University of California at Davis
Research in Evolutionary Genetics
|Biology 101||Introductory Biology II (2nd sem)||
Consider butterflies. To find a particular species, you have to visit its proper habitat. Some species are very localized in widely scattered sites and even in danger of extinction, whereas others are widespread and highly mobile; some are even economic pests. These differences in habitat use create fundamental differences in the ecologies of these butterflies, and they affect the ability of these species to evolve adaptations to changes in their local environments. The rules we learn from studying butterflies often apply generally to a broad diversity of organisms.
Whether we want to conserve a rare butterfly species or control the economic damage of a pest species, we need to understand the rules of how the ecologies of these butterflies affect their ability to evolve in the face of habitat change. In conserving butterflies, we want to manage their evolution so that they are able to survive inbreeding in local populations and adapt to local conditions that inevitably change. In managing pests, we want to control the evolutionary process to inhibit the spread of "adaptations" to our pest management techniques, whether they be pesticides, planting and harvesting practices, or predators and parasites that we introduce.
Genetic structure of populations
To manage the evolutionary process, we need a much more detailed understanding of the basic rules of evolutionary change in the kind of environments we are trying manage. This entails the knowledge of how evolutionary processes (natural selection, mutation, gene flow and genetic drift) create patterns of genetic differentiation within and among different populations, that is, how these processes affect genetic population structure. The rules we uncover are basic, and apply far beyond the management of butterfly populations per se.
My research program deals with genetic population structure in several ways.
Speciation and regulatory genes
It is well known that hybrids between species are usually sterile, if indeed they are able to survive at all. If we could explain how this low hybrid fitness evolves, than we would have explained an important mechanism of how new species form (i.e., speciation). We do know that this must be caused by genes that do not interact properly in the hybrid. It has to be the interactions among genes (called epistasis), not the individual genes themselves, because these same genes work perfectly well to produce the living, breeding parents. Nobody knows what causes these poor interactions to evolve, but it is widely suspected that they arise as an inadvertant consequence when spatially isolated populations adapt to their local environmental conditions. But, the link to epistasis has seemed arbitrary to many speciation biologists, and indeed, most evolutionary geneticists use an 'additive model' to represent genetically complex traits. Under this additive model, genes contribute small parts to the phenotype, and these add up (along with environmental and other contributions) to an individual's phenotypic score.
Johnson and I suspect that developmental biology
provides copious evidence of this link between epistasis
and adaptation (Johnson
& Porter 2001). When an organism develops,
genes turn on other genes in a regulatory cascade, and
regulatory gene interactions (a type of epistasis) are
the rule rather than the exception in biological
systems. We therefore simulated two populations with
phenotypes produced by regulatory interactions among
genes, instead of additively. We subjected these
populations to evolutionary pressures and hybridized
them to look at what happened to their hybrids. We found
that when these populations were subject to directional
selection, rapid speciation evolved in accordance with
some basic theoretical predictions (Johnson &
Porter 2000). This reproductive isolation evolves
even when there is substantial gene flow between
& Johnson 2002). We are now finding that the
evolutionary dynamics of branched regulatory pathways
reduce to those of simple linear pathways under simple,
realistic conditions. But, there are some
intriguing new wrinkles that involve the evolution of
Introgression and species boundaries
Species under the biological species concept are often defined as being unable to share genes. In practice, however, this is a very difficult thing to measure and we usually rely on morphological and behavioral traits (and a liberal dose of opinion) to distinguish species. I study genetic patterns at the boundary between species in an effort to develop a measure of the rates at which genes are exchanged across the boundary. Such a rate, if negligible, indicates that the species are evolving independently and are 'good species' under the biological species concept's definition. If the rate is not negligible, then then the species are not evolving independently, and adaptations can readily spread between them. Such species will need to be treated together when managing their evolution and when making inferences about how their traits have evolved. An especially interesting corollary of this work is that 'diagnostic' traits used by systematists to recognize species can sometimes be adaptations to local ecological conditions. These can be maintained by natural selection even under the homogenizing influence of gene flow, and much of the remainder of the genome may be shared. Examples of this phenomenon are discussed in many of the papers selected below.
