I am collecting a series of journal articles I have found addressing the topic of the genetic basis of adaptation and/or evolutionary change. Most of the studies I have found are focused on changes that lead to speciation (the origin of species). (Note that this is macroevolution as macroevolution is defined as evolution at or above the species level.) Interestingly, these studies are consistantly finding that adaptive differences are often controlled by relatively few genetic differences of large effect (along with larger numbers of genetic differences that have small effects upon the structure of interest). Most of the studies only determine the genetic regions that influence physical trait differences between species. This is often done using RAPD markers. In some of the more recent studies, researchers have begun to track down and sequence the regions that lead to physical differences that result in speciation. Such studies should become more common in the future. This site is very much under construction and should change frequently as I find more articles. It seems to me that the ultimate goal of these studies should be to link (1) genetic variations (both pre-existing variations and those generated through recent mutations) to  (2) variations in anatomy and phsiology that lead to increased survivability for different individuals due to (3) identified causes that explain why the anatomical / physilogical differences enhance survivability in particular environments.

Many of the studies on the page (see the Mimulus studies) attempt to work out the genetic differences between closely related species by studying the effects upon anatomy due to QTL (quantitative trait loci) differences in the offspring of hybrids of the two species.  Morphological innovation and developmental genetics, a paper in Proceedings of the National Academy of Sciences, addressed this process in 1999 (linked below). This process is leading to the conclusion that much of the anatomic differences between these species are explained by relatively few genetic differences that have a large effect upon the organism. To quote the authors of that paper , "...whereas many genes of small effect may be involved, a few factors of large effect might account for the lion's share of phenotypic differences between taxa." Additionally, Orr mentions that: "Such analyses routinely reveal that morphological differences involve a modest number of chromosome regions of substantial effect." Please follow the link to the paper to get the full context of these quotes.

The most recent paper on this topic that I have found was published in the Dec. 20^th issue of Nature. These researchers are using the techniques described here to work out the genetic basis of the anatomic differences between related species of the stickleback fish.

Morphological innovation and developmental genetics
Charles R. Marshall, H. Allen Orr, and Nipam H. Patel
Proc. Natl. Acad. Sci. USA, Vol. 96, Issue 18, 9995-9996, August 31, 1999

How do the actions of individual genes contribute to the complex morphologies of animals and plants? How widespread are these genes taxonomically? How many genes are involved in the morphological differences observed between species, and can we identify them? To what extent can empirical data and theory be reconciled? We provide an overview of some recent attempts to answer these questions, answers that have taken us to the threshold of understanding the mechanistic basis and evolutionary factors that underlie morphological innovation.

Stanford Researchers Develop System For Field Testing Mechanisms Of Evolution
December 20^th, 2001

STANFORD, Calif. - Evolutionary biology has always faced a major hurdle - how to test a process that takes place over thousands, if not millions, of years. Researchers at Stanford University may have come up with a solution. Genetic mutations and the possible mechanisms underlying evolution have been studied in laboratory animals for decades, said David Kingsley, PhD, professor of developmental biology and assistant investigator for the Howard Hughes Medical Institute. The challenge has been to find a means of applying what scientists know to be true in the lab to systems in the natural world. In a paper published Dec. 20 in the journal Nature, Kingsley and his team propose that a small spiny fish called the three-spine stickleback, and the gene-linkage map of the fish's chromosomes that the team has developed, may be the tools evolutionary biologists have been needing.

The key, according to Kingsley, was to find two populations, that unlike laboratory bred mice and rats, would have traits that had evolved naturally and yet could still be cross-bred.

"What we needed were two species that had diverged fairly recently, had distinct morphological differences, were fast-growing and easy to keep in the laboratory," said Kingsley. It was also important to find two species, Kingsley said, that could produce viable offspring in the lab even if they would not naturally mate in the wild. The group's intent was to develop a map of the inheritance patterns showing the links between genes from one generation to another. According to Kingsley, it is a system used to study genetics in laboratory-bred mice, but he wanted to develop a system that could test inheritance patterns, mutations, and ultimately the mechanisms underlying evolution in natural populations.

"It's part of an age-old debate," Kingsley said. "Does evolution occur through infinitesimally small genetic changes involving a very large number of genes, or does it occur through changes of large effect associated with a smaller number of genes?" In the lab, according to Kingsley, much of the focus is on single gene mutations of large effect, but how does this apply to evolution as it occurs naturally? Kingsley and his team turned to the genetic architecture of two populations of sticklebacks for some answers.

"What made sticklebacks so appealing was that not only did they meet our criteria from a molecular and genetics standpoint, but their ecology and  behavior has also been widely studied by many other researchers," Kingsley said.

