X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fdata%2Ftol_156.xml;h=40a316f2031b303d053a1f3fd26b28a8a7bf045a;hb=d7cffe43f06ee91484ca0d5fba57b9bc78fdb0f7;hp=1219c70ca57f43c94635fa0459be5df4caba8b94;hpb=10e9474a4613157a625a7d4596c40a9faccaf5cb;p=jalview.git
diff --git a/forester/data/tol_156.xml b/forester/data/tol_156.xml
index 1219c70..40a316f 100644
--- a/forester/data/tol_156.xml
+++ b/forester/data/tol_156.xml
@@ -1579,9 +1579,13 @@
50557
Insecta
- true insects
class
+
+ Advances in Insect Phylogeny at the Dawn of the Postgenomic Era
+
+
+
33340
@@ -1592,12 +1596,18 @@
33392
Endopterygota
+ Holometabola
infraclass
- Hymenoptera & Lepidoptera & Diptera
+ Mecopterida & Neuropteroidea
- Lepidoptera & Diptera
+
+ Mecopterida
+
+
+ The position of the Hymenoptera within the Holometabola as inferred from the mitochondrial genome of Perga condei
+
7147
@@ -1812,8 +1822,8 @@
- 104431
- Obtectomera
+ 37567
+ Ditrysia
@@ -1840,97 +1850,176 @@
- 7400
- Apocrita
- wasps, ants and bees
+ 41088
+ Cucujiformia
+ infraorder
- 7434
- Aculeata
- suborder
+ 217634
+ ANOGL
+ Anoplophora glabripennis
+ Asian longhorn beetle
+ Anoplophora nobilis
+ species
+ http://bugguide.net/images/cache/WZMLBZXL2Z2HTH4HHR2H3H2HJH9H9Z5LJH5LWZ7LAZSLTH4HPZXHDHKLVZEH9ZEHRRPHJH7LAZPHZR4L3H7H3H9HZR.jpg
+
+
+
+
+ 7070
+ TRICA
+ Tribolium castaneum
+ Red flour beetle
+ species
+ http://upload.wikimedia.org/wikipedia/commons/d/da/Tribolium_castaneum.jpg
+
+
+
+
+
+
+ 7400
+ Apocrita
+ wasps, ants and bees
+
+
+
+ 7434
+ Aculeata
+ suborder
+
+
+
+ 36668
+ Formicidae
+ family
- 36668
- Formicidae
- ants
- family
+ 34695
+ Myrmicinae
+ subfamily
- 143999
- Attini
- tribe
+ 12957
+ ATTCE
+ Atta cephalotes
+ Linnaeus, 1758
+ Leafcutter ant
+ species
+ http://upload.wikimedia.org/wikipedia/commons/4/4e/Leaf-cutting_ant.jpg
-
-
- 12957
- ATTCE
- Atta cephalotes
- Linnaeus, 1758
- Leafcutter ant
- species
- http://upload.wikimedia.org/wikipedia/commons/4/4e/Leaf-cutting_ant.jpg
-
-
-
-
- 103372
- ACREC
- Acromyrmex echinatior
- Forel, 1899
- Panamanian leafcutter ant
- Acromyrmex octospinosus echinatior
- species
- http://hymenopteragenome.org/acromyrmex/sites/hymenopteragenome.org.acromyrmex/files/Acromyrmex_echinatior2.jpg
-
-
- 104421
- CAMFO
- Camponotus floridanus
- Buckley, 1866
- Florida carpenter ant
+ 103372
+ ACREC
+ Acromyrmex echinatior
+ Forel, 1899
+ Panamanian leafcutter ant
+ Acromyrmex octospinosus echinatior
species
- http://bugguide.net/images/cache/5RLH6RRHXRALZZ9LZZ6L3LBLXZBL2RFZHZ9L7ZKH4RDZ3L3Z2RZHKZCLMZKH4R0H6R3Z6RSHMZBL5RRH5ROLKZELLZ.jpg
