Conclusions
The last decade has seen an explosion of development of new model systems
for the study of development, evolution and ecology. This has been due in part to the
increasing accessibility of medium- and large-scale sequencing, together with the
improvement of bioinformatics tools for their analysis, resulting in more genome and
EST databases. New model development has also gained momentum due to
demonstrability: the more community members are exposed to new models and learn
about how they were developed and the possibilities for new research areas they
afford, the more open researchers become to developing new models of their own.
We hope that this paper will encourage colleagues both to take advantage of newly
established or newly developing model systems, and also to consider developing new
models of their own.
Recently developed models have made an invaluable contribution to our
understanding of ecological and evolutionary processes. The introduction and/or
solidification of several paradigms that are now widely accepted could not have
happened without the development of new model systems. For example, the concept
of modularity in development has been refined with data from non-melanogaster
Drosophilids and sea urchins [1, 2]. (ANOTHER EXAMPLE HERE?)
New model systems have also permitted researchers to test predictions of, or
answer questions raised by, theoretical biology. For example, case studies of gene
duplications fitting the predictions of the duplication, duplication-degeneration and
DDC models [3, 4] have been provided by non-melanogaster Drosophilids,
columbines and other plant models [5, 6]. Beach mice, brine shrimp, finches and
non-melanogaster Drosophilids are being used to examine the relative roles of cisand trans-regulation of gene expression in the evolution of both novel morphologies
and adaptive radiations [7-12]. The molecular mechanisms underlying evolutionary
convergence and parallelism have been elucidated using sticklebacks (more
examples?) [13, 14]. New models can also inform phylogenetic relationships by
providing new data sets either in the form of sequence data [15-17], morphological or
developmental characters [18-20].
The availability of new model systems can allow new questions to be asked,
or old questions to be answered in newly informative ways. For example, the
developmental origins and evolutionary consequences of parthenogenesis have long
been a subject of discussion [21], and the development of the pea aphid as a model
species offers a promising new system to study this phenomenon [22]. The homology
concept and the ground pattern of the last common ancestors of various nodes of the
evolutionary tree, can be re-examined with the molecular data provided by new
models such as ferns, sea anemones, and annelid worms [23-26].
Finally, new systems can and should be developed to address questions of
practical and clinical significance, if current models prove inefficient or
unsatisfactory. For example, new insights into stem cell biology and regeneration are
promised by new flatworm models [27, 28], while transgenic advances in chickens
and cichlids have important applications in animal industry and trade [29, 30].
Establishing a new model system is not as laborious or expensive as even five
years ago, thanks both to the dropping prices and increasing efficiency of sequencing
technology, and to the growing integration of data on life histories and phylogenetic
relationships. We hope that our description of which characteristics should be sought
in a new model, in order to answer specific types of biological questions, will enable
researchers to more easily pinpoint candidate species for new model development.
Even if something cannot be cultured in the laboratory, as long as some samples can
be obtained, deep EST and possibly even genome sequencing is possible. However,
building a new model can present challenges: a pre-existing research community may
or may not exist, and specific tools may have to be targeted for development, possibly
requiring significant investments of time and/or money. For example, while RNAi
and morpholino advances mean that developing reverse genetics requires only some
extent of lab culture, the development of forward or classical genetics requires not
just a minimum of genetic map information, but also the space and culture facility to
keep dozens or more individual strains alive for the duration of the study, and
efficient lab breeding over several generations. Building a collaborative community
of researchers interested in a common model can greatly enhance the development of
new models. Ultimately, however, increased resources from funding agencies will
have to (continue to?) stretch beyond studies on well-established species, to support
both the development of new tools (e.g. transgenesis or culture facilities) for fledgling
models, and the creation of preliminary tools (e.g. EST collections or BAC libraries)
for potential new ones.
References
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
Ludwig, M.Z., N.H. Patel, and M. Kreitman, Functional analysis of eve stripe
2 enhancer evolution in Drosophila: rules governing conservation and
change. Development, 1998(125): p. 949-958.
Arnone, M.I. and E.H. Davidson, The hardwiring of development:
organization and function of genomic regulatory systems. Development, 1997.
124(10): p. 1851-64.
Ohno, S., Evolution by gene duplication. 1970, New York: Springer Verlag.
Lynch, M. and A. Force, The probability of duplicate gene preservation by
subfunctionalization. Genetics, 2000. 154(1): p. 459-73.
Kramer, E.M., M.A. Jaramillo, and V.S. Di Stilio, Patterns of gene
duplication and functional evolution during the diversification of the
AGAMOUS subfamily of MADS box genes in angiosperms. Genetics, 2004.
166(2): p. 1011-23.
