#NEXUS [written Tue Jul 14 11:01:06 EST 2009 by Mesquite version 2.6 (build 486) at SUB6287/127.0.0.1 (George D.F. (Buz) Wilson)] BEGIN TAXA; TITLE 'Poore 2005, no fossils'; DIMENSIONS NTAX=18; TAXLABELS Bathynellacea Anaspidacea Dendrobranchiata Caridea Euphausiacea Mysida Lophogastrida Thermosbaenacea Spelaeogriphus Potiicoara Mangkurtu Mictocaris Hirsutia Thetispelecaris Cumacea Tanaidacea Isopoda Amphipoda ; END; BEGIN CHARACTERS; TITLE Modified_Poore_2005_matrix; DIMENSIONS NCHAR=91; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 1 2 3 4 5"; CHARSTATELABELS 1 Cervical_groove / absent 'present (at least in part)', 2 'Cephalothoracic shield (thoracomeres)' / first_only involves_2_or_more absent, 3 Dorsal_fold / absent present, 4 Cephalic_pleural_fold / absent present, 5 'Segmental pleural folds (branchiostegal folds)' / absent thoracomere_1_only 'thoracomeres 2-6' 'thoracomeres 1-8', 6 Branchiostegal_flaps / absent present, 7 Pleonite_musculature / not_capable_of_caridoid_escape_response with_diagonal_muscles_crossing_pleonite_boundaries_enabling_caridoid_reverse_escape_response, 8 Eye_optics / 'apposition (no clear zone between crystalline cone and rhabdom)' 'superposition (clear zone formed by retinular cells and/or distal pigment cells separating cone and rhabdom)', 9 'Ommatidia, crystalline cone' / tetrapartite bipartite, 10 Ocular_lobe / present absent, 11 Naupliar_eye_of_adult / present absent, 12 'Antennula, outer ramus' / 'multiarticulate (more than 20 articles)' with_fewer_than_10_articles 'rudimentary, if present', 13 'Antennula, inner ramus' / 'multiarticulate (more than 20 articles)' rarely_more_than_6_articles, 14 Antennal_gland / present absent, 15 Antennula_statocyst / absent present, 16 Antenna_article_3 / 'about third as long as article 4 (or more)' shorter_than_article_4 'fused to article 4(?)', 17 Antenna_outer_ramus / present absent, 18 Antenna_outer_ramus / linear 'scale-like (scaphocerite)', 19 'Antenna scale (scaphocerite)' / 'as long or longer than articles 3+4' 'half length of articles 3+4', 20 Labrum / without_posterior_tooth with_posterior_tooth, 21 Mandibular_incisor / 'stout, tooth-like' 'thin, blade-like ', 22 'Mandible, lacinia mobilis (broad on right, narrower spine on left)' / absent present, 23 Mandibular_spine_row_and_lacinia_mobilis / 'short and compact, incisor and molar closely-set' 'long, incisor and molar widely-spaced', 24 mandibular_palp / with_lateral_setae_on_articles_2_and_3 with_distal_setae_on_article_3_only, 25 Labium / 'with apices rounded, without long seta, mesial faces smooth' 'with acute apices, each bearing long seta, mesial faces bearing tooth plus 2 denticulate setae', 26 Maxillula_palp / 'with palp (endopod)' 'without palp (endopod)', 27 'Maxillula palp (endopod)' / distally_produced reflexed, 28 Maxillula__proximal_endite / with_row_of_long_marginal_setae 'with 3-4 short pappose setae' with_2_apical_pappose_setae 'with 4-5 spiniform setae' with_few_distal_simple_setae, 29 Maxillula__distal_endite / without_distolateral_row_of_denticulate_setae_or_teeth 'with distolateral row of denticulate setae (longer and distinct from distal spiniform setae)', 30 Maxillula__distal_endite / 'without lateral pappose setae (usually pair of facial long pappose setae instead)' with_single_distolateral_or_facial_pappose_seta, 31 Maxillary_gland / present absent, 32 Maxilla__basal_endites / longer_than_wide about_a_wide_as_long, 