From dmerrill from ksu.edu Mon Feb 1 12:39:56 2010 From: dmerrill from ksu.edu (Arthropod Genomics) Date: Mon Feb 1 12:41:56 2010 Subject: [Arthropod] Registration OPEN - Arthropod Genomics Symposium, Kansas City, June 10-13, 2010 Message-ID: Arthropod Genomics: New Approaches and Outcomes 4th ANNUAL ARTHROPOD GENOMICS SYMPOSIUM June 10 ? 13, 2010, in Kansas City, USA www.k-state.edu/agc/symp2010 REGISTRATION is now open to attend the 4th Annual Arthropod Genomics Symposium, ?Arthropod Genomics: New Approaches and Outcomes,? June 10 to 13, 2010, in Kansas City. Early registration deadline: Friday, March 26, 2010 Keynote Speaker: Nora J. Besansky University of Notre Dame Population genomics of adaptation and speciation in malaria?s vector Featured Speakers: Michael Akam University of Cambridge, United Kingdom The genome of the Geophilomorph centipede, Strigamia maritima Scott J. Emrich University of Notre Dame Opportunities and challenges of non-model transcriptome sequencing: From corn to wild butterflies and moths Matthew Hudson University of Illinois at Urbana-Champaign Exploring the evolution of social behavior using genome sequencing and analysis Anthony A. James University of California Message in a battle, using whole genome expression analyses to fight vector-borne diseases Michael R. Kanost Kansas State University Functional genomics of cuticle sclerotization in Tribolium castaneum Fabrice Legeai INRA, Rennes, France Prediction and analyses of non coding RNA sequences in the pea aphid genome Barry R. Pittendrigh University of Illinois at Urbana-Champaign The Body Louse genome project Patrick D. Schloss University of Michigan Bugs within bugs: Understanding the influence of the microbiome on arthropod health Christian Schl?tterer Vetmeduni Vienna, Austria Next generation sequencing in population genetics: From experimental evolution to gene expression Zhijian Jake Tu Virginia Tech Anopheles stephensi genome assembly and transcriptome analysis John (Jack) H. Werren University of Rochester Functional and evolutionary insights from the genomes of three parasitoid Nasonia species Evgeny M. Zdobnov University of Geneva, Switzerland Genomics in the light of evolution FUNDING AGENCY PRESENTATIONS Representatives from national funding agencies will make short presentations about funding philosophies and opportunities within their programs. Following each presentation, the floor will be open for questions and discussion. Speakers include: Alan Christensen, NSF Adriana Costero, NIAID, NIH Mary F. Purcell-Miramontes, USDA, NIFA PRE-SYMPOSIUM WORKSHOP: Thursday afternoon, June 10, 4:00-6:00 pm Navigating NCBI?s resources for insect genomics. Terence Murphy, NCBI/NIH, will provide training on utilizing NCBI?s resources for insect genomics. Topics will include accessing data in the RefSeq and Entrez Gene databases, BLink, BLAST, NCBI?s Map Viewer, and other resources. Issues regarding the submission of data to NCBI and options for linking outside resources to NCBI?s databases will also be discussed. There is no cost to attend this optional workshop, but registration is requested. ORGANISM MEETINGS - Friday afternoon/evening, June 11, 5:15-? p.m. Meet with scientists who are also working with your organism of interest during small group gatherings. Group leaders will be identified to coordinate topics and lead discussions. Additional information will be posted to the conference website as details are finalized. POSTER SESSIONS: There will be two poster sessions. Six platform presentations will be chosen from submitted poster abstracts. Abstract Submission Deadline: Wednesday, May 19, 2010. SYMPOSIUM PROGRAM: The symposium sessions will begin Thursday evening, June 10, and continue on Friday and Saturday, with additional events Saturday evening and Sunday morning. Speakers will present new insights from genomic approaches in arthropods and describe the development of tools for genomic analysis. Workshops will be held Thursday prior to the Symposium and Saturday morning. Activities will conclude by noon on Sunday, June 13. ROUNDTABLE DISCUSSION: Sunday morning will highlight a roundtable discussion led by members of the ArthropodBase Consortium regarding the generation of integrated arthropod genome databases and tools for genome projects. Symposium attendees are invited to join the fun as we share our progress by providing feedback on these projects and proposing new possibilities. REGISTRATION: The early registration fee is $295 ($150 for graduate and undergraduate students) on or before Friday, March 26, and will include a welcome reception Thursday evening, breakfast and lunch on Friday and Saturday, and breakfast on Sunday. VENUE: The symposium will take place at the Kansas City Marriott on the beautiful Country Club Plaza. Participants are invited to dine Saturday night at an optional banquet at the BRIO Tuscan Grille. INFORMATION: Visit our website, www.k-state.edu/agc/symp2010, for complete details and brochure. Add your name to the Symposium mailing list, by sending your contact information to dmerrill@k-state.edu. DEADLINES: Early Discount Registration: Friday, March 26 Hotel Reservations: Wednesday, May 19 Poster Abstracts: Wednesday, May 19 Registration: Wednesday, May 19 QUESTIONS: Contact us at (785) 532-3482 or dmerrill@ksu.edu. Please share this announcement with colleagues and students! SPONSOR: Center for Genomic Studies on Arthropods Affecting Human, Animal and Plant Health, Kansas State University Susan J. Brown, Professor Director, Center for Genomic Studies on Arthropods Affecting Human, Animal and Plant Health and Robin E. Denell, Distinguished Professor Chair, AGC Symposium Organizing Committee by Doris Merrill, Program Coordinator K-State Arthropod Genomics Center Division of Biology, Kansas State University 116 Ackert Hall, Manhattan, KS 66506-4901 (785) 532-3482, dmerrill@k-state.edu www.k-state.edu/agc Join the Arthropod Genomics Consortium, formed to increase collaboration and information exchange among the community of scientists performing genomic studies on arthropods. Visit: http://arthropodgenomes.org , to register and learn more! From gilbertd from cricket.bio.indiana.edu Mon Feb 1 12:40:47 2010 From: gilbertd from cricket.bio.indiana.edu (Don Gilbert) Date: Mon Feb 1 12:41:57 2010 Subject: [Arthropod] Re: Daphnia has the most ancestral genes Message-ID: <201002011740.o11HelO12169@cricket.bio.indiana.edu> Scott, Yes, to be sure, I qualified it 'the most ancestral arthropod gene set (of those available)'.. It may be a slog thru many arthropod genomes to find "the ancestral" model; from insect genomes, it is clear even the phylogenetically basal ones are more derived than ixodes or daphnia, and that agrees with known phylogeny (?). Part of Ixodes lower score is its highly repetitive genome, subsequent poor assembly, and artifactually poorer gene models (missing in all or parts). But the distinction in Ixodes better score to mammal genes vs plant/worm suggests a real difference from Daphnia. Another thing I noticed in these stats of non-arthropod homology, I can't