Here is a factoid about Daphnia and Ixodes genes relative to insects: Daphnia has 21% of the best gene matches to human genes, Ixodes is second with 16%, with the best insect (tribolium) at 12%, and the Dipterans (drosophila, mosquitoes) trail at 3% best human gene matches. Considering other eukaroyte models (weed,worm,yeast), Daphnia remains with 21% best gene matches, but Ixodes falls to the insect level of 10%. This suggests Daphnia retains the most ancestral eukaryotic genes. This comes from blast-matching human and 5 other model gene sets from Swissprot to 14 arthropod gene sets. It includes 20000 human genes, 16000 mouse, 9000 weed, 7000 yeast, and 3000 worm genes. These results correspond with other, earlier arthropod x non-arthropod gene comparisons, see below for two such. These agree that Daphnia has about 2 times as many best Human gene orthologs than any insect. :: Don Gilbert, Jan/Feb 2010 BEST Arthropod Gene Matches to Uniprot 6 model organisms Uniprot-Swissprot subset for 6 model species, 2010 January Models: HUMAN, MOUSE, YEAST, ARATH = Arabidopsis, CAEEL = C.elegans, DROME = Drosophila mel. ==> Input Swissprot model genes <== 8823 ARATH 3278 CAEEL 3052 DROME 20276 HUMAN 16214 MOUSE 6912 YEAST blastp -i uniprot_mods1001.fa -d arthropods -e1e-5 -o arp2-unipmod6.blastp ==> Found Swissprot model genes <== 5029 ARATH 2492 CAEEL 3035 DROME 15345 HUMAN 13004 MOUSE 3575 YEAST Table of best match genes counting each arthropod species with bitscore >= 95% of highest bitscore per uniprot gene ngene = number of best match genes agene = proportion of found model genes sumbit = sum of bit scores avebit = average bit score / best genes query source ngene agene sumbit avebit HUMAN daphnia 3286 0.21 1189036 361.84 HUMAN ixodes 2465 0.16 725411 294.28 HUMAN triboli 1969 0.12 660884 335.64 HUMAN apis 1724 0.11 629472 365.12 HUMAN nasonia 1606 0.10 554965 345.55 HUMAN pedicul 1593 0.10 580960 364.69 HUMAN aphid 1286 0.08 371777 289.09 HUMAN aedes 696 0.04 184173 264.61 HUMAN anophel 622 0.04 156518 251.63 HUMAN drosmel 563 0.03 124598 221.31 HUMAN drosmoj 514 0.03 128012 249.05 HUMAN bombyx 479 0.03 97678 203.92 HUMAN culex 410 0.02 98223 239.56 HUMAN drospse 383 0.02 73653 192.3 MOUSE daphnia 2849 0.21 1034228 363.01 MOUSE ixodes 2180 0.16 651179 298.7 MOUSE triboli 1707 0.13 567672 332.55 MOUSE apis 1486 0.11 540619 363.8 MOUSE nasonia 1412 0.10 499058 353.44 MOUSE pedicul 1352 0.10 518101 383.21 MOUSE aphid 763 0.05 195391 256.08 MOUSE aedes 560 0.04 155506 277.68 MOUSE anophel 550 0.04 139306 253.28 MOUSE drosmoj 469 0.03 119250 254.26 MOUSE drosmel 463 0.03 106164 229.29 MOUSE bombyx 428 0.03 89616 209.38 MOUSE culex 368 0.02 91738 249.28 MOUSE drospse 314 0.02 66556 211.96 ARATH daphnia 1004 0.19 207021 206.19 ARATH triboli 524 0.10 100629 192.04 ARATH nasonia 506 0.10 111248 219.85 ARATH aphid 496 0.09 89749 180.94 ARATH apis 482 0.09 103948 215.66 ARATH ixodes 447 0.08 89762 200.81 ARATH pedicul 410 0.08 84654 206.47 ARATH drosmoj 350 0.06 60433 172.66 ARATH drosmel 330 0.06 50919 154.3 ARATH aedes 291 0.05 58683 201.66 ARATH anophel 282 0.05 46710 165.63 ARATH culex 253 0.05 46204 182.62 ARATH drospse 243 0.04 38424 158.12 ARATH bombyx 211 0.04 36630 173.6 CAEEL daphnia 573 0.23 176032 307.21 CAEEL triboli 283 0.11 83790 296.07 CAEEL ixodes 279 0.11 71289 255.51 CAEEL nasonia 249 0.10 90807 364.68 CAEEL apis 235 0.09 76915 327.29 CAEEL pedicul 204 0.08 70302 344.62 CAEEL aphid 166 0.06 43718 263.36 CAEEL drosmoj 137 0.05 35175 256.75 CAEEL anophel 135 0.05 34986 259.15 CAEEL drosmel 134 0.05 34419 256.85 CAEEL aedes 122 0.04 36683 300.68 CAEEL drospse 104 0.04 22190 213.36 CAEEL culex 103 0.04 27587 267.83 CAEEL bombyx 79 0.03 16393 207.51 DROME drosmel 2925 0.96 3183557 1088.39 DROME drospse 54 0.01 24546 454.55 DROME drosmoj 30 0 15328 510.93 DROME triboli 8 0 4557 569.62 DROME nasonia 7 0 3258 465.42 DROME culex 3 0 596 198.66 DROME apis 2 0 417 208.5 DROME aphid 2 0 441 220.5 DROME bombyx 1 0 380 380 DROME aedes 1 0 855 855 YEAST daphnia 714 