Species boundaries may be studied from two geographic contexts. The first is when geographic ranges of the species are adjacent, whereupon hybridization is spatially limited and occurs in hybrid zones. Examples of studies on this situation include Porter et al. (1997a), Porter (1997), and Porter & Geiger (1995, 1988). We are studying this problem in tiger swallowtail butterflies (Papilio glaucus and P. canadensis, Lepidoptera: Papilionidae), where most of the adaptive differences are on the X- and Y-chromosomes. We are mapping the genome using AFLP markers, and mapping these as they vary across the hybrid zone between these species. The results will tell us a lot about the evolutionary pressures on sex chromosomes, and the consequences of these pressures for introgression. The second is when species are sympatric, whereupon hybridization occurs throughout the geographic range. Examples of this include Porter & Ribi (1994) and Ribi & Porter (1995). I am currently doing theoretical work on this problem, using F-statistics to measure rates of introgression and gene flow in an extension of the work in Porter (1990) and Porter & Geiger (1995, 1988). We are currently applying this to the study of introgression between two sympatric Colias butterflies, Colias eurytheme and Colias philodice, that are economic pests of forage legume crops, particularly alfalfa and clover. Their hybridization indicates that adaptations conferring advantages to these crop habitats may readily spread between the species, and indicates they should perhaps be treated ecologically as a single species by pest management protocols. Baiqing Wang is using AFLP markers to map the genomes of these butterflies (Wang & Porter 2004), to determine which parts are shared and which are maintaining the separate identities of the species. Here too, most of the diagnostic differences between species seem to be on the X-chromosomes.
One major, longstanding hope of evolutionary geneticists is it might be possible to measure processes that cause evolutionary change from patterns of genetic variation within and among populations. This is really hard to do, because very often the same genetic patterns will be produced by different combinations of processes. Nevertheless, the discipline of ecological genetics exists to try to measure population sizes, selection coefficients, gene flow and mutation rates from statistical descriptions of genetic population structure. One common starting point for these measures is to assume a very simple population structure exists, namely Wright's island model. This model assumes, among other things, that there are a very large number of equal sized populations, and that individuals moving between populations have an equal chance to go to any other population. The result is pattern of allele frequency differences among populations that follows a fairly well-known statistical distribution, a beta-distribution. I have written software for a statistical test that treats the island model as a null hypothesis, instead of as a given assumption (Porter, 2003). I am currently modifying this method to permit a measure of gene flow, and a test of this null hypothesis, using dominant markers such as AFLPs. Stay tuned.
Managing adaptation to pesticides
Pesticides were long ago thought to be the panacea to agriculrural problems that arise when other species eat the food we grow for ourselves. Now we know that pesticides pose a whole host of problems, including toxicity to people and extensive collateral damage to natural (and agricultural) habitats. What's worse, the very same pest species are now evolving to be resistant to the toxic effects. This leads ultimately to failure of the crop, and before that, to larger, more frequent applications of pesticides on the fields. New ways have been invented to slow the evolution of resistance. Perhaps counterintuitively, these rely on planting areas of the crop, called refuges, that are then left untreated. Pests build up to large numbers in these refuges, and send emigrants out to the treated areas. The key idea is that these emigrants will tend to be susceptible to the pesticide (not having been exposed to it), and will mate with any new, resistant mutants that arise in the treated parts of the field. Their hybrid offspring will tend to be susceptible (or at least, not as resistant) and the treatment will kill them before the resistance can spread. It's a nice idea in theory, but it depends in practice on numerous assumptions about how resistance works physiologically, where the untreated refuges are placed in the field, and how individual pest organisms move about within and among fields. Currently, absent data on these factors, the typical recommendation is 20% of the field be planted as an untreated refuge (this is required when transgenic crops are planted).
Mitch Baker, Dave Ferro, Andrei Alyokhin and I have been working on this problem in Colorado potato bettles, which have evolved resistance to most pesticides used against them. Our trick has been to recognize that natural selection for resistance is very strong, and can evolve significantly in a single season (Baker et al. 2001). We can therefore treat half a field and leave the rest as a refuge, and by the end of the season, see a sharp change in resistance across the step. We then use cline theory to interpret details in the shape of this step at the boundary as being caused by the interaction between selection and dispersal (as the beetles move about). We have used this to measure in-field dispersal, as a prelude to the design of the size and placement of refuges in large fields. This is therefore an example of the use of ecological genetic principles to manage the rate of pest evolution in agricultural settings.
Species with small, spatially separated populations, especially those of concern to conservation biologists, are exposed to evolutionary conditions that have not been well studied by evolutionary biologists. I have been using computer simulation and mathematical modeling to address the evolution of such populations. One interesting case (Porter 1999) occurs during habitat loss when individuals can flee and become established in sites that remain. These refugees carry their genes and cause two effects. First, genetic variation within sites increases and populations are more able to adapt to ecological changes and survive the effects of inbreeding. Second, genetic variation among sites decreases due to this homogenizing effect. This refugee process throws the genetic structure out of equilibrium and it can be a very long time before equilibrium is re-established.