Wang, W., H. Yu, and M. Long, Duplication-degeneration as a mechanism of
gene fission and the origin of new genes in Drosophila species. Nat Genet,
2004. 36(5): p. 523-7.
Ronshaugen, M., N. McGinnis, and W. McGinnis, Hox protein mutation and
macroevolution of the insect body plan. Nature, 2002. 415(6874): p. 914-7.
Galant, R. and S.B. Carroll, Evolution of a transcriptional repression domain
in an insect Hox protein. Nature, 2002. 415(6874): p. 910-3.
Abzhanov, A., et al., Bmp4 and morphological variation of beaks in Darwin's
finches. Science, 2004. 305(5689): p. 1462-5.
Gompel, N., et al., Chance caught on the wing: cis-regulatory evolution and
the origin of pigment patterns in Drosophila. Nature, 2005. 433(7025): p. 4817.
Prud'homme, B., et al., Repeated morphological evolution through cisregulatory changes in a pleiotropic gene. Nature, 2006. 440(7087): p. 1050-3.
Hoekstra, H.E., et al., A single amino acid mutation contributes to adaptive
beach mouse color pattern. Science, 2006. 313(5783): p. 101-4.
Colosimo, P.F., et al., Widespread parallel evolution in sticklebacks by
repeated fixation of Ectodysplasin alleles. Science, 2005. 307(5717): p. 192833.
Shapiro, M.D., M.A. Bell, and D.M. Kingsley, Parallel genetic origins of
pelvic reduction in vertebrates. Proc Natl Acad Sci U S A, 2006. 103(37): p.
13753-8.
Theodorides, K., et al., Comparison of EST libraries from seven beetle
species: towards a framework for phylogenomics of the Coleoptera. Insect
Mol Biol, 2002. 11(5): p. 467-75.
Philippe, H., N. Lartillot, and H. Brinkmann, Multigene analyses of bilaterian
animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and
Protostomia. Mol Biol Evol, 2005. 22(5): p. 1246-53.
Savard, J., et al., Phylogenomic analysis reveals bees and wasps
(Hymenoptera) at the base of the radiation of Holometabolous insects.
Genome Res, 2006. 16(11): p. 1334-8.
Gabriel, W.N., et al., The tardigrade Hypsibius dujardini, a new model for
studying the evolution of development. Dev Biol, 2007. 312(2): p. 545-59.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
Stollewerk, A., M. Weller, and D. Tautz, Neurogenesis in the spider
Cupiennius salei. Development, 2001. 128(14): p. 2673-88.
Kadner, D. and A. Stollewerk, Neurogenesis in the chilopod Lithobius
forficatus suggests more similarities to chelicerates than to insects. Dev Genes
Evol, 2004. 214(8): p. 367-79.
Halvorson, H.O. and A. Monroy, The Origin and Evolution of Sex. MBL
Lectures in Biology. Vol. 7. 1985, New York: Alan R. Liss, Inc. 345.
Miura, T., et al., A comparison of parthenogenetic and sexual embryogenesis
of the pea aphid Acyrthosiphon pisum (Hemiptera : Aphidoidea). Journal of
Experimental Zoology Part B-Molecular and Developmental Evolution, 2003.
295B(1): p. 59-81.
Sano, R., et al., KNOX homeobox genes potentially have similar function in
both diploid unicellular and multicellular meristems, but not in haploid
meristems. Evol Dev, 2005. 7(1): p. 69-78.
Finnerty, J.R., et al., Origins of bilateral symmetry: Hox and dpp expression in
a sea anemone. Science, 2004. 304(5675): p. 1335-7.
Arendt, D., et al., Ciliary photoreceptors with a vertebrate-type opsin in an
invertebrate brain. Science, 2004. 306(5697): p. 869-71.
Seaver, E.C. and L.M. Kaneshige, Expression of 'segmentation' genes during
larval and juvenile development in the polychaetes Capitella sp. I and H.
elegans. Dev Biol, 2006. 289(1): p. 179-94.
Pfister, D., et al., The exceptional stem cell system of Macrostomum lignano:
Screening for gene expression and studying cell proliferation by hydroxyurea
treatment and irradiation. Frontiers in Zoology, 2007. 4: p. 9.
Sanchez Alvarado, A. and H. Kang, Multicellularity, stem cells, and the
neoblasts of the planarian Schmidtea mediterranea. Exp Cell Res, 2005.
306(2): p. 299-308.
Maclean, N., et al., Transgenic tilapia and the tilapia genome. Gene, 2002.
295(2): p. 265-77.
van de Lavoir, M.C., et al., Germline transmission of genetically modified
primordial germ cells. Nature, 2006. 441(7094): p. 766-9.