To develop the gene-linkage map of the fish's genome, Kingsley's team first designed a marking system that would allow them to follow the inheritance patterns of various genes from one generation to the next. Using the markers, the team crossbred two populations - a near-shore invertebrate feeding species and an open-water plankton feeding species. They followed the patterns of inheritance through several generations, developing a genome-wide gene linkage map. Next, they used the map to analyze the genetic basis for a number of evolutionary changes that occurred in the two populations, such as the amount of body armor, the number of gill rakers and the length of the stickleback's spines.

Kingsley said they found a number of parallels between traditional laboratory genetics and the traits they examined in the stickleback populations. For example, many of the traits could be traced to major chromosome regions - indicating that evolution can occur through changes of large effect, not just as a series of small changes. Their findings also indicate that genetic control of body regions appears to be modular. The genes that control the length of the first dorsal spine, for instance, are located on different chromosome regions from the genes that control the length of the second dorsal spine. This is not surprising, said Kingsley, because it follows previous findings of the genetic control of mouse skeleton development. As anyone who plays with Legos can testify to, a modular body plan greatly increases the options for tweaking designs over time.

"The goal of this project was to develop a system that makes it possible to bring what we know in the laboratory about molecular genetics and begin applying it in the field to evolutionary theory and ecology," said Kingsley. The initial results, he said, suggest that these fish can now be used for detailed genetic studies of the mechanisms that control vertebrate evolution.

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Environmental adaptations as windows on molecular evolution.
Schulte PM.
Department of Biology, University of Waterloo, 200 University Avenue West, Ontario, N2L 3G1, Waterloo, Canada
Comp Biochem Physiol B Biochem Mol Biol 2001 Mar;128(3):597-611

Changes in gene regulation may play an important role in adaptive evolution, particularly during adaptation to a changing environment. However, little is known about the molecular mechanisms underlying adaptively significant variation in gene regulation. To address this question, we are using environmental adaptations in populations of a fish, Fundulus heteroclitus as a window into the molecular evolution of gene regulation. F. heteroclitus are found along the East Coast of North America, with populations distributed along a steep thermal gradient. At the extremes of the species range, populations have undergone local adaptation to their habitat temperatures. A variety of genes differ in their regulation between these populations. We have determined the mechanism responsible for changes in lactate dehydrogenase-B (Ldh-B) gene regulation. A limited number of mutations in the regulatory sequence of this gene result in changes in its expression. Both the phenotypic (increased LDH activity) and genotypic (changes in Ldh-B regulatory sequences) differences between populations have been shown to be affected by natural selection, rather than genetic drift. Therefore, even a small number of mutations within important regulatory sequences can provide evolutionarily significant variation and have an impact on environmental adaptation.

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Evolutionary adaptations of gene structure and expression in natural populations in relation to a changing environment: a multidisciplinary approach to address the million-year saga of a small fish.
Powers DA, Schulte PM. Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA.
J Exp Zool 1998 Sep-Oct 1;282(1-2):71-94

We have used an experimentally based strategy to address molecular mechanisms underlying adaptation in Fundulus heteroclitus. In an attempt to falsify the hypothesis that selection is a major driving force in the maintenance of genetic diversity, we employed a multidisciplinary approach including allelic isozyme and mtDNA phylogeography, kinetic analyses of allelic isozymes, analysis of variation in coding and regulatory DNA sequences, metabolic biochemistry, organismal physiology, and selection experiments. Observed differences in gene structure and expression led us to make testable predictions about differences in metabolic flux, whole organism performance, and differential survival between allotypes. We have shown that variation in the lactate dehydrogenase-B (Ldh-B) protein results in differences in physiological function and is correlated with differences in survival at high temperatures. Recent work has investigated the role of variation in Ldh-B expression. There are differences in the levels of Ldh-B protein, mRNA, and transcription rate. We have addressed the mechanisms responsible for differences in transcription rate by a combination of sequence comparison, DNase I footprinting, and functional analyses both in vitro and in vivo. We have shown that variation in the regulatory sequence of Ldh-B is responsible for the differences in transcription rate between populations and that the patterns of variation are inconsistent with a neutral model of molecular evolution. This functional differentiation, coupled with departures from neutral expectations, suggests that natural selection has acted on the regulation of Ldh-B. This article illustrates the value of a multidisciplinary approach in addressing problems in gene structure, expression, and evolutionary adaptation.
 