+ http://hymenopteragenome.org/acromyrmex/sites/hymenopteragenome.org.acromyrmex/files/Acromyrmex_echinatior2.jpg
- 7460
- APIME
- Apis mellifera
- Honeybee
+ 104421
+ CAMFO
+ Camponotus floridanus
+ Buckley, 1866
+ Florida carpenter ant
species
- http://www.floridanature.org/photos/Apis_mellifera_6b_&_Trifolium_sp.,_TBP,_Tallahassee,_20030323.jpg
+ http://bugguide.net/images/cache/5RLH6RRHXRALZZ9LZZ6L3LBLXZBL2RFZHZ9L7ZKH4RDZ3L3Z2RZHKZCLMZKH4R0H6R3Z6RSHMZBL5RRH5ROLKZELLZ.jpg
- 7425
- NASVI
- Nasonia vitripennis
- Parasitic wasp
+ 7460
+ APIME
+ Apis mellifera
+ Honeybee
species
- http://www.freshpond.org/nasonia.jpg
+ http://www.floridanature.org/photos/Apis_mellifera_6b_&_Trifolium_sp.,_TBP,_Tallahassee,_20030323.jpg
+
+
+ 7425
+ NASVI
+ Nasonia vitripennis
+ Parasitic wasp
+ species
+ http://www.freshpond.org/nasonia.jpg
+
+
- 7070
- TRICA
- Tribolium castaneum
- Red flour beetle
- species
- http://upload.wikimedia.org/wikipedia/commons/d/da/Tribolium_castaneum.jpg
+ 33341
+ Orthopteroidea
+ infraclass
+
+
+ 6970
+ Dictyoptera
+ superorder
+
+
+
+ 6973
+ BLAGE
+ Blattella germanica
+ German cockroach
+ Blatta germanica
+ species
+ http://www.biopix.com/photosmedium/Blattella%20germanica%2000017.JPG
+
+
+
+
+ 136037
+ ZOONE
+ Zootermopsis nevadensis
+ Dampwood termite
+ species
+ http://bugguide.net/images/cache/GQA0PQ10VQPK4KAKRKWKSKEKLKWKPQZS5KBK1QCK7KJ05KOK8KAKRK9K4QUK6Q10RKWKHKT02QWKSKEK5Q9KPQD0PQ.jpg
+
+
+
+
+
+ 6993
+ Orthoptera
+ order
+
+
+
+ 7009
+ SCHAM
+ Schistocerca americana
+ American grasshopper
+ species
+ http://bugguide.net/images/cache/BH7HOHIHZRZLAZXLVZQL4ZKL4Z4H6Z4HRRNHLR5HZR2HAHGHAHSLAHKL1H7HDH7H3HUH1ZXLUZGL3H2HAHZLAHXH.jpg
+
+
+
+
+ 51074
+ GRYPE
+ Gryllus pennsylvanicus
+ Field cricket
+ species
+ http://bugguide.net/images/raw/GL9Z5L9Z8LJHWHHR6HRREHVZUHCHIH8Z7HVHMHGZ7HTHQL6ZXHOHWH3H5LUZ7L9ZRLVH5HDHQL.jpg
+
+
+
@@ -1947,6 +2036,32 @@
+ 33351
+ Panheteroptera
+
+
+
+ 7536
+ ONCFA
+ Oncopeltus fasciatus
+ Large milkweed bug
+ species
+ http://bugguide.net/images/cache/309QLSWQT0IKUKSK2KSKUKRKUKGKBKRKNK6QD05QC05Q6KZKPKGQD00K9KGQ2KLKWK8QV0KKO0EQV0EQNK8Q2KGQ10.jpg
+
+
+
+
+ 13249
+ RHOPR
+ Rhodnius prolixus
+ Triatomid bug
+ species
+ http://upload.wikimedia.org/wikipedia/commons/b/b9/Rhodnius_prolixus.jpg
+
+
+
+
+
7029
ACYPI
Acyrthosiphon pisum
@@ -1955,16 +2070,6 @@
http://www.agroatlas.ru/content/pests/Acyrthosiphon_pisum/Acyrthosiphon_pisum.jpg
-
-
- 13249
- RHOPR
- Rhodnius prolixus
- Triatomid bug
- species
- http://upload.wikimedia.org/wikipedia/commons/b/b9/Rhodnius_prolixus.jpg
-
-
@@ -2241,6 +2346,9 @@
roundworms
phylum
+
+ Nematodes: The Worm and Its Relatives
+
119089
@@ -2250,119 +2358,205 @@
