ASR OF TROPHIC HABITS IN CALLIPHORIDAE

# ASR OF TROPHIC HABITS IN CALLIPHORIDAE ## BUILDING THE DATASET after having the tree, you need a "traits file" with species sorted just like the tree; we do this in R ``` # this is how the traits file looked initially: Auchmeromyia_bequaerti P Auchmeromyia_luteola P Cordylobia_anthropophaga P Pachychoeromyia_praegrandis P # one column for the species and one for the trait (you can use only ONE letter for the trait) # R code to sort the species: tree <- read.nexus(file = "TREE5_zumpt.nex") data_zumpt <- read.table("phenotype_zumpt.txt") # is the tree tip order the same as the V1 order? phylo_species <- tree$tip.label data_zumpt_sorted <- data_zumpt[match(phylo_species, data_zumpt$V1),] sum(tree$tip.label == data_zumpt_sorted$V1) == nrow(data_zumpt_sorted) # prints TRUE, so ready to go: #write table write.table(data_zumpt_sorted, "data_zumpt_sorted.txt", quote=F, row.names=F, col.names=F, sep='\t') ``` We also need the help of R to make a "control file" with will be used to pass the analyses commands to bayestraits; first the packages I will be using: ``` library(here) library(posterior) library(tidybayes) library(coda) library(btw) # remotes::install_github('rgriff23/btw') library(tidytree) library(ape) library(tidyverse) library(patchwork) library(tidyr) library(dplyr) library(readr) library(phytools) library(EBImage) library(ggtree) ``` the next steps are necessary to tell bayestraits to reconstruct ALL internal nodes in the tree (it will not be done by default): ``` # convert tree to a dataframe tree_data <- as_tibble(tree) # create an empty column for tip labels d_nodes <- tibble(nodes = dplyr::filter(tree_data, is.na(label)) %>% pull(node), label = NA) for(i in 1:nrow(d_nodes)){ temp_node = d_nodes$nodes[i] temp_offspring <- offspring(tree_data, temp_node, tiponly = TRUE) d_nodes$label[i] <- temp_offspring$label %>% paste0(collapse = ' ') } d_nodes <- mutate(d_nodes, first_command = paste('AddTag', paste('T', nodes, sep = ''), label, sep = ' '), second_command = paste('AddNode', nodes, paste('T', nodes, sep = ''), sep = ' ')) to_save <- select(d_nodes, first_command, second_command) %>% pivot_longer(everything(), names_to = 'blah', values_to = 'command') %>% pull(command) write.table(to_save, "tags_zumpt", quote=FALSE, col.names = FALSE, row.names = FALSE) ``` Now we create the control file using these info generated by the previous R script; this is how the control file looks like (the big block starting with AddTag was the one built in R): ``` 1 # tells the program to run in multistate mode 2 # run in MCMC mode (1 would be ML) RJHP exp 0 2 # set a reverse jump hyperprior with an exponential distribution seeded from 0 to 2 Iterations 10000000 # number of iterations Sample 10000 # frequency of sampling Burnin 1000000 # set burnin Stones 100 10000 # this will be used to run a BayesFactor test LogFile LOG_zumpt_exp02 # name of output AddTag T55 Pachychoeromyia_praegrandis Auchmeromyia_luteola Auchmeromyia_bequaerti Cordylobia_anthropophaga Aldrichina_grahami Calliphora_vomitoria Calliphora_nigribarbis Calliphora_lata Calliphora_lopesi Calliphora_nigribasis Calliphora_vicina Calliphora_croceipalpis Sarconesia_chlorogaster Lucilia_silvarum Lucilia_richardsi Lucilia_sericata Lucilia_cuprina Lucilia_porphyrina Lucilia_ampullacea Lucilia_papuensis Lucilia_caesar Hemipyrellia_pulchra Hemipyrellia_fernandica