put too much weight on its biological accuracy but someone could investigate further: pediculus (mammal parasite) and aphid (plant parasite) are two relatively close insects, and should by phylogeny have about same gene distance from non-arthropods. Not quite: pediculus favors mammal genes over aphid by 2%, and aphid favors plant genes over pediculus by 1%, the only case I looked at where aphid exceeds louse. More details are here: http://arthropods.eugenes.org/arthropods/summaries/best-arp-model6genes.txt - Don |Subject: Re: Daphnia has the most ancestral genes | |Hi Don, | |I thought that was an interesting comparison you posted on Arthropod |Digest, but I wonder if there will be a non-parasitic arthropod genome |coming out that would be a better indicator of ancestral genes (eg a |spider?). Mites and ticks have a long history of parasitism and that |has been shown to be associated with gene loss, I believe. | |Scott Cornman |Beltsville Bee Research Lab |USDA-ARS | From mark.blaxter from ed.ac.uk Mon Feb 1 15:59:49 2010 From: mark.blaxter from ed.ac.uk (Mark Blaxter) Date: Mon Feb 1 16:59:28 2010 Subject: [Arthropod] Re: Daphnia has the most ancestral genes In-Reply-To: <201002011740.o11HelO12169@cricket.bio.indiana.edu> References: <201002011740.o11HelO12169@cricket.bio.indiana.edu> Message-ID: <60C24EAA-1155-4CAC-87FE-D9BB0E413F41@ed.ac.uk> Hi folks I'm always worried when BLAST is used as a phylogenetic tool... basically the 'scores' returned are contingent on the underlying model, which in BLAST is evolutionary/biological of course, but is generalised across all proteins. Statements of 'basal' imply a tree, and a tree implies a model driven reconstruction, and, well, BLAST doesnt reconstruct trees. A top blast match (or reciprocal best blast) algorithm is severely biased by - the relative rates of substitution in each genome all extant genomes are equally 'evolved'; the differences are in rates and patterns of rates of evolution across genes two genomes with relatively low substitution rates will appear more similar than expected when compared to their sister taxa, when sister taxa have elevated rates - the patterns of substitution that are driven by other forces, such as base composition its well known in mitochondrial genomes that protein substitution patterns are driven by genome AT content, resulting in significant and completely confounding homoplastic convergence at the amino acid level thus global comparisons using BLAST, using a single substitution matrix (that implicitly assumes equivalence of amino acid composition bias) will mislead It would be good to derive trees for all of the protein sets Don has generated and ask what their topologies are. Are these genes not in TreeFam, where there are trees derived that can be mined for data affirming this finding. Mark On 1 Feb 2010, at 17:40, Don Gilbert wrote: > > Scott, > > Yes, to be sure, I qualified it 'the most ancestral arthropod gene > set (of > those available)'.. > > It may be a slog thru many arthropod genomes to find "the ancestral" > model; > from insect genomes, it is clear even the phylogenetically basal > ones are > more derived than ixodes or daphnia, and that agrees with known > phylogeny (?). Part > of Ixodes lower score is its highly repetitive genome, subsequent > poor assembly, and > artifactually poorer gene models (missing in all or parts). But the > distinction > in Ixodes better score to mammal genes vs plant/worm suggests a real > difference > from Daphnia. > > Another thing I noticed in these stats of non-arthropod homology, I > can't put too much > weight on its biological accuracy but someone could investigate > further: > pediculus (mammal parasite) and aphid (plant parasite) are two > relatively close insects, > and should by phylogeny have about same gene distance from non- > arthropods. Not quite: > pediculus favors mammal genes over aphid by 2%, and aphid favors > plant genes over > pediculus by 1%, the only case I looked at where aphid exceeds > louse. More details are here: > http://arthropods.eugenes.org/arthropods/summaries/best-arp-model6genes.txt > > - Don > > |Subject: Re: Daphnia has the most ancestral genes > | > |Hi Don, > | > |I thought that was an interesting comparison you posted on Arthropod > |Digest, but I wonder if there will be a non-parasitic arthropod > genome > |coming out that would be a better indicator of ancestral genes (eg a > |spider?). Mites and ticks have a long history of parasitism and that > |has been shown to be associated with gene loss, I believe. > | > |Scott Cornman > |Beltsville Bee Research Lab > |USDA-ARS > | > > _______________________________________________ > Arthropod mailing list > Arthropod@net.bio.net > http://www.bio.net/biomail/listinfo/arthropod > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From mark.blaxter from ed.ac.uk Mon Feb 1 16:53:29 2010 From: mark.blaxter from ed.ac.uk (Mark Blaxter) Date: Mon Feb 1 16:59:29 2010 Subject: [Arthropod] Re: Daphnia has the most ancestral genes In-Reply-To: <859872d41002011342k1266b010i72bb92d17fed7dfe@mail.gmail.com> References: <201002011740.o11HelO12169@cricket.bio.indiana.edu> <60C24EAA-1155-4CAC-87FE-D9BB0E413F41@ed.ac.uk> <859872d41002011342k1266b010i72bb92d17fed7dfe@mail.gmail.com> Message-ID: <2D5E8A19-B279-4C7D-9D1C-B8FAF55E1536@ed.ac.uk> Hi Scott yes, I agree that defining sets of genes that we can hypothesise were present in the last common ancestor is a very valuable task. Indeed weve been doing it for nematodes, and its a fun and revealing game to get into, however done (domains/genes/etc). But I thought from Don's post that he was commenting on the best blast matches (vide "the best gene matches to human genes"), not presence/absence of members of inferred orthologue groups present in the LCA of humans and arthropods. Thus Daphnia, for human gene X, might 'win' the race, but this doesnt imply that Apis/Ixodes/Cupiennius DOESNT have a copy of the family X, just that whatever copies were present scored less highly than Daphnia's. Mark On 1 Feb 2010, at 21:42, scott cornman wrote: > Hi Mark, > > I agree with you that BLAST is not a proper method for inferring > phylogenies, but are tree topologies even needed to formulate sets of > ancestral genes? Perhaps I'm being naive, but can one just use a BLAST > threshold to estimate whether homologous genes are present/absent in a > clade, and then identify the arthropod with the most overlap with > vertebrates but not necessarily the most similar sequence by some > evolutionary model? And given the rate of multigene family evolution, > perhaps presence/absence of well defined domains is a better unit to > tabulate? > > Scott Cornman > Beltsville Bee Research lab > USDA-ARS > > On Mon, Feb 1, 2010 at 3:59 PM, Mark Blaxter > wrote: >> Hi folks >> I'm always worried when BLAST is used as a phylogenetic tool... >> basically >> the 'scores' returned are contingent on the underlying model, which >> in BLAST >> is evolutionary/biological of course, but is generalised across all >> proteins. Statements of 'basal' imply a tree, and a tree implies a >> model >> driven reconstruction, and, well, BLAST doesnt reconstruct trees. >> >> A top blast match (or reciprocal best blast) algorithm is severely >> biased by >> - the relative rates of substitution in each genome >> all extant genomes are equally 'evolved'; the differences >> are in >> rates and patterns of rates of evolution across genes >> two genomes with relatively low substitution rates will >> appear more >> similar than expected when compared to their sister taxa, when >> sister taxa >> have elevated rates >> - the patterns of substitution that are driven by other forces, >> such as base >> composition >> its well known in mitochondrial genomes that protein >> substitution >> patterns are driven by genome AT content, resulting in significant >> and >> completely confounding homoplastic convergence at the amino acid >> level >> thus global comparisons using BLAST, using a single >> substitution >> matrix (that implicitly assumes equivalence of amino acid >> composition bias) >> will mislead >> >> It would be good to derive trees for all of the protein sets Don has >> generated and ask what their topologies are. Are these genes not in >> TreeFam, >> where there are trees derived that can be mined for data affirming >> this >> finding. >> >> Mark >> >> >> On 1 Feb 2010, at 17:40, Don Gilbert wrote: >> >>> >>> Scott, >>> >>> Yes, to be sure, I qualified it 'the most ancestral arthropod gene >>> set (of >>> those available)'.. >>> >>> It may be a slog thru many arthropod genomes to find "the ancestral" >>> model; >>> from insect genomes, it is clear even the phylogenetically basal >>> ones are >>> more derived than ixodes or daphnia, and that agrees with known >>> phylogeny >>> (?). Part >>> of Ixodes lower score is its highly repetitive genome, subsequent >>> poor >>> assembly, and >>> artifactually poorer gene models (missing in all or parts). But the >>> distinction >>> in Ixodes better score to mammal genes vs plant/worm suggests a real >>> difference >>> from Daphnia. >>> >>> Another thing I noticed in these stats of non-arthropod homology, >>> I can't >>> put too much >>> weight on its biological accuracy but someone could investigate >>> further: >>> pediculus (mammal parasite) and aphid (plant parasite) are two >>> relatively >>> close insects, >>> and should by phylogeny have about same gene distance from non- >>> arthropods. >>> Not quite: >>> pediculus favors mammal genes over aphid by 2%, and aphid favors >>> plant >>> genes over >>> pediculus by 1%, the only case I looked at where aphid exceeds >>> louse. >>> More details are here: >>> >>> http://arthropods.eugenes.org/arthropods/summaries/best-arp-model6genes.txt >>> >>> - Don >>> >>> |Subject: Re: Daphnia has the most ancestral genes >>> | >>> |Hi Don, >>> | >>> |I thought that was an interesting comparison you posted on >>> Arthropod >>> |Digest, but I wonder if there will be a non-parasitic arthropod >>> genome >>> |coming out that would be a better indicator of ancestral genes >>> (eg a >>> |spider?). Mites and ticks have a long history of parasitism and >>> that >>> |has been shown to be associated with gene loss, I believe. >>> | >>> |Scott Cornman >>> |Beltsville Bee Research Lab >>> |USDA-ARS >>> | >>> >>> _______________________________________________ >>> Arthropod mailing list >>> Arthropod@net.bio.net >>> http://www.bio.net/biomail/listinfo/arthropod >>> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From gilbertd from cricket.bio.indiana.edu Mon Feb 1 17:27:37 2010 From: gilbertd from cricket.bio.indiana.edu (Don Gilbert) Date: Mon Feb 1 17:30:16 2010 Subject: [Arthropod] Re: Daphnia has the most ancestral genes Message-ID: <201002012227.o11MRbU13072@cricket.bio.indiana.edu> Mark, Yes, I agree genes counted from best matches to human, etc. using blast are not the best way to analyze phylogeny (this is a "factoid", implying you should take with some grains of salt). 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. So 600 Drosophila mel genes score as best matches to 15,000 human genes, Tribulium has 2,000 best, and 3,300 Daphnia genes are best matches. These are large differences. Using bitscore as a shorthand for quality of alignments, there are larger differences. I haven't the time just now to run this thru a more careful alignment and phylogenetic assessment, but I'll wager these differences remain. Some others folks have done such, but perhaps not with a recent set of arthropod genes. - Don From lawson from ebi.ac.uk Mon Feb 1 17:28:58 2010 From: lawson from ebi.ac.uk (Daniel Lawson) Date: Mon Feb 1 17:30:17 2010 Subject: [Arthropod] Re: Daphnia has the most ancestral genes In-Reply-To: <60C24EAA-1155-4CAC-87FE-D9BB0E413F41@ed.ac.uk> References: <201002011740.o11HelO12169@cricket.bio.indiana.edu> <60C24EAA-1155-4CAC-87FE-D9BB0E413F41@ed.ac.uk> Message-ID: <3bdfed711002011428j15dad5f9md4e8272e5c7549e9@mail.gmail.com> HI Well this is one of the aims for the Ensembl Genomes project (excuse the blatant advertising). All of Don's model organism genomes are represented and from an arthropod point of view we are missing Daphnia, Tribolium, Nasonia, Aphid, Apis and Bombyx (so 6 out of 14 species). Some of these will be incorporated during the spring so we could consider such an analysis in the summer. regards Dan -- Ensembl Genomes | VectorBase On 1 February 2010 20:59, Mark Blaxter wrote: > Hi folks > I'm always worried when BLAST is used as a phylogenetic tool... basically > the 'scores' returned are contingent on the underlying model, which in BLAST > is evolutionary/biological of course, but is generalised across all > proteins. Statements of 'basal' imply a tree, and a tree implies a model > driven reconstruction, and, well, BLAST doesnt reconstruct trees. > > A top blast match (or reciprocal best blast) algorithm is severely biased > by > - the relative rates of substitution in each genome > all extant genomes are equally 'evolved'; the differences are in > rates and patterns of rates of evolution across genes > two genomes with relatively low substitution rates will appear more > similar than expected when compared to their sister taxa, when sister taxa > have elevated rates > - the patterns of substitution that are driven by other forces, such as > base composition > its well known in mitochondrial genomes that protein substitution > patterns are driven by genome AT content, resulting in significant and > completely confounding homoplastic convergence at the amino acid level > thus global comparisons using BLAST, using a single substitution > matrix (that implicitly assumes equivalence of amino acid composition bias) > will mislead > > It would be good to derive trees for all of the protein sets Don has > generated and ask what their topologies are. Are these genes not in TreeFam, > where there are trees derived that can be mined for data affirming this > finding. > > Mark > > > > On 1 Feb 2010, at 17:40, Don Gilbert wrote: > > >> Scott, >> >> Yes, to be sure, I qualified it 'the most ancestral arthropod gene set (of >> those available)'.. >> >> It may be a slog thru many arthropod genomes