DOI: 10.5061/dryad.1ps0t
title: Data from: Testing for differences in rates of speciation, extinction, and morphological evolution in four tribes of cichlids endemic to Lake Tanganyika, East Africa

description: Patterns of morphological disparity yield important insight into the
 causes of diversification and adaptive radiation in East African cichlids.
 However, comparisons of cichlid disparity have often failed to consider
 the effects that differing clade ages or stochasticity may have on
 disparity before making interpretations. Here, a model of branching
 morphological evolution allows assessment of the relative contributions of
 differing turnover and morphological change rates, clade ages, and
 stochastic variation to the observed patterns of disparity in four endemic
 tribes of Lake Tanganyika cichlids. Simulations compare the likelihood of
 generating the observed disparity of the four tribes using 200 parameter
 combinations and four model conditioning variations, which allows
 inference of evolutionary rate differences among clades. The model is
 generally robust to model conditioning, the approach to data analysis, and
 model assumptions. Disparity differences among the first three cichlid
 tribes, Ectodini, Lamprologini, and Tropheini, can be explained entirely
 by stochasticity and age, whereas the fourth tribe, Cyprichromini, has
 likely experienced lower rates of turnover and morphological change. This
 rate difference is likely related to the low dietary diversity of the
 Cyprichromini. These results highlight the importance of considering both
 clade age and stochastic variation when interpreting morphological
 diversity and evolutionary processes.
description: Code for
 Speciation-based Model, MinMax variationSpeciation_MinMax_Model.txtCode for Speciation-based Model; No Condition, Extant, and Min variationsSpeciation_NoMax_Model.txtCode for Time-based Model, MinMax variationTime_MinMax_Model.txtCode for counting matches between simulated data and actual clade disparityThis code (written in R) counts the number of simulations generated under each parameter combination that match the actual disparity of the real clade, within 1 standard error. In order to use this code, input the morphological variance of the real clade as “var” and the standard error of this variance as “SE” by replacing the example numbers. In the next line, input the file name of the data output from the simulations between the quotation marks by replacing the example file name (minmaxvar.txt). Finally, replace the output file name between the quotation marks in the last line by replacing the example output name (minmaxvarcount.xls).Varcount.txtMorphometric data for East African Cichlids (Ectodini, Lamprologini, Tropheini, Cyprichromini, Perissodini, Limnochromini) downloaded from FishBaseThis spreadsheet contains the data downloaded from FishBase. Each species name also includes a link to the FishBase page for that species. The data is separated by tribe, and includes data for species from Ectodini, Lamprologini, Tropheini, Cyprichromini, Perissodini, and Limnochromini. The characters used include standard length (% total length), pre-anal length (% total length), pre-dorsal length (% total length), pre-pelvic length (% total length), pre-pectoral length (% total length), body depth (% total length), head length (% total length), eye diameter (% head length), pre-orbital length (% head length), and the aspect ratio (calculated as height squared divided by surface area) of the caudal fin.FishBase_data_compilation.xlsxCode for calculations for probability matrices and likelihoodMatrixcalcs.txt