33 Maxilla_basal_endites_2_and_3 / 'with simple, setulate or pectinate setae along distal margin' 'each with row of long setae with claw-shaped end along mesial margin (pectinate setae distally)', 34 'Maxilla endopod (palp)' / present absent, 35 Maxilla_palp / articular reduced_to_long_external_seta_at_base_of_outer_lobe, 36 Maxilla_exopod / present absent, 37 Maxilla_exopod / simply_lamelliform 'produced proximally (posteriorly into branchial chamber as scaphognathite)', 38 'Thoracopods 1-3' / undifferentiated_from_posterior_thoracopods first_differentiated_as_maxilliped_with_well_developed_basal_endite 'at least two (often three) differentiated as diverse maxillipeds from posterior thoracopods' all_three_differentiated_as_similar_maxillipeds_from_posterior_thoracopods, 39 'Thoracopod 2 (pereopod 1)' / 'ambulatory or not enclosing mouthparts as follows, ischium-merus articulation linear' 'enclosing mouthparts, ischium-merus articulation angled anteriorly; basis more elongate than that of pereopod 2', 40 'Thoracopod 1 (maxilliped) basal endite' / with_setae_variously_structured 'with about 8 short distomesial robust setae, lateral simple setae', 41 'Thoracopod 1 (maxillipedal) palp article 5' / aligned_with_article_4 at_right_angles_to_article_4, 42 'Thoracopod 1 (maxillipedal) palp articles 2 and 3' / 'not mesially expanded, with few mesial setae' 'mesial expanded, with mesial row of plumose setae', 43 'Thoracopod 1 (maxillipedal) epipod' / present absent, 44 'Thoracopod 1 (maxillipedal) epipod' / 'short, linear (or in Isopoda not expanded into branchial cavity)' expanded_into_branchial_cavity, 45 'Thoracopod thorax-coxa articulation' / thorax_and_coxa_articulating_on_transverse_hinge thorax_and_coxa_articulating_in_anteroposterior_axis coxa_immobilised, 46 'Thoracopod coxa-basis articulation' / dicondylic_along_anteroposterior_axis monocondylic, 47 'Thoracopods, intrabasal articulation' / absent present, 48 Pereopods / with_few_short_setae_on_articles with_row_of_long_setae_on_all_articles, 49 Pereopodal_unguis / 'short, curved' 'long, setiform', 50 Thoracopodal_Exopods_on_any_limb / present absent, 51 'Thoracopod 1 (maxillipedal) exopod' / present absent, 52 'Thoracopod 1 (maxillipedal) exopod' / linear with_expanded_basal_section, 53 'Thoracopod 2 (pereopod 1) exopod' / present absent, 54 'Thoracopod 3-4 (pereopods 2-3) exopods' / 'of at least 3-4 articles' of_2_articles, 55 'Thoracopod 5 (pereopod 4) exopod of female ' / 'of 2 (or more) articles ' of_1_article, 56 'Thoracopod 6 (pereopod 5) exopod' / 'of at least 2-4 articles' of_1_article, 57 'Thoracopod 7 (pereopod 6) exopod' / present absent, 58 'Thoracopod 7 (pereopod 6) exopod' / 'of at least 2-4 articles' of_1_article, 59 'Thoracopod 8 (pereopod 7) exopod' / present absent, 60 'Thoracopod 5-7 (pereopods 4-6) basis, pedunculate setae' / absent '2-3 present', 61 'Thoracopodal epipods (oostegites excluded)' / absent present, 62 Thoracopodal_epipods / 'one or two, linear' 'two or three (complex branchiae)' one_coxal_gill, 63 Oostegites / absent present, 64 Oostegites / with_marginal_setae without_marginal_setae, 65 'Oostegite on thoracopod 2 (pereopod 1)' / present absent, 66 'Oostegite on thoracopod 7 (pereopod 6)' / present absent, 67 'Pleopods 1-5' / 'well developed, biramous' 'small, uniramous (or further reduced)', 68 Pleopodal_sexual_dimorphism / 'Pleopods in males reduced or absent, at least