to find "the ancestral" >> model; >> from insect genomes, it is clear even the phylogenetically basal ones are >> more derived than ixodes or daphnia, and that agrees with known phylogeny >> (?). Part >> of Ixodes lower score is its highly repetitive genome, subsequent poor >> assembly, and >> artifactually poorer gene models (missing in all or parts). But the >> distinction >> in Ixodes better score to mammal genes vs plant/worm suggests a real >> difference >> from Daphnia. >> >> Another thing I noticed in these stats of non-arthropod homology, I can't >> put too much >> weight on its biological accuracy but someone could investigate further: >> pediculus (mammal parasite) and aphid (plant parasite) are two relatively >> close insects, >> and should by phylogeny have about same gene distance from non-arthropods. >> Not quite: >> pediculus favors mammal genes over aphid by 2%, and aphid favors plant >> genes over >> pediculus by 1%, the only case I looked at where aphid exceeds louse. >> More details are here: >> >> http://arthropods.eugenes.org/arthropods/summaries/best-arp-model6genes.txt >> >> - Don >> >> |Subject: Re: Daphnia has the most ancestral genes >> | >> |Hi Don, >> | >> |I thought that was an interesting comparison you posted on Arthropod >> |Digest, but I wonder if there will be a non-parasitic arthropod genome >> |coming out that would be a better indicator of ancestral genes (eg a >> |spider?). Mites and ticks have a long history of parasitism and that >> |has been shown to be associated with gene loss, I believe. >> | >> |Scott Cornman >> |Beltsville Bee Research Lab >> |USDA-ARS >> | >> >> _______________________________________________ >> Arthropod mailing list >> Arthropod@net.bio.net >> http://www.bio.net/biomail/listinfo/arthropod >> >> > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > Arthropod mailing list > Arthropod@net.bio.net > http://www.bio.net/biomail/listinfo/arthropod > -- Ensembl Genomes | VectorBase From mark.blaxter from ed.ac.uk Tue Feb 2 02:52:32 2010 From: mark.blaxter from ed.ac.uk (Mark Blaxter) Date: Tue Feb 2 09:04:54 2010 Subject: [Arthropod] Re: Daphnia has the most ancestral genes In-Reply-To: <3bdfed711002011428j15dad5f9md4e8272e5c7549e9@mail.gmail.com> References: <201002011740.o11HelO12169@cricket.bio.indiana.edu> <60C24EAA-1155-4CAC-87FE-D9BB0E413F41@ed.ac.uk> <3bdfed711002011428j15dad5f9md4e8272e5c7549e9@mail.gmail.com> Message-ID: <274F5582-2E3F-4F2A-90D8-7663CDA42A12@ed.ac.uk> Hi Dan could you get the genes into the TreeFam project also? Will the ensembl genomes project be 'doing' the trees? Mark On 1 Feb 2010, at 22:28, Daniel Lawson wrote: > HI > > Well this is one of the aims for the Ensembl Genomes project (excuse > the blatant advertising). All of Don's model organism genomes are > represented and from an arthropod point of view we are missing > Daphnia, Tribolium, Nasonia, Aphid, Apis and Bombyx (so 6 out of 14 > species). Some of these will be incorporated during the spring so we > could consider such an analysis in the summer. > > regards > Dan > -- > Ensembl Genomes | VectorBase > > On 1 February 2010 20:59, Mark Blaxter wrote: > Hi folks > I'm always worried when BLAST is used as a phylogenetic tool... > basically the 'scores' returned are contingent on the underlying > model, which in BLAST is evolutionary/biological of course, but is > generalised across all proteins. Statements of 'basal' imply a tree, > and a tree implies a model driven reconstruction, and, well, BLAST > doesnt reconstruct trees. > > A top blast match (or reciprocal best blast) algorithm is severely > biased by > - the relative rates of substitution in each genome > all extant genomes are equally 'evolved'; the differences are > in rates and patterns of rates of evolution across genes > two genomes with relatively low substitution rates will > appear more similar than expected when compared to their sister > taxa, when sister taxa have elevated rates > - the patterns of substitution that are driven by other forces, such > as base composition > its well known in mitochondrial genomes that protein > substitution patterns are driven by genome AT content, resulting in > significant and completely confounding homoplastic convergence at > the amino acid level > thus global comparisons using BLAST, using a single > substitution matrix (that implicitly assumes equivalence of amino > acid composition bias) will mislead > > It would be good to derive trees for all of the protein sets Don has > generated and ask what their topologies are. Are these genes not in > TreeFam, where there are trees derived that can be mined for data > affirming this finding. > > Mark > > > > On 1 Feb 2010, at 17:40, Don Gilbert wrote: > > > Scott, > > Yes, to be sure, I qualified it 'the most ancestral arthropod gene > set (of > those available)'.. > > It may be a slog thru many arthropod genomes to find "the ancestral" > model; > from insect genomes, it is clear even the phylogenetically basal > ones are > more derived than ixodes or daphnia, and that agrees with known > phylogeny (?). Part > of Ixodes lower score is its highly repetitive genome, subsequent > poor assembly, and > artifactually poorer gene models (missing in all or parts). But the > distinction > in Ixodes better score to mammal genes vs plant/worm suggests a real > difference > from Daphnia. > > Another thing I noticed in these stats of non-arthropod homology, I > can't put too much > weight on its biological accuracy but someone could investigate > further: > pediculus (mammal parasite) and aphid (plant parasite) are two > relatively close insects, > and should by phylogeny have about same gene distance from non- > arthropods. Not quite: > pediculus favors mammal genes over aphid by 2%, and aphid favors > plant genes over > pediculus by 1%, the only case I looked at where aphid exceeds > louse. More details are here: > http://arthropods.eugenes.org/arthropods/summaries/best-arp-model6genes.txt > > - Don > > |Subject: Re: Daphnia has the most ancestral genes > | > |Hi Don, > | > |I thought that was an interesting comparison you posted on Arthropod > |Digest, but I wonder if there will be a non-parasitic arthropod > genome > |coming out that would be a better indicator of ancestral genes (eg a > |spider?). Mites and ticks have a long history of parasitism and that > |has been shown to be associated with gene loss, I believe. > | > |Scott Cornman > |Beltsville Bee Research Lab > |USDA-ARS > | > > _______________________________________________ > Arthropod mailing list > Arthropod@net.bio.net > http://www.bio.net/biomail/listinfo/arthropod > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > Arthropod mailing list > Arthropod@net.bio.net > http://www.bio.net/biomail/listinfo/arthropod > > > > -- > Ensembl Genomes | VectorBase -------------- next part -------------- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From lawson from ebi.ac.uk Tue Feb 2 05:04:42 2010 From: lawson from ebi.ac.uk (Daniel Lawson) Date: Tue Feb 2 09:04:56 2010 Subject: [Arthropod] Re: Daphnia has the most ancestral genes In-Reply-To: <274F5582-2E3F-4F2A-90D8-7663CDA42A12@ed.ac.uk> References: <201002011740.o11HelO12169@cricket.bio.indiana.edu> <60C24EAA-1155-4CAC-87FE-D9BB0E413F41@ed.ac.uk> <3bdfed711002011428j15dad5f9md4e8272e5c7549e9@mail.gmail.com> <274F5582-2E3F-4F2A-90D8-7663CDA42A12@ed.ac.uk> Message-ID: <3bdfed711002020204y139ceb69p3fd5b1ba0b190b6f@mail.gmail.com> Hi Mark, TreeFam certainly picks up vertebrate genomes from Ensembl as a data source and my understanding is the Ensembl Genomes will be handled in the same manner. Treefam haven't made a release for almost a year. There is some convergence between the Treefam and Ensembl tree 'doing' systems with reference to the HMM approach but they are independent groups. So both Treefam and Ensembl Genomes will generate gene trees. Ensembl Genomes doesn't specifically aim to include all species in all trees like Treefam rather we aim to have coverage within broad taxonomic groupings (metazoa, protists, plants, bacteria, fungi etc.) and then a pan-compara which includes key species from all of the tree of life (a skeletal Treefam if you want). Another way of viewing this is that Treefam species coverage is analogous to the combination of metazoa and protists with some outgroups from fungi and plants. Due to our resource limitation we are prioritising inclusion of genomes into Ensembl Metazoa. Genomes which fall within a funded collaboration first and then the next candidate from a short list of published species. We are keen for this to be responsive to the community and so if people have wish lists then could they send them to me (offline from the list - I don't want to get into trouble). Personally, I have an arthropod leaning and with that scope in mind the list currently looks like this: Bombyx Tribolium Apis Acyrthosiphon Daphnia Nasonia spp. Some of these groups are actively working on the annotation of their genomes and so we are liaising with them as to when would be the appropriate time to incorporate the genome and it's updated annotations. regards Dan -- Ensembl Genomes | VectorBase ArthropodBase www.arthropodgenomes.org From gilbertd from bio.indiana.edu Tue Feb 2 13:37:44 2010 From: gilbertd from bio.indiana.edu (Don Gilbert) Date: Tue Feb 2 13:38:34 2010 Subject: [Arthropod] Recent arthropod orthology data sets (Re: Daphnia has the most ancestral genes) References: Message-ID: For those of you who want to look at recent Arthropod orthology analyses, here is a list I have, probably not complete, but a few of these include Daphnia and Ixodes and more recent insects, to balance the Dipteran perspective of arthropod genes. Of these, I think the phylomedb.org Acyrthosiphon set is perhaps the most valuable, even lacking Ixodes. Toni Gabaldon provides his alignment and tree data sets, so one can do post analyses such as measuring which species have more ancestral genes. -- Don 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 http://cegg.unige.ch/orthodb/ Evgeny Zdobnov and colleagues, recent gene sets for arthropods, includes Daphnia and Ixodes, and recent insects Aphid, Pediculus, Nasonia. http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/ current release has 2008/2009 data, with 1,200 completely sequenced genomes, includes daphnia, recent insects, but not ixodes 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 http://www.orthomcl.org/ OrthoMCL-DB, current release from 2009 has 138 genomes across the tree, however arthropods include only insect genomes From jlboore from calmail.berkeley.edu Tue Feb 2 21:40:24 2010 From: jlboore from calmail.berkeley.edu (Jeffrey Boore) Date: Tue Feb 2 21:54:08 2010 Subject: [Arthropod] Re: Daphnia has the most ancestral genes In-Reply-To: <274F5582-2E3F-4F2A-90D8-7663CDA42A12@ed.ac.uk> References: <201002011740.o11HelO12169@cricket.bio.indiana.edu> <60C24EAA-1155-4CAC-87FE-D9BB0E413F41@ed.ac.uk> <3bdfed711002011428j15dad5f9md4e8272e5c7549e9@mail.gmail.com> <274F5582-2E3F-4F2A-90D8-7663CDA42A12@ed.ac.uk> Message-ID: <1B8C6BDE-D625-452C-A69E-147EC65D3E1E@calmail.berkeley.edu> I cannot resist an advertisement here myself. We have a system called PHRINGE (Phylogenetic Resources for the Interpretation of Genomes) that uses a graph-based method for recognizing gene families that incorporates the evolutionary relationships among the organisms, reconstructs evolutionary trees for all genes in all considered genomes, and links this up with outside databases. Users can compare intron-exon structures, see the tree of each set of genes, download the multiple sequence alignments, see the relative physical arrangements of orthologous genes, and do other cool stuff. The best implementation is for oomycete genomes at . (Click on the links and/or plug in some random gene numbers if you want to see how it works.) We don't have anything yet for arthropods, because I have failed to convince DOE, NSF, or NIH to support this (rant suppressed here), but we intend to do that as part of our project sequencing the monarch butterfly genome. That sequencing will be complete in a few months. Jeff ___________________________ Jeffrey L. Boore, Ph.D. Chief Executive Officer Genome Project Solutions 1024 Promenade Street Hercules, CA 94547 http://GenomeProjectSolutions.com 1 (877) 867-0146 (toll free) Associate Adjunct Professor, University of California Berkeley Guest Researcher, Berkeley National Lab and DOE Joint Genome Institute On Feb 1, 2010, at 11:52 PM, Mark Blaxter wrote: > Hi Dan > could you get the genes into the TreeFam project also? Will the > ensembl genomes project be 'doing' the trees? > Mark > > On 1 Feb 2010, at 22:28, Daniel Lawson wrote: > >> HI >> >> Well this is one of the aims for the Ensembl Genomes project >> (excuse the blatant advertising). All of Don's model organism >> genomes are represented and from an arthropod point of view we are >> missing Daphnia, Tribolium, Nasonia, Aphid, Apis and Bombyx (so 6 >> out of 14 species). Some of these will be incorporated during the >> spring so we could consider such an analysis in the summer. >> >> regards >> Dan >> -- >> Ensembl Genomes | VectorBase >> >> On 1 February 2010 20:59, Mark Blaxter wrote: >> Hi folks >> I'm always worried when BLAST is used as a phylogenetic tool... >> basically the 'scores' returned are contingent on the underlying >> model, which in BLAST is evolutionary/biological of course, but is >> generalised across all proteins. Statements of 'basal' imply a >> tree, and a tree implies a model driven reconstruction, and, well, >> BLAST doesnt reconstruct trees. >> >> A top blast match (or reciprocal best blast) algorithm is severely >> biased by >> - the relative rates of substitution in each genome >> all extant genomes are equally 'evolved'; the differences are >> in rates and patterns of rates of evolution across genes >> two genomes with relatively low substitution rates will >> appear more similar than expected when compared to their sister >> taxa, when sister taxa have elevated rates >> - the patterns of substitution that are driven by other forces, >> such as base composition >> its well known in mitochondrial genomes that protein >> substitution patterns are driven by genome AT content, resulting in >> significant and completely confounding homoplastic convergence at >> the amino acid level >> thus global comparisons using BLAST, using a single >> substitution matrix (that implicitly assumes equivalence of amino >> acid composition bias) will mislead >> >> It would be good to derive trees for all of the protein sets Don >> has generated and ask what their topologies are. Are these genes >> not in TreeFam, where there are trees derived that can be mined for >> data affirming this finding. >> >> Mark >> >> >> >> On 1 Feb 2010, at 17:40, Don Gilbert wrote: >> >> >> Scott, >> >> Yes, to be sure, I qualified it 'the most ancestral arthropod gene >> set (of >> those available)'.. >> >> It may be a slog thru many arthropod genomes to find "the >> ancestral" model; >> from insect genomes, it is clear even the phylogenetically basal >> ones are >> more derived than ixodes or daphnia, and that agrees with known >> phylogeny (?). Part >> of Ixodes lower score is its highly repetitive genome, subsequent >> poor assembly, and >> artifactually poorer gene models (missing in all or parts). But >> the distinction >> in Ixodes better score to mammal genes vs plant/worm suggests a >> real difference >> from Daphnia. >> >> Another thing I noticed in these stats of non-arthropod homology, I >> can't put too much >> weight on its biological accuracy but someone could investigate >> further: >> pediculus (mammal parasite) and aphid (plant parasite) are two >> relatively close insects, >> and should by phylogeny have about same gene distance from non- >> arthropods. Not quite: >> pediculus favors mammal genes over aphid by 2%, and aphid favors >> plant genes over >> pediculus by 1%, the only case I looked at where aphid exceeds >> louse. More details are here: >> http://arthropods.eugenes.org/arthropods/summaries/best-arp-model6genes.txt >> >> - Don >> >> |Subject: Re: Daphnia has the most ancestral genes >> | >> |Hi Don, >> | >> |I thought that was an interesting comparison you posted on Arthropod >> |Digest, but I wonder if there will be a non-parasitic arthropod >> genome >> |coming out that would be a better indicator of ancestral genes (eg a >> |spider?). Mites and ticks have a long history of parasitism and that >> |has been shown to be associated with gene loss, I believe. >> | >> |Scott Cornman >> |Beltsville Bee Research Lab >> |USDA-ARS >> | >> >> _______________________________________________ >> Arthropod mailing list >> Arthropod@net.bio.net >> http://www.bio.net/biomail/listinfo/arthropod >> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> _______________________________________________ >> Arthropod mailing list >> Arthropod@net.bio.net >> http://www.bio.net/biomail/listinfo/arthropod >> >> >> >> -- >> Ensembl Genomes | VectorBase > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > _______________________________________________ > Arthropod mailing list > Arthropod@net.bio.net > http://www.bio.net/biomail/listinfo/arthropod From gilbertd from bio.indiana.edu Wed Feb 10 14:39:41 2010 From: gilbertd from bio.indiana.edu (Don Gilbert) Date: Wed Feb 10 14:41:00 2010 Subject: [Arthropod] New arthropod phylogeny study References: Message-ID: Here is a new study of phylogeny of arthropods from proteins, moving a few groups around (I hope the millipede genome is finished soon to compare). It has a nice figure 2 with pictures of these bugs, and fig 1 shows the new tree. Most insects here are ones I've never heard of by genus, but Daphnia magna is included as a crustacean. THe branch lengths in fig 2 agree that insect genes are farther out from the root than crustaceans like Daphnia, but arachnids/Chelicerata seem to be lower than crustaceans, as are millipedes. What I found with Ixodes somewhat higher than Daphnia doesn't agree, but then this new study has a much larger species set, and smaller (62 vs >10,000), common gene set. -- Don -------------------------------- Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences doi:10.1038/nature08742 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08742.html Jerome C. Regier1, Jeffrey W. Shultz1,2,3, Andreas Zwick1, April Hussey1, Bernard Ball4, Regina Wetzer5, Joel W. Martin5 & Clifford W. Cunningham4 Abstract The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed1, 2, 3, 4, 5, 6, 7. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes2, 8 (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions7, 9, 10. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41*kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata11 (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata)2, 5, 12. In addition to Hexapoda, Pancrustacea includes three major extant lineages of *crustaceans*, each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that *crustaceans* are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships. From gilbertd from bio.indiana.edu Fri Feb 19 12:07:14 2010 From: gilbertd from bio.indiana.edu (Don Gilbert) Date: Fri Feb 19 12:08:52 2010 Subject: [Arthropod] Butterfly gene duplication ties extra UV opsin to wing colors Message-ID: Here is a new study of how bugs are using gene duplications: Butterflies that have a duplicate gene allowing them to see ultraviolet colors also have UV-yellow pigment on their wings. Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies. Adriana Briscoe, Seth Bybee and colleagues. doi:10.1073/pnas.0910085107 We now find that Heliconius erato has a second UV opsin mRNA (UVRh2)???a previously undescribed duplication of this gene among Lepidoptera. ... Along with the additional UV opsin, Heliconius have also evolved 3-hydroxy-DL-kynurenine (3-OHK)-based yellow wing pigments not found in close relatives ... Functional diversification of the UV-sensitive visual pigments may help explain why the yellow wing pigments of Heliconius are so colorful in the UV range compared to the yellow pigments of close relatives lacking the UV opsin duplicate. --------- Daphnia and Aphid have lots of gene duplications. The best general explanation we've found for Daphnia is these are often functionally diversified, even when newly duplicated. It would be useful to find better ways to study evolution in co-regulated groups of genes, and see where duplication fits in. Do gene duplications offer a cost-effective way to adapt to environments, or differentiate into ecological niches? - Don From gilbertd from bio.indiana.edu Fri Feb 19 13:15:53 2010 From: gilbertd from bio.indiana.edu (Don Gilbert) Date: Fri Feb 19 13:17:03 2010 Subject: [Arthropod] New crustacean gene set: Porcelain crab transcriptome paper Message-ID: This new paper helps flesh out more of the arthropod gene sets: Tagmount A, Wang M, Lindquist E, Tanaka Y, Teranishi KS, et al. (2010) The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database. PLoS ONE 5(2): e9327. doi:10.1371/journal.pone.0009327 Among other results here, they support the pancrustacea hypothesis and suggest that branchiopod crustaceans (daphnia) may be more closely related to insects than other malacostracan