Products by NESCent
Scientists
Publication,
Software/Databases, and Proposals/Grants
December 2004 –
February 2008
I. PUBLICATIONS
Postdoctoral Fellows
Published / In Press
Johnson
N.C., Hoeksema J.D., Umbanhowar J.A., Bever J., Chaudhary V.B., Gehring C.A., Klironomos J.N., Koide R., Moore J., Miller M., Moutoglis P., Schwartz M.W., Simard S., Swenson W., Wilson G.W., and Zabinski C.. 2006.
From Lilliput to Brobdingnag:
Extending models of mycorrhizal function across
scales. Bioscience 56(11):889-900.
Hoeksema, J.D., Forde, S.E. 2008. A meta-analysis of factors affecting local adaptation between
interacting species. Am. Nat. 171:276-290.
Hoeksema J.D., and J.N. Thompson. 2007. Evolved geographic
structure in a widespread plant-ectomycorrhizal interaction: Pines and false truffles. Journal of Evolutionary Biology
20:1148-1163.
Kidd, D. M., and
M. G. Ritchie. 2006. Phylogeographic information systems; Putting the geography
into phylogeography. Journal of Biogeography 33:1851-1865.
Kidd, D. M., and X. Liu. in press.
GEOPHYLOBUILDER 1.0: an ArcGIS extension for creating
'geophylogenies'. Molecular Ecology
Notes.
McCall, L.W. 2007. Individual invention vs. socioecological innovation: Unifying the behavioral and
evolutionary sciences. Brain and Behavior Sciences. In press.
Sidlauskas, Brian L. 2007. Testing for
unequal rates of morphological diversification in the absence of a detailed
phylogeny: a case study from characiform fishes. Evolution 61(2):299-316.
Sidlauskas, Brian L., Julío Cesar Garavello and Jennifer Jellen. 2007. A new Schizodon (Characiformes: Anostomidae)
from the Río Orinoco system, with a redescription of
S. isognathus from the Rio Paraguay system. Copeia 2007(3):711-725.
Sidlauskas, Brian L. and Richard Vari. 2008 (in press). Phylogenetic relationships within the South American fish family Anostomidae (Teleostei, Ostariophysi, Characiformes).
Zoological Journal of the Linnean Society, 384
manuscript pages
In Prep / Submitted
Harmon,
Luke J., Jonathan B. Losos, Jonathan Davies, Rosemary
G. Gillespie, John L. Gittleman, W. Bryan Jennings,
Kenneth Kozak, Mark A. McPeek, Franck Moreno-Roarck, Tom J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, James A. Schulte II, Ole Seehausen,
Hoeksema J.D., and S. Forde. A meta-analysis of factors affecting local adaptation
between species. In review, The American Naturalist.
Horvath,
J.E., D.W. Weisrock, S.L. Embry, I. Fiorentino, J.P.
Balhoff, P. Kappeler, G.A. Wray, H.F. Willard,
and A.D. Yoder. 2007. Developing a Genomic Toolkit to Resolve Deep
Species Relationships: Lemur Phylogeny and Divergence Estimation. (In preparation)
McCall, L.W. Studying cultural evolution at the
tips: Human cross-cultural ecology. In review.
McCall, L.W. Vertebrate locomotor diversification and the hominin brain. In review.
Brian Sidlauskas, Omar Torres-Carvajal,
Jason T. Weir, & Arne Mooers. (in review). Constraints and the scaling of evolutionary rates. Submitted to Nature.
Sabbatical Scholars
and Visitors
Published / In Press
Agrawal, A. F. and S. P. Otto (2006) Host-parasite coevolution and selection on sex
through the effects of segregation. American Naturalist,
168: 617-629.
Barrett, R.
D. H., L. K. M'Gonigle, and S. P. Otto (2006) The distribution of
beneficial mutant effects under strong selection. Genetics, 174: 2071-2079.
Beldade, P., A. Papanicolaou,
and W. O. McMillan. (2007) Butterfly Genomics Eclosing. Heredity (in press).