posteriorly' Pleopods_1_and_2_forming_petasma_in_male Pleopods_undifferentiated Pleopod_2_of_male_differentiated, 69 Male_pleopod_2_endopod / undifferentiated 'single non-setose article' with_appendix_masculina, 70 Pleopodal_exopods / annulate of_2_articles of_1_article obsolete, 71 Uropodal_rami / 'flattened (most setae on lateral margins)' 'styliform (most setae on upper margin)', 72 Uropod_endopod / of_1_article of_2_articles of_3_or_more_articles, 73 Uropodal_exopod / of_2_articles of_only_1_article, 74 Uropodal_exopodal_proximal_article / longer_than_distal_article shorter_than_distal_, 75 Telson / not_fused_to_pleonite_6 fused_to_pleonite_6, 76 Embryo_flexion / ventral dorsal, 77 Yolk_in_posterior_part_of_embryo / none present, 78 Development_of_appendages / advanced_development_of_anterior_head_appendages continuous_anteroposterior_decrease_in_degree_of_appendage_formation_, 79 'Manca stage (juvenile lacking p7)' / absent present, 80 Dorsal_frontal_organ / absent present, 81 Ventral_frontal_organ / absent present, 82 Foregut_shape / anterior_section_of_similar_dimension_to_posterior anterior_section_enlarged, 83 'Foregut, dorsolateral and midventral ridges' / with_setae with_teeth_or_ossicles, 84 'Foregut, fine filter channels' / 1_or_2 numerous, 85 'Foregut, superomedianum' / absent present, 86 'Foregut, entoderm plates' / unpaired paired, 87 'Foregut, dorsal caeca' / absent present, 88 arterial_system / arteries_arising_only_from_anterior_and_posterior_ends_of_heart several_segmental_arteries_arising_from_heart, 89 'Heart, arteria subneuralis' / absent present, 90 Spermatophore / present absent, 91 'Sperm, cross-striated perforatorium' / absent present '/' ; MATRIX Bathynellacea 21111121?2?2221111-1211212-511111112-11---2-1111111112221211211---23-4211121?11??1?????112? Anaspidacea 211111222111122111-11111111111111112-21111111111111111111111211---12-1111111111211112121121 Dendrobranchiata 222141221111112112111111111111211111231---121111111212221211221---12-3111111111222222121211 Caridea 221241221111112112111111111111211111231---121111111211111111221---1413111111111222222121211 Euphausiacea 212241222111111112111111111111211111111---121111111122221111221---12-3111111111122222121211 Mysida 21222222212111211212121112-1112111111(1 3)1---1221211111211111112121111(1 4)111111112111122122212(1 2)2 Lophogastrida 212222222121111112121211112111111111111---2-21211111111111112221111(1 4)11111111?11111222?21222 Thermosbaenacea 1122211??1?1121?2--122211111112211111211111232111111121111111-1---23-211111121(1 2)??1112221122 Spelaeogriphus 2122211??1?11??21221222112-212?222-2-21222123211112-122212211-2?12141311111???????????????2 Potiicoara 2122211??1?11??21211222112-312?222-2-21221113211112-122212211-2?12142311121???????????????? Mangkurtu 2122211??1?112121211222112-212?22112-21222113211112-122212121-22121423111112??2???????????2 Mictocaris 1112211??1?22??11221222112-311?11112-211112-3211112-12112-221-22122414121212??2???????????? Hirsutia 1112211??2?22?111221222222-421?11122-221112-3212212-211111221-212124?4231?1???????????????? Thetispelecaris 1112211??2?222111221222222-421?11122-221112-3212212-111111221-21212??4231?1???2??1????????? Cumacea 12123111?22222112--112211121111112-1141---1232111111211111211-221211-22211(1 2)2222111112?12122 Tanaidacea 111221112(1 2)22211111-112212121111112-2-21111123211112-111111111-221213-2231?22222111112212122 Isopoda 23----1122231211122112{1 