crustaceans (por. crab). - DOn From gilbertd from cricket.bio.indiana.edu Fri Feb 19 16:24:36 2010 From: gilbertd from cricket.bio.indiana.edu (Don Gilbert) Date: Fri Feb 19 16:25:42 2010 Subject: [Arthropod] New crustacean gene set: Porcelain crab transcriptome paper Message-ID: <201002192124.o1JLOab20847@cricket.bio.indiana.edu> Darren, This Porcelain crab transcriptome is compared to only Daphnia and two insects (in the figure I looked at), so it is much narrower in species scope than that recent Arthropod phylogeny paper. On the other hand it is comparing 19,000 EST clusters (~genes), whereas the Nature paper compared only ~60 genes. My take, and I'm not a phylogenist, is these are both accurate interpretations of their data, but neither is a complete or final determination of the phylogenies. We need more data for that :) I just took another look at the phylo tree in Regier et al Nature paper and it seems in agreement with malacostracan (crab) being more distant from insects than branchiopoda (daphnia). -- Don |From dobbard@staffmail.ed.ac.uk Fri Feb 19 16:01:30 2010 |Date: Fri, 19 Feb 2010 21:01:14 +0000 |From: Darren Obbard |To: Don Gilbert |Subject: Re: [Arthropod] New crustacean gene set: Porcelain crab | transcriptome paper | |> Among other results here, they support the pancrustacea hypothesis and |> suggest that branchiopod crustaceans (daphnia) may be more closely related |> to insects than other malacostracan crustaceans (por. crab). | |Does this mean we don't believe "Xenocarida as the long-sought sister |group to the Hexapoda"? |http://www.nature.com/nature/journal/vaop/ncurrent/pdf/nature08742.pdf | | | |-- |Darren Obbard |Institute of Evolutionary Biology |Ashworth Labs |Kings Buildings |University of Edinburgh, UK From mark.blaxter from ed.ac.uk Sat Feb 20 08:13:29 2010 From: mark.blaxter from ed.ac.uk (Mark Blaxter) Date: Sat Feb 20 13:10:13 2010 Subject: [Arthropod] New crustacean gene set: Porcelain crab transcriptome paper In-Reply-To: <201002192124.o1JLOab20847@cricket.bio.indiana.edu> References: <201002192124.o1JLOab20847@cricket.bio.indiana.edu> Message-ID: Hi Both a further comment on the porcelain crab analysis. The EST dataset is stunning, and looks really useful for lots of things, but the claim that the data as presented support one tree over another is in fact not there. The claim is based on a pair of venn diagrams (the figure 5 in the paper) that show the numbers of EST clusters or genes match between the porcelain crab (Pc), Daphnia pulex (Dp), and either Drosophila melanogaster (Dm) or Apis mellifera (Am). The venn diagram shows clearly that more Dp genes match Dm or Am than do Pc EST clusters. Hence Dp must be closer to Hexapoda. However, like is not being compared with like. The Dp, Dm and Ap datasets are hopefully-near-complete proteomes from the respective genomes, while the Pc data are a partial transcriptome. Thus a Dp gene that matches Dm but doesnt match Pc could simply be due to missing data in the Pc dataset. The correct comparison is to look at the number of Pc genes that match ONLY Dp versus ONLY Dm, or ONLY Dp versus ONLY Am. These genes are presumed to be present in the last common ancestor of the species compared, and the tree that implies the fewest gene losses is arguably the better tree. The data are: Pc clusters in Dahnia pulex but NOT in Dm or Am: 2449 Pc clusters NOT in Daphnia pulex but in Apis: 2811 Pc clusters NOT in Daphnia pulex but in Dm: 2071 So the comparison to Drosophila places Pc closer to Dm than Dp (2811>2449): Pc is closer to Hexapoda But he comparison to Apis places Pc closer to Dm than Dp (2071<2449): Daphnia is closer to Hexapoda So, actually the data as presented are entirely equivocal, but since 2811>2071 could be used to argue the opposite of the authors conclusions (I wouldnt recommend doing so). As I have posted earlier, BLAST is not a good phylogenetic tool, and phylogenies should be addressed using model-driven phylogenetic methods. In addition it is very dangerous to use presence-absence data such as these in cases where there are incomplete data (such as the Pc 'partial genome') or there is an ascertainment bias of any kind (eg: were not many of the Apis and Daphnia gene models inferred partly on the basis of the wonderfully dense annotation of the Drosophila genomes? So isnt there a circularity: Daphnia looks more like Drosophila because Daphnia was modeled on Drosophila). In this comment I do not intend to make any claims as to the truth or falsity of the hypothesis of relationships within Pancrustacea, just to say that the data in the Pc paper do not address it cogently... they could though! Mark On 19 Feb 2010, at 21:24, Don Gilbert wrote: > > Darren, > > This Porcelain crab transcriptome is compared to only Daphnia and > two insects > (in the figure I looked at), so it is much narrower in species scope > than that > recent Arthropod phylogeny paper. On the other hand it is comparing > 19,000 EST > clusters (~genes), whereas the Nature paper compared only ~60 > genes. My take, > and I'm not a phylogenist, is these are both accurate > interpretations of their > data, but neither is a complete or final determination of the > phylogenies. > We need more data for that :) > > I just took another look at the phylo tree in Regier et al Nature > paper and > it seems in agreement with malacostracan (crab) being more distant > from > insects than branchiopoda (daphnia). > > -- Don > > |From dobbard@staffmail.ed.ac.uk Fri Feb 19 16:01:30 2010 > |Date: Fri, 19 Feb 2010 21:01:14 +0000 > |From: Darren Obbard > |To: Don Gilbert > |Subject: Re: [Arthropod] New crustacean gene set: Porcelain crab > | transcriptome paper > | > |> Among other results here, they support the pancrustacea > hypothesis and > |> suggest that branchiopod crustaceans (daphnia) may be more > closely related > |> to insects than other malacostracan crustaceans (por. crab). > | > |Does this mean we don't believe "Xenocarida as the long-sought sister > |group to the Hexapoda"? > |http://www.nature.com/nature/journal/vaop/ncurrent/pdf/ > nature08742.pdf > | > | > | > |-- > |Darren Obbard > |Institute of Evolutionary Biology > |Ashworth Labs > |Kings Buildings > |University of Edinburgh, UK > > _______________________________________________ > Arthropod mailing list > Arthropod@net.bio.net > http://www.bio.net/biomail/listinfo/arthropod > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From tcrease from uoguelph.ca Sat Feb 20 14:55:57 2010 From: tcrease from uoguelph.ca (Teresa Crease) Date: Sat Feb 20 15:27:31 2010 Subject: [Arthropod] Re: Arthropod Digest, Vol 5, Issue 6 In-Reply-To: <1963440878.943761266695726082.JavaMail.root@erie.cs.uoguelph.ca> Message-ID: <2069598355.943811266695757538.JavaMail.root@erie.cs.uoguelph.ca> The tree in the Reiger et al. paper puts Branchiopoda and Malacostraca together in the Vericrustacea, while insects are the sister group to the Xenocarida (as Darren mentioned).? Thus, Branchiopoda and Malacostraca are more closely related to each other than either?group is?to the insects.? This does not agree with the hypothesis that branchiopods and insects are more closely related to one another, than branchiopods are to malacostracans , as suggested by the porcelain crab paper.? Both scenarios are consistent with?Pancrustacea, which includes all crustaceans plus insects.? The?unresolved question seems to be to which crustacean group the insects are most closely related.? teri? Teresa Crease Professor and Acting Chair Department of Integrative Biology University of Guelph 488 Gordon Street Guelph, ON N1G 2W1 phone: 519-824-4120 x52723 FAX: ? 