Charlesworth, J. & Eyre-Walker, A.
(2007) The other side of the neutral theory, evidence
for slightly advantageous back-mutations. Proc. Natl. Acad. Sci.
USA (in press)
Charlesworth, J. & Eyre-Walker, A. (2006) The rate of adaptive evolution in enteric
bacteria. Mol. Biol. Evol. 23:1348-1356.
Citerne HL, Pennington RT, Cronk QC. An
apparent reversal in floral symmetry in the legume Cadia is a homeotic transformation. Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12017-20. Epub 2006 Jul 31.
Cronk QC. Legume
flowers bear fruit. Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4801-2. Epub
2006 Mar 27.
Cronk Q, Ojeda I, Pennington RT. Legume
comparative genomics: progress in phylogenetics and phylogenomics. Curr Opin Plant Biol. 2006
Apr;9(2):99-103. Epub 2006
Feb 15. Review.
Cronk, Q. 329 page synthesis manuscript, The
Molecular Organography of Plants, written while at
NESCENT (to be published by Oxford University Press).
Cui, L., J.
Leebens-Mack, L. Wang, J. Tang, L. Rymarquis, D. Stern, and C.W. dePamphilis.
2006. Adaptive Evolution of Chloroplast Genome Structure Inferred Using a
Parametric Bootstrap Approach. BMC Evolutionary Biology 6:13.
Eyre-Walker, A. (2006) Size does not matter for
mitochondrial DNA. Science 312, 537-538.
Eyre-Walker, A. (2006) The rate of adaptive evolution at the molecular level. TREE 21, 569-575.
Eyre-Walker, A. & Keightley,
P.D. (2007) The distribution of fitness effects of new
mutations. Nature Reviews Genetics 8:610-618.
Eyre-Walker, A., Woolfit,
M. & Phelps, T. (2006) The distribution of fitness
effects of new deleterious amino acid mutations in humans. Genetics 173:891-900.
Gandon,
S., and S. P. Otto (2007) The evolution of sex and recombination in response to abiotic or coevolutionary fluctuations in epistasis. Genetics, 175:1835-1853.
Gerstein,
A. C., H.-J. E. Chun, A. Grant, and S.
P. Otto (2006) Genomic convergence toward diploidy in Saccharomyces cerevisiae. PLoS Genetics, 2: e145.
Gilchrist EJ, Haughn GW, Ying CC, Otto SP, Zhuang J,
Cheung D, Hamberger B, Aboutorabi F, Kalynyak T, Johnson L, Bohlmann J, Ellis
BE, Douglas CJ, Cronk QC. Use of
Ecotilling as an efficient SNP discovery tool to survey genetic variation in
wild populations of Populus trichocarpa. Mol Ecol. 2006 Apr;15(5):1367-78.
Guillaume, F., and M. C. Whitlock. 2007. Effects of migration on the
genetic covariance matrix. In press, Evolution. (http://www.blackwell-synergy.com/doi/full/10.1111/j.1558-5646.2007.00193.x)
Hadany,
L. and S. P. Otto (2007) The evolution of condition-dependent sex in the face of high
costs. Genetics, in press.
Harper, G. R. Jr. & Pfennig,
D. W. 2008. Selection overrides gene flow to break down maladaptive mimicry. Nature 451:
1103-1106.
Hill, J.
A., and S. P. Otto (2007) The role of pleiotropy in the
maintenance of sex in yeast. Genetics,
175: 1419-1427.
Joron,
M., C. D. Jiggins, A. Papanicolaou, and W. O McMillan. (2006) Heliconius wing patterns: an evo-devo model
for understanding phenotypic diversity. Heredity 97: 157-167.
Joron,
M., R. Papa, M. Beltran, J. Mavarez, R. Papa, E. Bermingham, J. Mallet, W.
O. McMillan and C. D. Jiggins. (2006) A conserved supergene locus controls color pattern convergence and divergence in Heliconius
butterflies. PLoS Biology 4(10): e303.