- nematode Clade V
+ nematode clades IV and V
-
- 6237
- Caenorhabditis
- genus
-
-
- Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss
-
+ nematode clade V
- CAEBR & CAERE & CAEBE & CAEEL
+
+ 6236
+ Rhabditida
+ order
+
- CAEBR & CAERE & CAEBE
+
+ 6237
+ Caenorhabditis
+ genus
+
+
+ Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss
+
- CAEBR & CAERE
+ CAEBR & CAERE & CAEBE & CAEEL
+
+ 6238
+ Caenorhabditis briggsae
+ species
+
+ CAEBR & CAERE & CAEBE
6238
- CAEBR
Caenorhabditis briggsae
species
- http://www.life.umd.edu/biology/haag/briggsae_herm.jpg
+
+ CAEBR & CAERE
+
+ 6238
+ Caenorhabditis briggsae
+ species
+
+
+
+ 6238
+ CAEBR
+ Caenorhabditis briggsae
+ species
+ http://www.life.umd.edu/biology/haag/briggsae_herm.jpg
+
+
+
+
+ 31234
+ CAERE
+ Caenorhabditis remanei
+ Caenorhabditis vulgaris
+ species
+ http://lemur.amu.edu.pl/share/php/mirnest_1.0/species_images/Caenorhabditis_remanei.jpg
+
+
+
+
+
+ 135651
+ CAEBE
+ Caenorhabditis brenneri
+ Nematode worm
+ Caenorhabditis CB5161
+ species
+
+
- 31234
- CAERE
- Caenorhabditis remanei
- Caenorhabditis vulgaris
+ 6239
+ CAEEL
+ Caenorhabditis elegans
species
- http://lemur.amu.edu.pl/share/php/mirnest_1.0/species_images/Caenorhabditis_remanei.jpg
+ http://www.easternct.edu/~adams/images/celegansmain.jpg
- 135651
- CAEBE
- Caenorhabditis brenneri
- Nematode worm
- Caenorhabditis CB5161
+ 281687
+ CAEJA
+ Caenorhabditis japonica
species
- 6239
- CAEEL
- Caenorhabditis elegans
+ 53326
+ Ancylostoma ceylanicum
species
- http://www.easternct.edu/~adams/images/celegansmain.jpg
- 281687
- CAEJA
- Caenorhabditis japonica
+ 54126
+ PRIPA
+ Pristionchus pacificus
+ Parasitic nematode
species
+ http://smithlabdb.usc.edu/images/Pristionchus_pacificus.jpg
- 54126
- PRIPA
- Pristionchus pacificus
- Parasitic nematode
- species
- http://smithlabdb.usc.edu/images/Pristionchus_pacificus.jpg
+ 189290
+ Meloidogyne
+ genus
+
+
+ 6306
+ MELIC
+ Meloidogyne incognita
+ Southern root-knot nematode
+ species
+
+
+
+
+ 6305
+ MELHA
+ Meloidogyne hapla
+ Root-knot nematode worm
+ species
+
+
-
- 6296
- Onchocercidae
- family
-
+ nematode clade III
- 6279
- BRUMA
- Brugia malayi
- Filarial nematode worm
- species
- http://upload.wikimedia.org/wikipedia/commons/4/4a/Brugia_malayi.JPG
+ 6296
+ Onchocercidae
+ family
+
+
+ 6279
+ BRUMA
+ Brugia malayi
+ Filarial nematode worm
+ species
+ http://upload.wikimedia.org/wikipedia/commons/4/4a/Brugia_malayi.JPG
+
+
+
+
+ 6293
+ WUCBA
+ Wuchereria bancrofti
+ species
+ http://upload.wikimedia.org/wikipedia/commons/a/a9/Wuchereria_bancrofti_1_DPDX.JPG
+
+
+
+
- 6293
- WUCBA