2}112-2211112-2-2111111221112---------11-22111432212-22222111112212222 Amphipoda 13----112(1 2)2111112--112111111112112-2-211112-321112---------123212213-1221111221111111222122 ; END; BEGIN TREES; Title Use_Trees_from_Separate_NEXUS_File; LINK Taxa = 'Poore 2005, no fossils'; TRANSLATE 1 Bathynellacea, 2 Anaspidacea, 3 Dendrobranchiata, 4 Caridea, 5 Euphausiacea, 6 Mysida, 7 Lophogastrida, 8 Thermosbaenacea, 9 Spelaeogriphus, 10 Potiicoara, 11 Mangkurtu, 12 Mictocaris, 13 Hirsutia, 14 Thetispelecaris, 15 Cumacea, 16 Tanaidacea, 17 Isopoda, 18 Amphipoda; TREE PAUP_1 = (1,(2,(((3,4),5),((6,7),(8,((((9,(10,11)),17),((12,(13,14)),(15,16))),18)))))); TREE PAUP_2 = (1,(2,(((3,4),5),((6,7),(8,((((((9,(10,11)),17),(12,(13,14))),15),16),18)))))); TREE PAUP_3 = (1,(2,(((3,4),5),((6,7),(8,((((((9,(10,11)),17),(12,(13,14))),16),15),18)))))); TREE PAUP_4 = (1,(2,(((3,4),5),((6,7),(8,((((9,(10,11)),17),(((12,(13,14)),16),15)),18)))))); TREE PAUP_5 = (1,(2,(((3,4),5),((6,7),(8,((((9,(10,11)),17),(((12,(13,14)),15),16)),18)))))); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 91; END; BEGIN NOTES; TEXT CHARACTER = 50 TEXT = 'This addresses the unfounded strength of the exopod absent state - if scored absent here, all other characters for that taxon becomes inapplicable^n^n '; AN C = 2 A = Buz DC = 2008.3.11.12.44.55 DM = 2009.5.1.12.20.32 ID = Buz1189b82fb103 I = _ TF = (CM '"involves 2 or more" is too vague as the carapace of Cumaceans is quite different from Tanaids^nAdded a state for no shield as in carapaceless taxa') ; AN C = 5 A = Buz DC = 2009.5.21.11.35.52 DM = 2009.5.21.11.35.56 ID = Buz12160cf63cd37 I = _ TF = (CM 'composition of chrs 2-5 should be re-examined. Chr 5 mixes segmental homologies of pereonal pleural folds. ^n') ; AN C = 12 A = Buz DC = 2009.5.21.11.39.25 DM = 2009.5.21.11.39.40 ID = Buz12160d2a26d38 I = _ TF = (CM 'Isopods were scored AI exopod multiarticulate (as in Amphipods), whereas in a few it is only a single rudimentary article, most taxa lack it altogether (Brusca & Wilson (1991); personal observations) ') ; AN C = 16 A = Buz DC = 2009.5.1.12.13.57 DM = 2009.5.1.12.15.10 ID = Buz120f9f3105c82 I = _ TF = (CM 'Because the protopod is not identified here, the scoring is uncertain. Given the scoring, one can assume that Poore means article 4 and 5, not article 3 and 4 (article 1 is missing in many taxa). ') ; AN C = 17 A = Buz DC = 2009.5.21.11.40.24 DM = 2009.5.21.11.40.26 ID = Buz12160d3889739 I = _ TF = (CM 'Antenna outer ramus absent, but it is present in isopods! and should be scored in chr 18 & 19') ; AN C = 18 A = Buz DC = 2009.5.21.11.41.43 DM = 2009.5.21.11.41.54 ID = Buz12160d4bf2341 I = _ TF = (CM '?linear? and ?scale-like? are debatable, as most asellotans, where present, have a exite that is scale-like ^n') ; AN C = 19 A = Buz DC = 2009.5.21.11.42.32 DM = 2009.5.21.11.43.18 ID = Buz12160d57b8e42 I = _ TF = (CM 'use of ?peduncle? renders this character equivocal as homologous landmarks are not being discussed. R^n') ; AN C = 24 A = Buz DC = 2009.5.21.11.45.8 DM = 2009.5.21.11.45.12 ID = Buz12160d7dcfd43 I = _ TF = (CM 'lateral and distal setae are not homologous states. Character should be split into two binary characters, but also note that both can occur in isopods ') ; AN C = 25 A = Buz DC = 2009.5.1.12.9.22 DM = 2009.5.1.12.9.26 ID = Buz120f9eedf8c78 I = _ TF = (CM paragnaths) ; AN C = 28 A = Buz DC = 2009.5.21.11.46.17 DM = 2009.5.21.11.46.20 ID = Buz12160d8ec2b44 