Ledon-Rettig, C., Pfennig, D. W., & Nascone-Yoder, N.
2008. Ancestral
variation and the potential for genetic accommodation in larval amphibians:
Implications for the evolution of novel feeding strategies. Evolution and
Development (in press).
Maddison,
W. P., P. E. Midford and S. P. Otto (2007) Estimating a binary character's effect on
speciation and extinction. Systematic Biology, in press.
Mandegar,
M. A., and S. P. Otto (2007) Mitotic
recombination counteracts the benefits of genetic segregation. Proceedings of the Royal Society,
Otto, S. P. (2007) The evolutionary consequences of polyploidy. Cell, in press.
Otto, S. P. and T. Day (2007) A Biologist’s
Guide to Mathematical Modeling.
Papanicolaou , A., S. Gebauer-Jung,
M. L. Blaxter, W.
O. McMillan and C. D. Jiggins. (2008) ButterflyBase:
a platform for Lepidoptera genomics. Nucleic Acids Research 36(Database issue):D582–D587.
Ramirez, M.J., Coddington,
J.A., Maddison, W.P., Midford,
P.E., Prendini, L., Miller, J., Griswold, C.E., Hormiga, G., Sierwald, P., Scharff, N., Benjamin, S.P., Wheeler, W.C. 2007. Linking of digital images to phylogenetic data matrices using a
morphological ontology. Syst. Biol 56(2):1-12.
Reed, R. D., W. O. McMillan,
and L. M. Nagy. (2007) Gene expression underlying adaptive variation in Heliconius wing
patterns: non-modular regulation of overlapping cinnabar and vermilion
patterns. Proceedings of the Royal
Society of London, Series B, accepted.
Rice. A.
M. & Pfennig, D. W. 2008.
Analysis of range expansion in two species undergoing character displacement:
Why might invaders generally "win" during character displacement? Journal
of Evolutionary Biology (in press, published online March 13, 2008).
Servedio, M. R. Male versus female mate choice: sexual selection and the evolution of
species recognition via reinforcement. Evolution, in press.
Servedio, M. R., S. A. Saether and G.-P. Satre. Reinforcement and learning. Evolutionary Ecology, in press.
Stoletzki, N. & Eyre-Walker, A. (2007) Synonymous Codon Use in Escherichia coli - Selection for translational accuracy. Mol. Biol. Evol.
24:374-381.
Tuskan G, Cronk Q, et al. The
genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313 (5793),
1596. [DOI: 10.1126/science.1128691]
Whitlock, M. C. Founder effects. Encyclopedia of
Whitlock, M. C., B. H. Davis, and S. Yeaman. 2007. The costs and benefits of altruistic resource
sharing. Journal of Evolutionary Biology 20:1772-1782.
Whitlock, M. C., and D. Schluter. 2008. The analysis of biological
data. Roberts & Co., ~870pp.
Whitton,
J., Sears, C. J., Baack, E. J., and S. P. Otto (2007) The dynamic nature of apomixis in the angiosperms.
International Journal of Plant Sciences, in press.
Williams, D. and Clamp, J.C.
2007. A Molecular Phylogenetic Investigation of Opisthonecta and Related Genera (Ciliophora, Peritrichia, Sessilida). Journal of Eukaryotic Microbiology 54:317-323.
Zeyl, C.
W., and S. P. Otto (2007) A short
history of recombination in yeast. Trends in Ecology and Evolution, 22:
223-225.
In Prep / Submitted
Davis, B. H., A. F. Y. Poon, and M. C. Whitlock. Compensatory mutations cluster in
gene sequence: General properties and support for the cotranslational model of protein folding. To be submitted to Proceedings of the National
Academy of Sciences.
Nuismer, S. L., S. P. Otto, and F. Blanquart (2007)
Host-parasite interactions and the evolution of non-random mating and parasite
speciation. Nature, in prep.