Hemipyrellia_ligurriens Lucilia_lucigerens Lucilia_cluvia Lucilia_mexicana Lucilia_eximia Lucilia_caeruleiviridis Protophormia_terraenovae Phormia_regina Protocalliphora_sialia Protocalliphora_azurea Chrysomya_villeneuvi Chrysomya_rufifacies Chrysomya_albiceps Chrysomya_marginalis Chrysomya_putoria Chrysomya_chloropyga Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes Chrysomya_megacephala Chrysomya_bezziana Chrysomya_chani Compsomyiops_verena Cochliomyia_minima Cochliomyia_macellaria Cochliomyia_hominivorax Paralucilia_pseudolyrcea Paralucilia_fulvinota Paralucilia_paraensis Hemilucilia_semidiaphana Hemilucilia_segmentaria AddNode 55 T55 AddTag T56 Pachychoeromyia_praegrandis Auchmeromyia_luteola Auchmeromyia_bequaerti Cordylobia_anthropophaga AddNode 56 T56 AddTag T57 Pachychoeromyia_praegrandis Auchmeromyia_luteola Auchmeromyia_bequaerti AddNode 57 T57 AddTag T58 Auchmeromyia_luteola Auchmeromyia_bequaerti AddNode 58 T58 AddTag T59 Aldrichina_grahami Calliphora_vomitoria Calliphora_nigribarbis Calliphora_lata Calliphora_lopesi Calliphora_nigribasis Calliphora_vicina Calliphora_croceipalpis Sarconesia_chlorogaster Lucilia_silvarum Lucilia_richardsi Lucilia_sericata Lucilia_cuprina Lucilia_porphyrina Lucilia_ampullacea Lucilia_papuensis Lucilia_caesar Hemipyrellia_pulchra Hemipyrellia_fernandica Hemipyrellia_ligurriens Lucilia_lucigerens Lucilia_cluvia Lucilia_mexicana Lucilia_eximia Lucilia_caeruleiviridis Protophormia_terraenovae Phormia_regina Protocalliphora_sialia Protocalliphora_azurea Chrysomya_villeneuvi Chrysomya_rufifacies Chrysomya_albiceps Chrysomya_marginalis Chrysomya_putoria Chrysomya_chloropyga Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes Chrysomya_megacephala Chrysomya_bezziana Chrysomya_chani Compsomyiops_verena Cochliomyia_minima Cochliomyia_macellaria Cochliomyia_hominivorax Paralucilia_pseudolyrcea Paralucilia_fulvinota Paralucilia_paraensis Hemilucilia_semidiaphana Hemilucilia_segmentaria AddNode 59 T59 AddTag T60 Aldrichina_grahami Calliphora_vomitoria Calliphora_nigribarbis Calliphora_lata Calliphora_lopesi Calliphora_nigribasis Calliphora_vicina Calliphora_croceipalpis Sarconesia_chlorogaster Lucilia_silvarum Lucilia_richardsi Lucilia_sericata Lucilia_cuprina Lucilia_porphyrina Lucilia_ampullacea Lucilia_papuensis Lucilia_caesar Hemipyrellia_pulchra Hemipyrellia_fernandica Hemipyrellia_ligurriens Lucilia_lucigerens Lucilia_cluvia Lucilia_mexicana Lucilia_eximia Lucilia_caeruleiviridis AddNode 60 T60 AddTag T61 Aldrichina_grahami Calliphora_vomitoria Calliphora_nigribarbis Calliphora_lata Calliphora_lopesi Calliphora_nigribasis Calliphora_vicina Calliphora_croceipalpis AddNode 61 T61 AddTag T62 Calliphora_vomitoria Calliphora_nigribarbis Calliphora_lata Calliphora_lopesi Calliphora_nigribasis Calliphora_vicina Calliphora_croceipalpis AddNode 62 T62 AddTag T63 Calliphora_vomitoria Calliphora_nigribarbis Calliphora_lata Calliphora_lopesi Calliphora_nigribasis AddNode 63 T63 AddTag T64 Calliphora_vomitoria Calliphora_nigribarbis Calliphora_lata Calliphora_lopesi AddNode 64 T64 AddTag T65 Calliphora_nigribarbis Calliphora_lata Calliphora_lopesi AddNode 65 T65 AddTag T66 Calliphora_nigribarbis Calliphora_lata AddNode 66 T66 AddTag T67 Calliphora_vicina Calliphora_croceipalpis AddNode 67 T67 AddTag T68 Sarconesia_chlorogaster Lucilia_silvarum Lucilia_richardsi Lucilia_sericata Lucilia_cuprina