519-767-1656 ----- arthropod-request@oat.bio.indiana.edu wrote: > Send Arthropod mailing list submissions to > ????????arthropod@net.bio.net > To subscribe or unsubscribe via the World Wide Web, visit > ????????http://www.bio.net/biomail/listinfo/arthropod > or, via email, send a message with subject or body 'help' to > ????????arthropod-request@net.bio.net > You can reach the person managing the list at > ????????arthropod-owner@net.bio.net > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Arthropod digest..." > Today's Topics: > ?? 1. Butterfly gene duplication ties extra UV opsin to wing????????colors > ?? ? ?(Don Gilbert) > ?? 2. New crustacean gene set: Porcelain crab transcriptome????????paper > ?? ? ?(Don Gilbert) > ?? 3. Re: New crustacean gene set: Porcelain crab transcriptome > ?? ? ?paper (Don Gilbert) > ---------------------------------------------------------------------- > Message: 1 > Date: Fri, 19 Feb 2010 11:07:14 -0600 > From: Don Gilbert > Subject: [Arthropod] Butterfly gene duplication ties extra UV opsin to > ????????wing????????colors > To: bionet-biology-vectors@moderators.isc.org > Message-ID: > Content-Type: text/plain; charset=iso-8859-1 > Here is a new study of how bugs are using gene duplications: > Butterflies that have a duplicate gene allowing them to see > ultraviolet colors also have UV-yellow pigment on their wings. > ??Positive selection of a duplicated UV-sensitive visual pigment > ??coincides with wing pigment evolution in Heliconius butterflies. > ??Adriana Briscoe, Seth Bybee and colleagues. doi:10.1073/pnas.0910085107 > ?? > ??We now find that Heliconius erato has a second UV opsin mRNA > ??(UVRh2)???a previously undescribed duplication of this gene among > ??Lepidoptera. ... Along with the additional UV opsin, Heliconius > ??have also evolved 3-hydroxy-DL-kynurenine (3-OHK)-based yellow > ??wing pigments not found in close relatives ... Functional > ??diversification of the UV-sensitive visual pigments may help > ??explain why the yellow wing pigments of Heliconius are so > ??colorful in the UV range compared to the yellow pigments of close > ??relatives lacking the UV opsin duplicate. > ??--------- > Daphnia and Aphid have lots of gene duplications. The best > general explanation we've found for Daphnia is these are often > functionally diversified, even when newly duplicated. ?It would > be useful to find better ways to study evolution in co-regulated > groups of genes, and see where duplication fits in. Do gene > duplications offer a cost-effective way to adapt to > environments, or differentiate into ecological niches? > - Don > ------------------------------ > Message: 2 > Date: Fri, 19 Feb 2010 12:15:53 -0600 > From: Don Gilbert > Subject: [Arthropod] New crustacean gene set: Porcelain crab > ????????transcriptome????????paper > To: bionet-biology-vectors@moderators.isc.org > Message-ID: > This new paper helps flesh out more of the arthropod gene sets: > Tagmount A, Wang M, Lindquist E, Tanaka Y, Teranishi KS, et al. (2010) > The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray > and Sequence Database. PLoS ONE 5(2): e9327. doi:10.1371/journal.pone.0009327 > Among other results here, they support the pancrustacea hypothesis and > suggest that branchiopod crustaceans (daphnia) may be more closely related > to insects than other malacostracan crustaceans (por. crab). > - DOn > ------------------------------ > Message: 3 > Date: Fri, 19 Feb 2010 16:24:36 -0500 (EST) > From: Don Gilbert > Subject: Re: [Arthropod] New crustacean gene set: Porcelain crab > ????????transcriptome????????paper > To: dobbard@staffmail.ed.ac.uk, gilbertd@bio.indiana.edu > Cc: arthropod@magpie.bio.indiana.edu > Message-ID: <201002192124.o1JLOab20847@cricket.bio.indiana.edu> > Darren, > This Porcelain crab transcriptome is compared to only Daphnia and two insects > (in the figure I looked at), so it is much narrower in species scope than that > recent Arthropod phylogeny paper. On the other hand it is comparing 19,000 EST > clusters (~genes), whereas the Nature paper compared only ~60 genes. ?My take, > and I'm not a phylogenist, is these are both accurate interpretations of their > data, but neither is a complete or final determination of the phylogenies. > We need more data for that :) > I just took another look at the phylo tree in Regier et al Nature paper and > it seems in agreement with malacostracan (crab) being more distant from > insects than branchiopoda (daphnia). > -- Don > |From dobbard@staffmail.ed.ac.uk ?Fri Feb 19 16:01:30 2010 > |Date: Fri, 19 Feb 2010 21:01:14 +0000 > |From: Darren Obbard > |To: Don Gilbert > |Subject: Re: [Arthropod] New crustacean gene set: Porcelain crab > |????????transcriptome paper > | > |> Among other results here, they support the pancrustacea hypothesis and > |> suggest that branchiopod crustaceans (daphnia) may be more closely related > |> to insects than other malacostracan crustaceans (por. crab). > | > |Does this mean we don't believe "Xenocarida as the long-sought sister ? > |group to the Hexapoda"? ? > |http://www.nature.com/nature/journal/vaop/ncurrent/pdf/nature08742.pdf > | > | > | > |-- > |Darren Obbard > |Institute of Evolutionary Biology > |Ashworth Labs > |Kings Buildings > |University of Edinburgh, UK > ------------------------------ > _______________________________________________ > Arthropod mailing list > Arthropod@net.bio.net > http://www.bio.net/biomail/listinfo/arthropod > End of Arthropod Digest, Vol 5, Issue 6 > *************************************** From gilbertd from bio.indiana.edu Mon Feb 22 21:11:05 2010 From: gilbertd from bio.indiana.edu (Don Gilbert) Date: Mon Feb 22 21:12:37 2010 Subject: [Arthropod] Aphid genome paper is available Message-ID: Here is a new arthropod genome paper: Genome Sequence of the Pea Aphid Acyrthosiphon pisum. The International Aphid Genomics Consortium 2010 PLoS Biol 8(2): e1000313. http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000313 Aphid has a lot of genes: 35,000 compared to 15,000 to 20,000 in other insects. There are various speculations on this large number (including artifacts) but I see evidence that species gene sets are often missing what expression and orthology searches says is there. The asexual biology of aphid also provides opportunity for keeping extra gene copies perhaps more readily than in sexual bugs. As there is rather large variation in genome sizes, and gene numbers in other phyla, it isn't unexpected to see this range in arthropods, from 10,000 in the louse to over 30,000 in aphid and daphnia. -- Don