I = _ TF = (CM 'maxillula - what is meant by ?proximal endite?? If inner lobe, this is misscored for isopods and other taxa. ^n') ; AN C = 34 A = Buz DC = 2009.5.21.11.47.18 DM = 2009.5.21.11.47.21 ID = Buz12160d9dc1945 I = _ TF = (CM 'debatable, as the maxilla has 3 lobes, each representing a segment. This would put the most lateral lobe as the endite of the third article, which would be definitely endopodal. ^n') ; AN C = 38 A = Buz DC = 2009.5.21.11.48.20 DM = 2009.5.21.11.48.40 ID = Buz12160dacdfb46 I = _ TF = (CM could_be_split_into_characters_for_each_limb._Also_state_3_overlaps_state_4_) ; AN C = 46 A = Buz DC = 2009.5.1.12.1.5 DM = 2009.5.21.11.49.49 ID = Buz120f9e74a7275 I = _ TF = (CM 'oversimplified, amphipods and mysidaceans have a modifed state on some legs. This character has been misinterpreted, as the coxa is not immobilised but flexes on the anterior posterior axis as in Mysidacea. Delete state 3, assign all of peracarids to state 2 ^n') ; AN C = 52 A = Buz DC = 2009.5.1.11.37.40 DM = 2009.5.1.11.37.59 ID = Buz120f9d1d72c69 I = _ TF = (CM 'New cnaracter introduced to avoid incompatible character states^n') ; AN C = 59 A = Buz DC = 2009.5.21.11.52.59 DM = 2009.5.21.11.53.9 ID = Buz12160df0cf547 I = _ TF = (CM 'exopod ThVIII originally scored absent for iso/amph and other taxa. even in Kalliapseudes mancas ThVIII lacks the exopod. ^n') ; AN C = 68 A = Buz DC = 2009.5.21.11.55.56 DM = 2009.5.21.11.56.10 ID = Buz12160e1c32b48 I = _ TF = (CM 'Chr 70 mixes states from pleopods I and II, which are not part of the same homologous character ^n') ; AN C = 71 A = Buz DC = 2009.5.21.11.58.21 DM = 2009.5.21.11.58.24 ID = Buz12160e3f75150 I = _ TF = (CM 'Chr 73 runs in to the problem that the terminals are ground patterned, whereas both states occur in both amphipods and isopods ^n^n') ; AN C = 72 A = Buz DC = 2009.5.21.11.58.55 DM = 2009.5.21.11.59.9 ID = Buz12160e47ef051 I = _ TF = (CM 'Chr 74 misses that Hirsutiids have a multiarticulate endopod, and certain Cumacea have three ') ; AN C = 73 A = Buz DC = 2009.5.1.11.51.54 DM = 2009.5.21.12.0.2 ID = Buz120f9dee0f173 I = _ TF = (CM 'This character was modified because uropodal expods are not greater than 2 articles in the peracarids. The endopods, however, can be multiarticulate in a few taxa, like Cumacea, Tanaidacea, Hirsutiidae') ; AN C = 83 A = Buz DC = 2009.5.21.11.32.5 DM = 2009.5.21.11.32.9 ID = Buz12160cbea3633 I = _ TF = (CM 'not certain about whether one can see a distinct separation between ?setae? (probably spines), and ?teeth or ossicles?. Strictly speaking setae do not occur on the lining of the fore gut. ') ; AN C = 85 A = Buz DC = 2009.5.21.11.32.37 DM = 2009.5.21.11.32.40 ID = Buz12160cc688e34 I = _ TF = (CM 'Foregut, superomedianum is listed as absent for for iso/amph only, but I think that it is present in the isopods as the valvula esophagus dorsalis. This char is from Richter & Scholtz, but Kobusch in the thesis (p.144) agrees with my position: "The mediodorsal invagination described for Mesamphlsophus capensis (Isopoda, Phreatoicidea) was thought to be a valvula dorsalis oesophagi (Wagele, 1987: 28-29, 1989). However, the location of this infolding is definitely not an invagination of the esophageal passage at the cardio esophageal transition, but a mediodorsal invagination of the cardiac chamber, posterior to the anterodorsal apodemes (Fig. 59; ADA, SM). Therefore - in relation to all the other