Conservation biology of butterflies
Makiri Sei is studying the population and community ecology of the Maritime Ringlet Butterfly, Coenonympha tullia nipisiquit (Lepidoptera: Satyrinae), known from a few salt marshes in New Brunswick, Canada. The caterpillar of this butterfly is especially interesting because it must survive complete submergence in salt water during high tides (Sei 2004). Within the salt marsh, microhabitat differences that seem subtle to casual human observers turn out to have major impacts on the ability of the young caterpillars to survive (Sei & Porter 2003).
|Entomol. 697Q||Simulation of Evolutionary Problems|
|Entomol. 326||Insect Biology|
|Entomol. 597 B||
(ENT 326 + extra assignments for graduate credit)
|Entomol. 597Q||Ecological Genetics|
|Makiri Sei||Conservation Biology of Insects|
|Baiqing Wang||Evolutionary Genetics of Insects|
|Clayton Winter||Evolutionary Genetics of Insects|
<Museum page under construction>
I am curating the Lepidoptera in the Entomology Museum.
32. Wang, B. and A. H. Porter. 2004. An AFLP-based interspecific linkage map of sympatric, hybridizing Colias butterflies. Genetics 168:215-225.
31. Sei, M., & A. H. Porter. 2003. Microhabitat-specific early larval survival of the maritime ringlet (Coenonympha tullia nipisiquit, Nymphalidae, Lepidoptera). Animal Conservation 6: 55-61.
30. Porter, A. H. 2003.
A test for deviation from island-model population structure. Molecular
Ecology 12: 903-916. [See software
29. Porter, A. H., & N. A. Johnson. 2002. Speciation despite gene flow when developmental pathways evolve. Evolution 56:2103-2111.
28. Jakob, E. M., A. H. Porter & G. W. Uetz. 2001. Site fidelity and the costs of movement among territories: an example from colonial web-building spiders. Canadian Journal of Zoology 79: 2094-2100.
27. Johnson, N. A. & A. H. Porter. 2001. Toward a new synthesis: Population genetics and evolutionary developmental biology. Genetica 112-113: 45-58.
26. Baker, M. B., D. N. Ferro & A. H. Porter. 2001. Management of a well established crop pest: Colorado potato beetle invasions on large and small scales. Biological Invasions 3: 295-306.
25. Johnson, N. A. & A. H. Porter. 2000. Rapid speciation via parallel, directional selection on regulatory genetic pathways. Journal of Theoretical Biology 205: 527-542.
24. Porter, A. H. 1999. Refugees from lost habitat and reorganization of genetic population structure. Conservation Biology 13: 850-859.
23. Porter, A. H., & J. C. Mueller. 1998. Partial genetic isolation between Phyciodes tharos and P. cocyta (Nymphalidae). Journal of the Lepidopterists' Society 52: 182-205.
22. Jakob, E. M., G. Uetz, & A. H. Porter. 1998. The effect of conspecifics on the timing of orb construction in a colonial spider. J. Arachnology 26: 335-341.
21. Porter, A. H., R. Wenger, H. J. Geiger, A. Scholl, & A. M. Shapiro. 1997. The Pontia daplidice-edusa hybrid zone in northwestern Italy. Evolution 52: 1561-1573.
20. Porter, A. H. 1997. The Pieris napi/bryoniae hybrid zone at Pont de Nant, Switzerland: broad overlap in the range of suitable host plants. Ecological Entomology 22: 189-196.
19. Porter, A. H., H. J. Geiger, D. L. A. Underwood, J. Llorente-Bousquets, & A. M. Shapiro. 1997. Relatedness and population differentiation in a colonial Mexican butterfly, Eucheira socialis (Lepidoptera: Pieridae). Annals of the Entomological Society of America 90: 230-236.
18. Porter, A. H., S. J. Cadaret, S. A. Johnson, H. Mizohata, A. I. Benedetter, C. L. Bester, J. L. Borash, S. D. Kelly, G. S. Buehner, & M. L. Sherman. 1997. Relatedness and gregariousness in the orange-striped oakworm, Anisota senatoria (Lepidoptera: Saturniidae). Journal of the Lepidopterists' Society 51: 208-217.
17. Porter, A. H. & H. J. Geiger. 1995. Limitations to the inference of gene flow at regional geographic scales - an example from the Pieris napi group (Lepidoptera: Pieridae) in Europe. Biological Journal of the Linnean Society 54: 329-348.
16. Porter, A. H., R. Schneider & B. Price. 1995. Wing pattern and allozyme relationships in the Coenonympha arcania group, emphasising the C. gardetta-darwiniana contact area at Bellwald, Switzerland. Nota Lepidopterologica 17: 155-174.