Pfennig, K.
S. & Pfennig, D. W. Character
displacement: Ecological and reproductive solutions to a common evolutionary
problem. Quarterly Review of
Biology (in review).
Pfennig, D. W. Character displacement: ecology, development, and the origins of diversity.
Pfennig, D. W. Perspective: Causes and consequences of allopatry in
mimicry complexes. To be submitted to Journal of Evolutionary Biology.
Pfennig, D. W. & Martin, R. A. A maternal effect mediates divergence between populations of spadefoot toads undergoing character displacement. To be submitted to Evolution.
Otto, S. P., S. L. Nuismer,
and M. R. Servedio (2007)
Frequency-dependent selection and the evolution of assortative mating. Genetics, in prep.
Whitlock, M. C. Evolutionary inference from QST. To be
submitted to Molecular Ecology.
Working Groups
Published / In Press
Beder, J. H., and Gomulkiewicz, R. 2007. Optimizing selection for function-valued traits. J. Mathematical Biology (to appear).
Brenner, E.
& D. Stevenson. 2005. Using genomics to study evolutionary origins
of seeds. Pp. 1- 21 in C. Williams (ed), Landscapes, Genomics, and Transgenic Conifers.
Brenner,E.D.,
M.S. Katari, D.W.
Stevenson, S.A. Rudd, A.W. Douglas, W.N. Moss, R.W. Twigg,
S.J. Runko, G.M. Stellari,
R. W. McCombie, & G. M. Coruzzi.
2005. EST analysis in Ginkgo biloba: an assessment of
conserved developmental regulators and gymnosperm specific genes. BMC Genomics
6:143-152.
Grimm, G. W., S. S. Renner,
A. Stamatakis, and V. Hemleben. 2006. A nuclear ribosomal DNA phylogeny
of Acer inferred with maximum likelihood, splits
graphs, and motif analysis of 606 sequences. Evolutionary Bioinformatics Online
2:279-294.
Haendel, M.A., F. Neuhaus, D.S. Osumi-Sutherland,
P.M. Mabee, J.L.V. Mejino, C.J. Mungall and B. Smith. 2007. CARO - The Common Anatomy Reference Ontology. In: Anatomy
Ontologies for Bioinformatics: Principles and Practice, A. Burger, D. Davidson
and R. Baldock (eds).
Kelly, J.K. [
Leebens-Mack,J., T. Vision, E. Brenner, J. E.
Bowers, S. Cannon, M. J. Clement, C. W. Cunningham, C. DePamphilis,
R. DeSalle, J. J. Doyle, J. A. Eisen, Xun Gu, J. Harshman, R. K. Jansen, E. A. Kellogg, E. V. Koonin, B. D. Mishler, H.
Philippe, J. C. Pires, Y-L. Qiu,
S. Y. Rhee, K. Silander, D. E. Soltis,
P. S. Soltis, D.
W. Stevenson, K. Wall. 2006. Taking the First Steps towards a Standard for
Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis
(MIAPA). OMICS 10:231-237.
Little, D.
P. & D. W. Stevenson. 2007. A comparison of algorithms for the
identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 22:1-21.
Little, D. P., R. C. Moran, E. D. Brenner, & D. W. Stevenson. 2007.
Nuclear genome size in Selaginella. Genome 50:351-356.
Mabee, P.M., Arratia,
G., Coburn, M., Haendel, M., Hilton, E.J., Lundberg, J.G., Mayden, R.L., Rios, N., and Westerfield, M. (2007) Connecting evolutionary morphology to genomics
using ontologies: a case study from Cypriniformes including zebrafish. J. Exp. Zoolog. B Mol. Dev. Evol.
Mabee, P.M., Ashburner,
M., Cronk, Q., Gkoutos, G.V., Haendel, M., Segerdell, E., Mungall,
C., and Westerfield, M. (2007)
Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol. Evol. 22(7):345-350.
Manchester, S.