peracaridan superomediana - this infolding has to be interpreted as superomedianum, too." ( Kobusch 1999:144) ^n') ; AN C = 88 A = Buz DC = 2009.5.1.11.46.54 DM = 2009.5.1.11.47.29 ID = Buz120f9da4d9e72 I = _ TF = (CM Haemocircirculatory_system_characters_need_to_be_updated_with_data_from_Wirkner_&_Richter) ; AN C = 89 A = Buz DC = 2009.5.21.11.33.22 DM = 2009.5.21.11.33.28 ID = Buz12160cd18a435 I = _ TF = (CM 'isopods scored as having arteria subneuralis, but see Wirkner & Richter 2002 ') ; AN C = 90 A = Buz DC = 2008.3.11.13.29.16 DM = 2009.5.21.11.34.7 ID = Buz1189bab97ea13 I = _ TF = (CM 'not sure what this means as the peracarid sperm comes in bundles with a protein cap. ?Spermatophore? includes nonhomologous states and appears to be misscored throughout. ^n') ; AN C = 91 A = Buz DC = 2008.3.11.13.27.16 DM = 2009.5.21.11.34.41 ID = Buz1189ba9c28e12 I = _ TF = (CM 'I have to assume that this means the acrosomal process - or pseudoflagellum, in which case much of this was misscored. Not certain what Poore (2005) means by cross-striated perforatorium but if he means Wirth''s ?pennant sperm? this is present in all peracarids. ^n') ; AN T = 18 C = 1 A = Buz DC = 2009.5.1.12.21.44 DM = 2009.5.1.12.21.59 ID = Buz120f9fa31dc84 I = _ TF = (CM see_Phreatoicidea_) ; AN T = 16 C = 2 A = Buz DC = 2008.3.11.12.45.36 DM = 2008.3.11.12.46.30 ID = Buz1189b839a2e4 I = _ TF = (CM 'Involves 2 or more is wrong for tanaids as it is the same as Hirsutia and Thetispelicaris. Scored first only, although this is not exactly correct either as T2 is involved in all three taxa.') ; AN T = 16 C = 5 A = Buz DC = 2008.3.11.12.42.54 DM = 2008.3.11.12.43.52 ID = Buz1189b81215e2 I = _ TF = (CM 'Poore 2005 says thoracomeres 2-6 but this is wrong, as Hirsutia and Thetispelicaris have exactly the same state as Tanaids') ; AN T = 16 C = 12 A = Buz DC = 2009.5.1.12.17.18 DM = 2009.5.1.12.17.39 ID = Buz120f9f620c983 I = _ TF = (CM antennular_lateral_ramus_is_fairly_small_in_most_tanaids) ; AN T = 17 C = 12 A = Buz DC = 2008.3.11.12.49.29 DM = 2008.3.11.12.50.52 ID = Buz1189b8728956 I = _ TF = (CM 'Poore 2005 has the antennular exite as multiarticulate, but this is wrong!^n^nScored as fewer than 10 articles but in actuality it needs to be scored rudimentary (one nubbin)') ; AN T = 18 C = 12 A = Buz DC = 2008.3.11.12.49.23 DM = 2008.3.11.12.49.23 ID = Buz1189b87121f5 I = _ TF = (CM ) ; AN T = 18 C = 17 A = Buz DC = 2008.3.11.12.52.51 DM = 2008.3.11.12.53.49 ID = Buz1189b8a3e417 I = _ TF = (CM 'Another miscoring! Poore 2005 lists antennal exit absent, whereas it is present! Rescored to present, and adjusted subsequent characters^n^n^n^n') ; AN T = 17 C = 18 A = Buz DC = 2009.5.21.11.40.40 DM = 2009.5.21.11.40.44 ID = Buz12160d3c8ec40 I = _ TF = (CM 'Antenna outer ramus absent, but it is present in isopods! and should be scored in chr 18 & 19') ; AN T = 17 C = 23 A = Buz DC = 2009.5.1.12.11.2 DM = 2009.5.21.11.44.26 ID = Buz120f9f0640981 I = _ TF = (CM both_conditions_are_observed_in_Phreatoicidea_and_Asellota._Original_data_had_lacinia_&_spine_row_misscored_for_isopods._) ; AN T = 18 C = 23 A = Buz DC = 2009.5.1.12.10.57 DM = 2009.5.1.12.10.57 ID = Buz120f9f052c380 I = _ TF = (CM ) ; AN T = 16 C = 25 A = Buz DC = 2009.5.1.12.9.51 DM = 2009.5.1.12.10.8 ID = Buz120f9ef4ec079 I = _ TF = (CM changed_to_observed_condition) ; AN T = 17 C = 25 A = Buz DC = 2009.5.1.12.9.17 DM = 2009.5.1.12.9.17 ID = Buz120f9eecc0477 I = _ TF = (CM ) ; AN T = 17 C = 29 A = Buz DC = 2009.5.1.12.7.37 DM = 2009.5.1.12.7.44 ID = Buz120f9ed424776 I = _ TF = (CM See_Phreatoicidea_and_Asellota) ; AN T = 17 C = 45 A = Buz DC = 2009.5.1.11.36.36 DM = 2009.5.1.11.37.14 ID = Buz120f9d0df8e68 I = _ TF = (CM The_coxa_is_free_to_move_in_many_basal_isopods._Only_in_the_more_derived_groups_do_you_see_a_completely_immobilised_coxa) ; AN T = 17 C = 64 A = Buz DC = 2008.3.11.15.16.48 DM = 2009.5.1.11.58.41 ID = Buz1189c0e0a1015 I = _ TF = (CM 'amphipods have marginal setae and I know isopods don''t') ; AN T = 18 C = 64 A = Buz DC = 2008.3.11.15.16.9 DM = 2008.3.11.15.16.32 ID = Buz1189c0d6fe314 I = _ TF = (CM 'I''ll have to check but I think amphipods have marginal setae and I know isopods don''t') ; AN T = 17 C = 66 A = Buz DC = 2009.5.1.11.57.58 DM = 2009.5.1.11.58.20 ID = Buz120f9e46f3e74 I = _ TF = (CM 'although true for some advanced groups, it is absent in the Phreatoicidea and Asellota^n') ; AN T = 16 C = 68 A = Buz DC = 2008.3.11.13.5.14 DM = 2008.3.11.13.14.5 ID = Buz1189b9594d89 I = _ TF = (CM 'Poore 2005 scored this as 1 reduced or absent, whereas the pleopods are more present in males than in females, rescored to 3') ; AN T = 17 C = 68 A = Buz DC = 2008.3.11.13.3.40 DM = 2008.3.11.13.14.23 ID = Buz1189b94279c8 I = _ TF = (CM 'Poore 2005 scored 2 (petasma) whereas isopods basally have only pleopod II modified in the male. Rescored to 4, pl II differentiated^n^n') ; AN T = 12 C = 71 A = Buz DC = 2008.3.11.13.22.59 DM = 2008.3.11.13.24.16 ID = Buz1189ba5d53e10 I = _ TF = (CM 'This was scored styliform, but as defined (setae on lateral margins) Mictocaris has flattened rami') ; AN T = 17 C = 71 A = Buz DC = 2008.3.11.12.24.45 DM = 2008.3.11.13.15.43 ID = Buz1189b7083962 I = _ TF = (CM '^n') ; AN T = 18 C = 79 A = Buz DC = 2008.3.11.13.24.58 DM = 2009.5.21.12.1.12 ID = Buz1189ba7a61611 I = _ TF = (CM 'manca was scored present and absent here, whereas amphipods do not have a manca') ; AN T = 17 C = 85 A = Buz DC = 2009.5.1.11.45.33 DM = 2009.5.1.11.45.43 ID = Buz120f9d911c270 I = _ TF = (CM 'See Kobusch (1999) thesis') ; AN T = 17 C = 88 A = Buz DC = 2009.5.1.11.46.46 DM = 2009.5.1.11.46.50 ID = Buz120f9da2cd771 I = _ TF = (CM circ) ; AN T = 11 C = 91 A = Buz DC = 2009.5.21.11.34.54 DM = 2009.5.21.11.34.58 ID = Buz12160ce7f4936 I = _ TF = (CM personal_observations) ; AN ST = 0 C = 1 A = Buz DC = 2009.5.21.11.57.52 DM = 2009.5.21.11.57.55 ID = Buz12160e3872249 I = _ TF = (CM 'this term needs definition. It is used in old-fashioned taxonomy, but what it means precisely is unclear.') ; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord; TYPESET * UNTITLED = unord: 1 - 91; TYPESET untitled = unord: 1 - 91; END; begin PAUP; log file = Poore_modified.out; SET MSTAXA = POLYMORPH TCOMPRESS = YES INCREASE = AUTO TAXLABELS = FULL TORDER = RIGHT OUTROOT = MONOPHYL AUTOCLOSE = YES; outgroup 1 2; cstatus full; set maxtrees = 1000 increase = no; pset mstaxa = polymorph; hsearch addseq = random nchuck = 3 chuckscore = 1 nreps = 1000 randomize = trees; hsearch start = current nchuck = 0 chuckscore = 0; savetrees file = Poore_modified.tre; describetrees 1 / outroot = polytomy apolist = yes; describetrees 1; contree / majrule = no treefile = Poore_modified_con.tre; log stop; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 91; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 