Lucilia_porphyrina Lucilia_ampullacea Lucilia_papuensis Lucilia_caesar Hemipyrellia_pulchra Hemipyrellia_fernandica Hemipyrellia_ligurriens Lucilia_lucigerens Lucilia_cluvia Lucilia_mexicana Lucilia_eximia Lucilia_caeruleiviridis AddNode 68 T68 AddTag T69 Lucilia_silvarum Lucilia_richardsi Lucilia_sericata Lucilia_cuprina Lucilia_porphyrina Lucilia_ampullacea Lucilia_papuensis Lucilia_caesar Hemipyrellia_pulchra Hemipyrellia_fernandica Hemipyrellia_ligurriens Lucilia_lucigerens Lucilia_cluvia Lucilia_mexicana Lucilia_eximia Lucilia_caeruleiviridis AddNode 69 T69 AddTag T70 Lucilia_silvarum Lucilia_richardsi Lucilia_sericata Lucilia_cuprina Lucilia_porphyrina Lucilia_ampullacea Lucilia_papuensis Lucilia_caesar Hemipyrellia_pulchra Hemipyrellia_fernandica Hemipyrellia_ligurriens AddNode 70 T70 AddTag T71 Lucilia_silvarum Lucilia_richardsi Lucilia_sericata Lucilia_cuprina AddNode 71 T71 AddTag T72 Lucilia_silvarum Lucilia_richardsi Lucilia_sericata AddNode 72 T72 AddTag T73 Lucilia_silvarum Lucilia_richardsi AddNode 73 T73 AddTag T74 Lucilia_porphyrina Lucilia_ampullacea Lucilia_papuensis Lucilia_caesar Hemipyrellia_pulchra Hemipyrellia_fernandica Hemipyrellia_ligurriens AddNode 74 T74 AddTag T75 Lucilia_porphyrina Lucilia_ampullacea Lucilia_papuensis Lucilia_caesar AddNode 75 T75 AddTag T76 Lucilia_porphyrina Lucilia_ampullacea Lucilia_papuensis AddNode 76 T76 AddTag T77 Lucilia_porphyrina Lucilia_ampullacea AddNode 77 T77 AddTag T78 Hemipyrellia_pulchra Hemipyrellia_fernandica Hemipyrellia_ligurriens AddNode 78 T78 AddTag T79 Hemipyrellia_pulchra Hemipyrellia_fernandica AddNode 79 T79 AddTag T80 Lucilia_lucigerens Lucilia_cluvia Lucilia_mexicana Lucilia_eximia Lucilia_caeruleiviridis AddNode 80 T80 AddTag T81 Lucilia_lucigerens Lucilia_cluvia AddNode 81 T81 AddTag T82 Lucilia_mexicana Lucilia_eximia Lucilia_caeruleiviridis AddNode 82 T82 AddTag T83 Lucilia_mexicana Lucilia_eximia AddNode 83 T83 AddTag T84 Protophormia_terraenovae Phormia_regina Protocalliphora_sialia Protocalliphora_azurea Chrysomya_villeneuvi Chrysomya_rufifacies Chrysomya_albiceps Chrysomya_marginalis Chrysomya_putoria Chrysomya_chloropyga Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes Chrysomya_megacephala Chrysomya_bezziana Chrysomya_chani Compsomyiops_verena Cochliomyia_minima Cochliomyia_macellaria Cochliomyia_hominivorax Paralucilia_pseudolyrcea Paralucilia_fulvinota Paralucilia_paraensis Hemilucilia_semidiaphana Hemilucilia_segmentaria AddNode 84 T84 AddTag T85 Protophormia_terraenovae Phormia_regina Protocalliphora_sialia Protocalliphora_azurea Chrysomya_villeneuvi Chrysomya_rufifacies Chrysomya_albiceps Chrysomya_marginalis Chrysomya_putoria Chrysomya_chloropyga Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes Chrysomya_megacephala Chrysomya_bezziana Chrysomya_chani AddNode 85 T85 AddTag T86 Protophormia_terraenovae Phormia_regina AddNode 86 T86 AddTag T87 Protocalliphora_sialia Protocalliphora_azurea Chrysomya_villeneuvi Chrysomya_rufifacies Chrysomya_albiceps Chrysomya_marginalis Chrysomya_putoria Chrysomya_chloropyga Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes Chrysomya_megacephala Chrysomya_bezziana Chrysomya_chani AddNode 87 T87 AddTag T88 Protocalliphora_sialia Protocalliphora_azurea AddNode 88 T88 AddTag T89 Chrysomya_villeneuvi Chrysomya_rufifacies Chrysomya_albiceps Chrysomya_marginalis Chrysomya_putoria