- Wuchereria bancrofti
+ 6253
+ ASCSU
+ Ascaris suum
+ Pig roundworm
+ Ascaris lumbricoides
species
- http://upload.wikimedia.org/wikipedia/commons/a/a9/Wuchereria_bancrofti_1_DPDX.JPG
- 6334
- TRISP
- Trichinella spiralis
- Trichina worm
- species
- http://upload.wikimedia.org/wikipedia/commons/e/e8/Trichinella_larv1_DPDx.JPG
+ 119088
+ Enoplea
+ class
+
+
+ 6334
+ TRISP
+ Trichinella spiralis
+ Trichina worm
+ species
+ http://upload.wikimedia.org/wikipedia/commons/e/e8/Trichinella_larv1_DPDx.JPG
+
+
+
+
+ 319952
+ Enoplus communis
+ species
+
+
@@ -4327,6 +4521,7 @@
91835
fabids
+ eurosids I
Rosales & Cucurbitales & Fabales
@@ -4340,17 +4535,33 @@
- 57918
- FRAVE
- Fragaria vesca
- Woodland strawberry
- Fragaria vesca L.
- European strawberry
- alpine strawberry
- species
- http://www.boga.ruhr-uni-bochum.de/html/Fragaria.vesca.ja6.jpg
- http://caliban.mpiz-koeln.mpg.de/thome/band3/tafel_092_small.jpg
+ 171638
+ Rosoideae
+ subfamily
+
+
+ 57918
+ FRAVE
+ Fragaria vesca
+ Woodland strawberry
+ Fragaria vesca L.
+ European strawberry
+ alpine strawberry
+ Potentilla vesca
+ species
+ http://calphotos.berkeley.edu/imgs/512x768/0000_0000/1106/0659.jpeg
+
+
+
+
+ 211815
+ Rubus fruticosus
+ shrubby blackberry
+ species
+ http://www.plant-identification.co.uk/images/rosaceae/rubus-fruticosus-1.jpg
+
+
@@ -4372,6 +4583,7 @@
Cucumis sativus
Cucumber
species
+ http://bioweb.uwlax.edu/bio203/s2009/olson_eri2/clip_image001.jpg
@@ -4390,6 +4602,7 @@
Soybean
Glycine hispida
species
+ http://upload.wikimedia.org/wikipedia/commons/thumb/e/ef/Soja.jpg/400px-Soja.jpg
@@ -4485,6 +4698,7 @@
Lyre-leaved rock-cress
Arabis lyrata
species
+ http://www.illinoiswildflowers.info/savanna/photos/sand_cress1.jpg
@@ -4494,18 +4708,37 @@
Arabidopsis thaliana
Mouse-ear cress
species
+ http://www.calflora.net/bloomingplants/images/mouseearcress4.jpg
- 98038
- THEHA
- Thellungiella halophila
- Salt cress
- species
- http://mplant.oxfordjournals.org/content/2/1/3/F1.large.jpg
+ 98005
+ Eutrema
+ genus
+
+
+ 98038
+ THEHA
+ Thellungiella halophila
+ Salt cress
+ species
+ http://mplant.oxfordjournals.org/content/2/1/3/F1.large.jpg
+
+
+
+
+ 75806
+ EUTJA
+ Eutrema japonica
+ Wasabi plant
+ Eutrema wasabi
+ species
+ http://aoki2.si.gunma-u.ac.jp/BotanicalGarden/PICTs/wasabi3.jpeg
+
+
@@ -4522,53 +4755,98 @@
- 2706
- Citrus
- genus
+ 41937
+ Sapindales
+ order
- 85681
- CCLXX
- Citrus clementina
- Citrus clementina hort. ex Tanaka
+ 2706
+ Citrus
+ genus
+
+
+
+ 85681
+ CCLXX
+ Citrus clementina
+ Citrus clementina hort. ex Tanaka
+ species
+ http://www.citrusgenomedb.org/sites/default/files/tripal/tripal_organism/images/Citrus_clementina.jpg