0.20 160801 225.21 YEAST triboli 403 0.11 102607 254.61 YEAST nasonia 374 0.10 82341 220.16 YEAST ixodes 322 0.09 64085 199.02 YEAST apis 318 0.08 68593 215.7 YEAST pedicul 282 0.07 56938 201.91 YEAST aphid 266 0.07 48694 183.06 YEAST drosmel 220 0.06 38538 175.17 YEAST aedes 202 0.05 44266 219.14 YEAST anophel 195 0.05 36538 187.37 YEAST drosmoj 193 0.05 39726 205.83 YEAST drospse 171 0.04 29670 173.51 YEAST bombyx 171 0.04 31062 181.65 YEAST culex 156 0.04 34289 219.8 # combined HUMAN|CAEEL|ARATH|YEAST at 95% best query source ngene agene sumbit avebit UNIMOD4 daphnia 5577 0.21 1732891 310.72 UNIMOD4 ixodes 3513 0.13 950548 270.58 UNIMOD4 triboli 3179 0.12 947912 298.17 UNIMOD4 apis 2759 0.10 878930 318.56 UNIMOD4 nasonia 2735 0.10 839362 306.89 UNIMOD4 pedicul 2489 0.09 792856 318.54 UNIMOD4 aphid 2214 0.08 553940 250.19 UNIMOD4 aedes 1311 0.04 323806 246.99 UNIMOD4 drosmel 1247 0.04 248476 199.25 UNIMOD4 anophel 1234 0.04 274753 222.65 UNIMOD4 drosmoj 1194 0.04 263347 220.55 UNIMOD4 bombyx 940 0.03 181765 193.36 UNIMOD4 culex 922 0.03 206304 223.75 UNIMOD4 drospse 901 0.03 163938 181.95 #---- Comparison to Other Recent Orthology Analyses ------ I agree with others views that genes counted from matches using blast is not the best way to analyze phylogeny. However, these are for all the genes of these genomes, giving it a bit more strength from numbers, than for instance if it were for one gene family. It is also a straightforward, simple (less costly) and reproducible way to assess orthology for complete gene sets. Here is another look at arthropod x HUMAN genes, using two phylogenetic orthology analyses. However these two use different gene sets, and methods making them not quite comparable to the above. One reason we do not have more current, complete all x all phylogenetic assessments of orthology is the cost in effort to produce those. See http://www.bio.net/bionet/mm/arthropod/2010-February/000038.html http://phylomedb.org/ Acyrthosiphon pisum phylome Toni Gabaldon and colleagues using phylogenetic orthology include 14 recent arthropod genomes up to daphnia, aphid, nasonia, but not ixodes, along with human, worm, ciona outgroups review of methods: http://genomebiology.com/2008/9/10/235 phigs.org, ca 2006-2007 arthropod and eukaryote genomes using phylogenetic orthology methods, Jeff Boore and JGI colleagues, now offline, but I've a subset including Daphnia, several insects, and vertebrates (no ixodes) http://www.biomedcentral.com/1471-2105/7/201 For this summary, I used the alignment trees with gene distance values from the above two data sets. I measured minimum distance between Human genes and each arthropod for each gene tree. Number of Human gene trees with minimum distance to each arthropod (NBest) is tabulated. Average distance per species corresponds in rank order w/ the Nbest count. ABest here corresponds to "agene" in the above tables, as portion of best-match genes per human gene set. The Phylomedb turns out to have a problem for use in this analysis: it was not done as an all x all analysis, but only produced alignment trees that included Aphid genes. To adjust for that, I counted only gene trees that included all 6 arthropods + Human. PhIGs results (2007 data) HUMAN gene trees with at least 1 of 4 Arps species = 14818 Arp subset: Daphnia, DrosMel, Anopheles, Tribolium This is using an early Tribulium gene subset (~ 1/2 current) Ngenes Nbest ABest (of 14,800) Daphnia 30907 9156 0.61 Tribolium 9161 2623 0.18 Drosophila 14039 1262 0.09 Anopheles 12457 2649 0.18 #------------------------- Phylomedb results (2008 data) HUMAN gene trees with all of 6 Arp species = 6281 Arp subset: Daphnia, Aphid, Pediculus, Tribolium, DrosMel, Anopheles This Phylomedb set is produced only for those including Aphid (i.e. all are insect-centric), so only groups having all 6 Arp species are counted here. Nbest ABest (of 6300) Daphnia 2888 0.46 Tribolium 1324 0.21 Pediculus 1117 0.18 Aphid 441 0.07 Drosophila 191 0.03 Anopheles 320 0.05 #-------------------------