R., Q.-Y. (J.) Xiang, Q. P. Xiang. 2007. Curtisia (Cornales) from the Eocene of Europe and its phytogeographic significance. Botanical
Journal of Linnean Society. 155:127-134.
Petersen, G., O. Seberg, J. Davis, & D. Stevenson, 2006. RNA editing and
phylogenetic reconstruction in two monocot mitochondrial genes. Taxon 55:871-886.
Petersen,
G., O. Seberg, J. Davis, D. Stevenson, M. Chase, J. Pires, M. Fay,
L. Campbell, J. Freudenstein, D. Goldman, C. Hardy,
F. Michelangeli, M. Simmons, & C. Specht. 2006. Mitochondrial data in monocot phylogenetics.
Aliso:52-62.
Pires,
J., I. Maureira, T. Givnish,
K. Sytsma, O. Seberg, G.
Petersen, J. Davis, D. Stevenson, P. Rudall, M. Fay, & M. Chase. 2006. Phylogeny,
genome size, and chromosome evolution of Asparagales.
Aliso:287-304.
Ree, R. H. and S. A. Smith. 2007. Maximum-likelihood inference of geographic range evolution by
dispersal, local extinction, and cladogenesis. Systematic Biology (in press).
Renner, S. S., L. Beenken,
G. W. Grimm, A. Kocyan, and R. E. Ricklefs. The evolution of dioecy, heterodichogamy, and
labile sex expression in Acer. Evolution (in press).
Sargent, R.D., C. Goodwillie,
de la Torre, J.,
M. G. Egan, M. Katari, E. D. Brenner, D.
W. Stevenson, G. M. Coruzzi, & R. DeSalle. 2006. Estimating plant phylogeny: lessons from partitioning.
BMC Evolutionary Biology 6:48-87.
Xiang, Q.-Y. (J.), David
T. Thomas, Wenheng Zhang, Steven R. Manchester, and Zack Murrell.
2006. Species level phylogeny of the
Dogwood genus Cornus (Cornaceae)
based on molecular and morphological evidence - implication in taxonomy and
Tertiary intercontinental migration. TAXON 55:9-30.
In Prep / Submitted
Eckert, C.G.,
Goodwillie, C., P.-O. Cheptou,
C.G. Eckert, E. Elle, M.A. Geber, M.O.
Johnston, S. Kalisz, J.K. Kelly,
D.A. Moeller, E. Porcher, R.H. Ree, R.D. Sargent, M. Vallejo-Mara, A.A. Winn.
Mating-system evolution and floral allocation: macro- and microevolutionary
patterns. Planned for Evolution.
Lahti, D. C.,
Johnson, N. A., Otto, S. P., Ajie, B. C., Blumstein,
D. T., Bull, J. J., Burch, C. L., Coss, R. G., Day,
T., Donohue, K., Foster, S. A., Jeffery, W. R., Richards, A., Stock, D. W., Thibert-Plante, X. Relaxed selection and trait loss:
patterns and processes (proposal in review for Nature).
Moeller, D.A., R.D. Sargent, P.-O. Cheptou, C.G. Eckert, E.
Elle, M.A. Geber, C. Goodwillie, M.O. Johnston, S. Kalisz,
J.K. Kelly, E. Porcher, R.H. Ree, M. Vallejo-Mara, A.A. Winn. Comparative analysis of plant mating-systems.
Porcher, E., J.K. Kelly, P.-O. Cheptou,
C.G. Eckert, E. Elle, M.A. Geber, C. Goodwillie, M.O. Johnston, S. Kalisz, D.A. Moeller, R.H. Ree, R.D. Sargent, M. Vallejo-Mara, A.A. Winn. The
genetic consequences of fluctuating inbreeding depression and the evolution of
plant mating systems. Planned for fall 2007 submission
to Journal of Evolutionary Biology or Genetical Research.