Chrysomya_chloropyga Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes Chrysomya_megacephala Chrysomya_bezziana Chrysomya_chani AddNode 89 T89 AddTag T90 Chrysomya_villeneuvi Chrysomya_rufifacies Chrysomya_albiceps Chrysomya_marginalis Chrysomya_putoria Chrysomya_chloropyga AddNode 90 T90 AddTag T91 Chrysomya_villeneuvi Chrysomya_rufifacies Chrysomya_albiceps Chrysomya_marginalis AddNode 91 T91 AddTag T92 Chrysomya_villeneuvi Chrysomya_rufifacies Chrysomya_albiceps AddNode 92 T92 AddTag T93 Chrysomya_rufifacies Chrysomya_albiceps AddNode 93 T93 AddTag T94 Chrysomya_putoria Chrysomya_chloropyga AddNode 94 T94 AddTag T95 Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes Chrysomya_megacephala Chrysomya_bezziana Chrysomya_chani AddNode 95 T95 AddTag T96 Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes Chrysomya_megacephala Chrysomya_bezziana AddNode 96 T96 AddTag T97 Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes Chrysomya_megacephala AddNode 97 T97 AddTag T98 Chrysomya_thanomthini Chrysomya_pinguis Chrysomya_nigripes AddNode 98 T98 AddTag T99 Chrysomya_pinguis Chrysomya_nigripes AddNode 99 T99 AddTag T100 Compsomyiops_verena Cochliomyia_minima Cochliomyia_macellaria Cochliomyia_hominivorax Paralucilia_pseudolyrcea Paralucilia_fulvinota Paralucilia_paraensis Hemilucilia_semidiaphana Hemilucilia_segmentaria AddNode 100 T100 AddTag T101 Compsomyiops_verena Cochliomyia_minima Cochliomyia_macellaria Cochliomyia_hominivorax Paralucilia_pseudolyrcea Paralucilia_fulvinota Paralucilia_paraensis AddNode 101 T101 AddTag T102 Cochliomyia_minima Cochliomyia_macellaria Cochliomyia_hominivorax Paralucilia_pseudolyrcea Paralucilia_fulvinota Paralucilia_paraensis AddNode 102 T102 AddTag T103 Cochliomyia_minima Cochliomyia_macellaria Cochliomyia_hominivorax AddNode 103 T103 AddTag T104 Cochliomyia_minima Cochliomyia_macellaria AddNode 104 T104 AddTag T105 Paralucilia_pseudolyrcea Paralucilia_fulvinota Paralucilia_paraensis AddNode 105 T105 AddTag T106 Paralucilia_pseudolyrcea Paralucilia_fulvinota AddNode 106 T106 AddTag T107 Hemilucilia_semidiaphana Hemilucilia_segmentaria AddNode 107 T107 Run ``` To run bayestraits: ``` ./BayesTraitsV4 TREE5_zumpt.nex data_zumpt_sorted.txt < control_zumpt_covarion.txt ``` Now we take the output and remove all unecessary data keeping only the reconstructed states and calculate the average. Easy to do in excel. Then parse an awk to get the following format: ``` awk -v RS='\t' '{printf $0 "\t"} NR%3 == 0 {print ""}' input.txt > output ``` The final file should look like: ``` 0.409900477777777 0.173865247777778 0.416234034444443 0.252614996666667 0.500092979999999 0.247291871111112 0.197729334444445 0.612524225555555 0.189746361111111 0.155221598888889 0.694552817777778 0.150225552222222 ``` where each row is a node in the phylogeny and each column is the probability of one of the 3 states Lastly we add a new column with the corresponding node number. Nodes will always start with n+1 where n is the number of taxa in the phylogeny. So in this case, where we have 54 taxa, node numbers start with 55; the output will look like: ``` X0 X1 X2 node 0.409900477777777 0.173865247777778 0.416234034444443 55 0.252614996666667 0.500092979999999 0.247291871111112 56 0.197729334444445 0.612524225555555 0.189746361111111 57 0.155221598888889 0.694552817777778 0.150225552222222 58 0.421222236666667 0.107296277777778 0.471481452222222 59 ```