 4B) using data in character mapping R data filesummarize_simmap_results.R