9183389056920785940; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7844763347885263202; tell It; setDefaultOrder 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 45 46 47 48 49 50 51 42 43 44 52 54 56 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93; attachments ; endTell; checksumv 0 2 3382251345 null; endTell; getWindow; tell It; suppress; setResourcesState false false 8; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 946; setLocation -4 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.ManageTrees.ManageTrees; tell It; showTreeBlocks #mesquite.lists.TreeblockList.TreeblockList; tell It; getWindow; tell It; newAssistant #mesquite.lists.TreeblocksListNumber.TreeblocksListNumber; newAssistant #mesquite.lists.TreeblocksListTaxa.TreeblocksListTaxa; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1272 879; setLocation -4 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #9183389056920785940 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1153.1241144773703.8953014664182634806; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1272 879; setLocation -4 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientRight; toggleCorners off; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setFontSize 24; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 3; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; newAssistant #mesquite.ancstates.TraceCharOverTrees.TraceCharOverTrees; tell It; suppress ; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #7844763347885263202; endTell; endTell; setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; toggleMPRsMode off; endTell; endTell; setCharacter 1; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setNumTrees 100; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels off; toggleGray off; endTell; toggleShowLegend on; toggleShowNodeAbsent on; toggleShowEquivocal on; setMode Count_Trees_with_Uniquely_Best_States; setInitialOffsetX 337; setInitialOffsetY -419; setLegendWidth 142; setLegendHeight 196; desuppress ; endTell; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #7844763347885263202 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1272 879; setLocation -4 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; colorCells #mesquite.charMatrices.NoColor.NoColor; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleShowDefaultCharNames off; toggleConstrainCW on; setColumnWidth 16; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor; tell It; makeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1272 879; setLocation -4 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam; endTell; rowsAreCharacters on; toggleConstrainChar on; toggleConstrainCharNum 3; togglePanel on; toggleSummaryPanel off; endTell; showWindow; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel on; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.silk.AnnotSummary.AnnotSummary; tell It; togglePanel off; endTell; getEmployee #mesquite.silk.CellImages.CellImages; tell It; showColors off; togglePanel off; toggleAnnotations off; toggleSums off; toggleHistory off; toggleLocations off; endTell; getEmployee #mesquite.silk.StateImages.StateImages; tell It; showColors off; togglePanel off; toggleStateAnnotations off; toggleCharAnnotations off; toggleLocations off; endTell; getEmployee #mesquite.silk.aaManageImageIndices.aaManageImageIndices; tell It; setLocal; reset; endTell; getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; endTell; end;