15. Ribi, G. & A. Porter. 1995. Mating between two hybridizing species, Viviparus ater and V. contectus (Mollusca: Prosobranchia). Animal Behaviour 49: 1389-1398.
14. Porter, A. H., & G. Ribi. 1994. Population genetics of Viviparus (Mollusca: Prosobranchia): homogeneity of V. ater and apparent introgression into V. contectus. Heredity 73: 170-176.
13. Porter, A. H. 1994. Implications of introduced garlic mustard (Alliaria petiolata) in the habitat of Pieris virginiensis. Journal of the Lepidopterists' Society 48: 171-172.
12. Orr, M., A. H. Porter, H. Dingle, & T. Mousseau. 1994. Molecular and morphological evidence for gene flow between the grasshoppers Melanoplus sanguinipes and M. devastator (Orthoptera: Acrididae). Heredity 72: 42-54.
11. Ward, P., & A. H. Porter. 1993. Relative roles of habitat segregation and sexual selection in the mating system of Gammarus pulex (Amphipoda: Gammaridae): a simulation study. Animal Behaviour 45: 119-133.
10. Porter, A. H., & A. M. Shapiro. 1991. Genetics and biogeography of the Oeneis chryxus complex (Satyrinae) in California. Journal of Research on the Lepidoptera 28: 263-276.
9. Porter, A. H. 1990. Testing nominal species boundaries using gene flow statistics: the taxonomy of two hybridizing admiral butterflies (Limenitis; Nymphalidae). Systematic Zoology 39: 131-148.
8. Porter, A. H., & E. M. Jakob. 1990. Allozyme variation in the introduced pholcid spider Holocnemus pluchei (Araneae: Pholcidae) in California. Journal of Arachnology 18: 313-319.
7. Porter, A. H., & A. M. Shapiro. 1990. Genitalia and arthropod taxonomy: lack of mechanical isolation in a butterfly hybrid zone (Lepidoptera: Pieridae). Annals of the Entomological Society of America 82: 107-114.
6. Porter, A. H. 1989. Genetic evidence for reproductive isolation between hybridizing Limenitis butterflies (Lepidoptera: Nymphalidae) in southwestern New Mexico. American Midland Naturalist 122: 275-280.
5. Porter, A. H., & S. O. Mattoon. 1989. A new subspecies of Coenonympha tullia (Müller) confined to the coastal dunes of northern California. Journal of the Lepidopterists' Society 43: 229-238.
4. Shapiro, A. M., & A. H. Porter. 1989. The lock-and-key hypothesis: evolutionary and biosystematic interpretation of insect genitalia. Annual Review of Entomology 34: 231-245.
3. Porter, A. H. 1989. A courtship of a model (Adelpha; Nymphalidae) by its probable Batesian mimic (Limenitis, Nymphalidae). Journal of Research on the Lepidoptera 26: 255-256.
2. Porter. A. H., & H. J. Geiger. 1988. Genetic and phenotypic population structure of the Coenonympha tullia group (Lepidoptera: Nymphalidae; Satyrinae) in California: no evidence for species boundaries. Canadian Journal of Zoology 66: 2751-2765.
1. Porter, A. H. 1986. Life history of Nemoria glaucomarginaria B. & McD. (Lepidoptera: Geometridae; Geometrinae), with notes on larval taxonomy in the tribe Nemoriini. Journal of the Lepidopterists' Society 41: 304-314.
Porter, A H. 1993. Review of Terrestrial Ecosystems through Time: Evolutionary Paleoecology of Terrestrial Plants and Animals by A. K. Behrensmeyer, J. D. Damuth, W.A. DiMichele, R. Potts, H.-D. Sues, & S. L. Wing. 1992. University of Chicago Press, Chicago. 568 pp. Ohio Journal of Science 93: 153-154.
Porter, A H. 1993. Review of The Owlet Moths of Ohio (Order Lepidoptera, Family Noctuidae). Bulletin IX(2) NS by R. W. Rings, E. H. Metzler, F. J. Arnold, & D. H. Harris. 1992. Ohio Biological Survey, Columbus, OH. 219 pp, 16 plates. Ohio Journal of Science 93: 115-116.
Porter, A. H. 1989. The status of the federally endangered
Smith's Blue butterfly (Euphilotes enoptes smithi:
at Burns Creek, Monterey County, California. Prepared for: PAR
& Associates, PO Box 160756, Sacramento CA 95816-0756; ph.
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Updated: 04 February 2005 by A. Porter