Renner, S. S., G. W. Grimm, G. Schneeweiss, T. F. Stuessy, and
R. E. Ricklefs. Rooting and dating maples (Acer) via a Bayesian
evolutionary analysis: Implications for North American/Asian range
disjunctions. (manuscript close to submission)
Vallejo-Mara, M., M. Uyenoyama, P.-O. Cheptou,
C.G. Eckert, E. Elle, M.A. Geber, C. Goodwillie, M.O. Johnston, S. Kalisz, J.K. Kelly, D.A. Moeller, E. Porcher, R.H. Ree, R.D. Sargent,
A.A. Winn. Clonality, population structure and inbreeding depression.
Winn, A.A.,
Catalysis Meetings
Published / In Press
Russell, A. L., J. Ranivo,
E. P. Palkovacs, S. M. Goodman, and A. D. Yoder. 2007. Working at the interface of
phylogenetics and population genetics: a biogeographical analysis of Triaenops spp.
(Chiroptera: Hipposideridae).
Molecular Ecology 16:839-851.
In Prep / Submitted
C. Kremen, A. Cameron, A. Moilanen,
S. Phillips, H. Beentje, J. Dransfeld,
B. L. Fisher, F. Glaw, R. Hijmans,
D. C. Lees, E. Louis, C. Raxworthy, G. Schatz, M. Vences, D. R. Vieites, P. C. Wright , M.L.Zjhra.
2007. Aligning conservation priorities across taxa in
Russell, A. L., S. M. Goodman, and M. P. Cox. In prep. Coalescent analyses support multiple main-to-island dispersals in the evolution
of Malagasy Triaenops bats (Chiroptera: Hipposideridae). Systematic
Biology.
Other Meetings and
Activities
Published / In Press
Beder, J. H., and R. Gomulkiewicz. Optimizing selection for function-valued traits. Journal of Mathematical
Biology. (Accepted
Gilchrist, G. W., and C. Lee. 2007. All stressed out and nowhere
to go: does evolvability limit adaptation in invasive
species? Genetica 129:127-132.
Jones, C.B. 2007. The evolution of exploitation in
humans: "surrounded by strangers I thought were my friends". Ethology 113:499-510.
Kohn, David. 2008.
Lapp H, Bala S,
Balhoff JP, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katamaya T, Lewis
PO, Mackey A, Osborne BI, Piel WH, Kosakovsky-Pond
SL, Poon A, Qiu W-G, Stajich JE, Stoltzfus A, Thierer T, Vilella AJ, Vos RA, Zmasek CM, Zwickl D, Vision TJ (accepted pending
revision) The 2006 NESCent Phyloinformatics Hackathon: A field report. Evolutionary
Bioinformatics.
Leebens-Mack
J, Vision T, Brenner E, Bowers JE,
Cannon S and 21 others (2006) Taking the first steps towards a standard for
reporting in phylogenies: Minimal Information About a Phylogenetic Analysis
(MIAPA). OMICS 10, 231-237. doi:10.1089/omi.2006.10.231
Terry, M. 2008 (2004). One nation, under the Designer. Pp. 402-411 in . J.W. Noll, ed. Taking sides: clashing
views on educational issues. 14th ed., expanded. McGraw-Hill,
Terry, M. 2007. What’s design got to do
with it?: Independent schools and the teaching of
science.
Terry, M. 2005. Tending the tree of life
in the high school garden. Pp. 78-82 in
J. Cracraft and R. Bybee, eds. Evolutionary science and society: educating a new generation. BSCS/AIBS,
Terry, M. 2005. Art and evolution. The Science Teacher 72:22-25.
Terry, M. 2004. One nation, under the
Designer. Phi Delta Kappan 86:264-270.
Terry, M. and S. Linneman. 2003. Watching the Wedge: How the Discovery
Institute seeks to change the teaching of science.
In Prep / Submitted
Griswold, C. K., R. Gomulkiewicz, and N. Heckman. Hypothesis testing in comparative and experimental studies
of function-valued traits. Evolution. (In revision; submitted
Ahmed Moustafa and Debashish Bhattacharya. 2007. Phylogenomic analysis identifies Plantae genes
with chlamydia origin. (Preparing)
Tsai YE, Fox JR, Kidd D. 2007. PhyloGeoViz:
A Phylogeographic visualization tool. In prep.