+
+
+
+
+ 2711
+ CITSI
+ Citrus sinensis
+ Sweet orange
+ Citrus x sinensis
+ Citrus aurantium var. sinensis
+ species
+ http://www.west-crete.com/flowers/photos/citrus_sinensis-1.jpg
+
+
+
+
+
+ 29780
+ MANIN
+ Mangifera indica
+ Mango
species
- http://www.citrusgenomedb.org/sites/default/files/tripal/tripal_organism/images/Citrus_clementina.jpg
+ http://www.starrenvironmental.com/images/images/plants/600/09/10/starr-091020-8414.jpg
- 2711
- CITSI
- Citrus sinensis
- Sweet orange
- Citrus x sinensis
- Citrus aurantium var. sinensis
+ 151069
+ LITCN
+ Litchi chinensis
+ Lychee
species
- http://www.west-crete.com/flowers/photos/citrus_sinensis-1.jpg
+ http://ars.usda.gov/images/docs/12623_12817/litchi.jpg
- 71139
- EUCGR
- Eucalyptus grandis
- Flooded gum
- species
- http://www.calflora.net/losangelesarboretum/images/eucalyptus_grandis.jpg
+ 41944
+ Myrtales
+ order
+
+
+ 71139
+ EUCGR
+ Eucalyptus grandis
+ Flooded gum
+ species
+ http://www.calflora.net/losangelesarboretum/images/eucalyptus_grandis.jpg
+
+
+
+
+ 22663
+ PUNGR
+ Punica granatum
+ Pomegranate
+ species
+ http://www.biolib.cz/IMG/GAL/14132.jpg
+
+
- 582304
+ 29760
VITVI
Vitis vinifera
Grape
species
+ http://upload.wikimedia.org/wikipedia/commons/f/f2/Vitis-vinifera-2.JPG
@@ -4576,78 +4854,110 @@
91888
lamiids
+ Gentiananae
+ euasterids I
- 4070
- Solanaceae
- family
+ 4069
+ Solanales
+ order
- 4107
- Solanum
- genus
+ 4070
+ Solanaceae
+ family
- 49274
- Lycopersicon
- subgenus
+ 4107
+ Solanum
+ genus
- 4081
- SOLLC
- Solanum lycopersicum
- Tomato
- Lycopersicon esculentum
+ 49274
+ Lycopersicon
+ subgenus
+
+
+
+ 4081
+ SOLLC
+ Solanum lycopersicum
+ Tomato
+ Lycopersicon esculentum
+ species
+ http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0905/1214.jpeg
+
+
+
+
+ 4084
+ SOLPI
+ Solanum pimpinellifolium
+ Currant tomato
+ Lycopersicon pimpinellifolium
+ species
+ http://upload.wikimedia.org/wikipedia/commons/b/b8/Currant_tomato.jpg
+
+
+
+
+
+ 4113
+ SOLTU
+ Solanum tuberosum
+ Potato
species
- http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0905/1214.jpeg
+ http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0508/0344.jpeg
- 4084
- SOLPI
- Solanum pimpinellifolium
- Currant tomato
- Lycopersicon pimpinellifolium
+ 4111
+ SOLME
+ Solanum melongena
+ Eggplant
+ Aubergine
species
- http://upload.wikimedia.org/wikipedia/commons/b/b8/Currant_tomato.jpg
+ http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0905/1170.jpeg
- 4113
- SOLTU
- Solanum tuberosum
- Potato
+ 4097
+ TOBAC
+ Nicotiana tabacum
+ Common tobacco
species
- http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0508/0344.jpeg
+ http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0105/2073.jpeg
- 4097
- TOBAC
- Nicotiana tabacum
- Common tobacco
+ 4120
+ IPOBA
+ Ipomoea batatas
+ Sweet potato
+ Convolvulus batatas
species
- http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0105/2073.jpeg
+ http://www.starrenvironmental.com/images/images/plants/600/05/04/starr-050407-6234.jpg
4155
- MIMGU
- Mimulus guttatus
+ ERYGU
+ Erythranthe guttata
Yellow monkey flower
- Yellow monkey flower
+ Mimulus guttatus
species
+ http://www.laspilitas.com/images/grid24_18/7128/plants/pictures/a1000.jpg
@@ -4669,6 +4979,7 @@
4447
Liliopsida
+ monocotyledons
class
@@ -4745,53 +5056,69 @@
- 4527
- Oryza
- genus
+ 147368
+ Pooideae
+ subfamily
- 4530
- ORYSA
- Oryza sativa
- Rice
- species
+ 147389
+ Triticeae
+ tribe
+
+
+ 112509
+ HORVD
+ Hordeum vulgare var. distichum
+ Two-rowed barley
+ subspecies
+ http://www.missouriplants.com/Grasses/Hordeum_vulgare_plant.jpg
+
+
+
+
+ 4565
+ WHEAT
+ Triticum aestivum
+ Wheat
+ species
+
+
- 39947
- ORYSJ
- Oryza sativa subsp. japonica
- Rice
+ 15368
+ BRADI
+ Brachypodium distachyon
+ Purple false brome
+ Trachynia distachya
+ species
+ http://upload.wikimedia.org/wikipedia/commons/0/01/Brachypodium_distachyon_Bd21-3.jpg
- 147368
- Pooideae
- subfamily
+ 4527
+ Oryza
+ genus
- 15368
- BRADI
- Brachypodium distachyon
- Purple false brome
- Trachynia distachya
+ 4530
+ ORYSA
+ Oryza sativa
+ Rice
species
- http://upload.wikimedia.org/wikipedia/commons/0/01/Brachypodium_distachyon_Bd21-3.jpg
- 112509
- HORVD
- Hordeum vulgare var. distichum
- Two-rowed barley
- subspecies
- http://www.missouriplants.com/Grasses/Hordeum_vulgare_plant.jpg
+ 39947
+ ORYSJ
+ Oryza sativa subsp. japonica
+ Rice
@@ -5048,7 +5375,6 @@
38254
Glaucocystophyceae
- Glaucophyta
class
@@ -5079,7 +5405,8 @@
Emiliania huxleyi
Pontosphaera huxleyi
species
- http://research.kahaku.go.jp/zoology/kaisei/hp-2/images/hapto.jpg
+ http://www.nhm.ac.uk/resources-rx/images/1049/emiliania-huxleyi-light-microscope-image_68318_1.jpg
+ http://cmore.soest.hawaii.edu/education/kidskorner/images/emiliania_600px.jpg
@@ -5667,11 +5994,28 @@
- 71427
- Allogromia laticollaris
- species
- http://forambarcoding.unige.ch/system/pictures/424/s600/A.laticollaris1.jpg
+ 29178
+ Foraminifera
+ foraminifers
+ class
+
+
+ 71427
+ Allogromia laticollaris
+ species
+ http://forambarcoding.unige.ch/system/pictures/424/s600/A.laticollaris1.jpg
+
+
+
+
+ 46433
+ RETFI
+ Reticulomyxa filosa
+ species
+ http://forambarcoding.unige.ch/system/pictures/269/s600/R.filosa2.jpg
+
+