II. Software and
databases
Postdoctoral Fellows
Bolker et al. [B.
O’Meara] 2008. Phylobase. http://r-forge.r-project.org/projects/phylobase/ . A new R package produced at the R hackathon;
my contribution was to help add the ability for R to read data and trees from
Nexus files.
Ganeshkumar Ganapathy, Nihshanka Debroy. DQ: A python package for multilocus disequilibria. http://www.nescent.org/software/LD.zip
Hoeksema J. D. SAS code for conducting mixed-model
meta-regression analysis in SAS.
Hoeksema J. D. and S. Forde. 2007. Summary data on local
adaptation, species traits, and experimental design across 29 cross-inoculation
studies of species interactions.
Kidd, D. M., and X. Liu. GEOPHYLOBUILDER 1.0
http://www.nescent.org/informatics/software.php
Lewis, Holder, et al. 2008. Nexus Class Library. http://sourceforge.net/projects/ncl/ . I've been added
as an author for relatively minor contributions to reading multiple Nexus
blocks of the same type.
Tsai YE, Fox JR, Kidd D. 2007. PhyloGeoViz: A Phylogeographic visualization tool. http://phylogeoviz.org.
Sabbatical Scholars
and Visitors
Jones, C.B., R.H. Horwich,
and R.C. Brockett, R.C. 2006. Demography of black howler monkeys (Alouatta pigra) in two habitats
at the Community "Baboon" Sanctuary (CBS),
Maddison, W. P., and M. J. Ramirez. 2006. Simple Image LinKing (SILK): A
Ramirez, M. J., J. A. Coddington, P. Midford.
2007. Spider comparative biology: Ontology of terms. Version control and tracker available at
http://obo.cvs.sourceforge.net.
Working Groups
Johnston and Kalicz. The final database will comprise four separate databases.
1) The
mating system database contains information on estimates of selfing/outcrossing rate and/or the inbreeding coefficient measured at the population level for 475
species.
2) The
inbreeding depression database contains information on estimates inbreeding
depression measured across the life history (3-stage or 4-stage IBD) measured
at the population level.
3) The
experimental pollination database contains information at the population level
on experimental tests of selfing, outcrossing,
pollen limitation, reproductive assurance, timing of selfing,
etc.
4) The species
traits database contains data on the average morphological, phenological,
life history and habitat characteristics for all 475 species in the mating
system database.
Significantly,
all four databases contain citations to the original publications from which
the data
were extracted.
Kowalewski. Maximum Body Size
Database - A database of maximum body size of organisms across major taxonomic
groups and through time. In final stages of
completion. We expect the first edition to be published online in 2008.
Mark Gibson and Nicole Washington. [M. Haendel] 2007. Phenote working group. www.phenote.org
Ree, R. H. and S. A. Smith. 2007. Lagrange: likelihood analysis of geographic range evolution.
http://code.google.com/p/lagrange
Other Meetings and
Activities
Carrier, S., Dube, J., Greenberg, J. 2007. The DRIADE project: Phased
application profile development in support of open science. Proc. Int’l Conf. on
S., Dube, Carrier, S., Greenberg, J. 2007. DRIADE: A data
repository for evolutionary biology. JCDL. Pg. 481.
James C. Estill, Hilmar Lapp, William Piel. 2007. Command line topological query application for BioSQL. https://www.nescent.org/wg_phyloinformatics/
PhyloSoC:Command_Line_Topological_Query_Application_for_BioSQL
James Leung. ImageMagick Studio LLC. 2007.
ImageMagick. http://www.imagemagick.org
Osborne, B.I., and S. Cain. 2007. The new GMOD Wiki with
complete GMOD documentation. http://www.gmod.org
Jason E Stajich