The Population Genetics of the Origin and Divergence of the Drosophila simulans Complex Species
Richard M. Kliman, Peter Andolfatto, Jerry A. Coyne, Frantz Depaulis, Martin Kreitman, Andrew J. Berry, James McCarter, John Wakeley, and Jody Hey
Genetics, Vol. 156, 1913-1931, December 2000

The origins and divergence of Drosophila simulans and close relatives D. mauritiana and D. sechellia were examined using the patterns of DNA sequence variation found within and between species at 14 different genes. D. sechellia consistently revealed low levels of polymorphism, and genes from D. sechellia have accumulated mutations at a rate that is 50% higher than the same genes from D. simulans. At synonymous sites, D. sechellia has experienced a significant excess of unpreferred codon substitutions. Together these observations suggest that D. sechellia has had a reduced effective population size for some time, and that it is accumulating slightly deleterious mutations as a result. D. simulans and D. mauritiana are both highly polymorphic and the two species share many polymorphisms, probably since the time of common ancestry. A simple isolation speciation model, with zero gene flow following incipient species separation, was fitted to both the simulans/mauritiana divergence and the simulans/sechellia divergence. In both cases the model fit the data quite well, and the analyses revealed little evidence of gene flow between the species. The exception is one gene copy at one locus in D. sechellia, which closely resembled other D. simulans sequences. The overall picture is of two allopatric speciation events that occurred quite near one another in time.
 

Divergence of larval morphology between Drosophila sechellia and its sibling species caused by cis-regulatory evolution of ovo/shaven-baby
Élio Sucena and David L. Stern
Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 9, 4530-4534, April 25, 2000

We report an extreme morphological difference between Drosophila sechellia and related species of the pattern of hairs on first-instar larvae. On the dorsum of most species, the posterior region of the anterior compartment of most segments is covered by a carpet of fine hairs. In D. sechellia, these hairs have been lost and replaced with naked cuticle. Genetic mapping experiments and interspecific complementation tests indicate that this difference is caused, in its entirety, by evolution at the ovo/shaven-baby locus. The pattern of expression of the ovo/shaven-baby transcript is correlated with this morphological change. The altered dorsal cuticle pattern is probably caused by evolution of the cis-regulatory region of ovo/shaven-baby in the D. sechellia lineage.
 
 

The Genetic Basis of Drosophila sechellia's Resistance to a Host Plant Toxin Corbin D. Jones
Genetics, Vol. 149, 1899-1908, August 1998

Unlike its close relatives, Drosophila sechellia is resistant to the toxic effects of the fruit of its host plant, Morinda citrifolia. Using 15 genetic markers, I analyze the genetic basis of D. sechellia's resistance to this fruit's primary toxin, octanoic acid. D. sechellia's resistance is dominant in F1 hybrids between it and its sister species D. simulans. All chromosomes, except the Y and the dot fourth, carry genes affecting resistance. The third chromosome has the greatest effect and carries at least two factors. The X chromosome has an intermediate effect and harbors at least two genes, whereas the second chromosome carries at least one gene of weak effect. Thus, at least five loci are involved in this adaptation. However, I also identified large chromosome regions having no effect on resistance, suggesting that D. sechellia's resistance is neither very simple nor highly polygenic. Instead, resistance appears to have an oligogenic basis. D. sechellia's resistance to its host may contribute to ecological isolation between it and D. simulans.
 

 Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus)
Douglas W. Schemske, and H. D. Bradshaw Jr.
Proceedings of the National Academy of Sciences, Vol. 96, Issue 21, 11910-11915, October 12, 1999

A paradigm of evolutionary biology is that adaptation and reproductive isolation are caused by a nearly infinite number of mutations of individually small effect. Here, we test this hypothesis by investigating the genetic basis of pollinator discrimination in two closely related species of monkeyflowers that differ in their major pollinators. This system provides a unique opportunity to investigate the genetic architecture of adaptation and speciation because floral traits that confer pollinator specificity also contribute to premating reproductive isolation. We asked: (i) What floral traits cause pollinator discrimination among plant species? and (ii) What is the genetic basis of these traits? We examined these questions by using data obtained from a large-scale field experiment where genetic markers were employed to determine the genetic basis of pollinator visitation. Observations of F2 hybrids produced by crossing bee-pollinated Mimulus lewisii with hummingbird-pollinated Mimulus cardinalis revealed that bees preferred large flowers low in anthocyanin and carotenoid pigments, whereas hummingbirds favored nectar-rich flowers high in anthocyanins. An allele that increases petal carotenoid concentration reduced bee visitation by 80%, whereas an allele that increases nectar production doubled hummingbird visitation. These results suggest that genes of large effect on pollinator preference have contributed to floral evolution and premating reproductive isolation in these monkeyflowers. This work contributes to growing evidence that adaptation and reproductive isolation may often involve major genes.
 

Quantitative Trait Loci Affecting Differences in Floral Morphology Between Two Species of Monkeyflower (Mimulus)
H. D. Bradshaw, Jr, Kevin G. Otto, Barbara E. Frewen, John K. McKay, and Douglas W. Schemske
Genetics, Vol. 149, 367-382, May 1998

Conspicuous differences in floral morphology are partly responsible for reproductive isolation between two sympatric species of monkeyflower because of their effect on visitation of the flowers by different pollinators. Mimulus lewisii flowers are visited primarily by bumblebees, whereas M. cardinalis flowers are visited mostly by hummingbirds. The genetic control of 12 morphological differences between the flowers of M. lewisii and M. cardinalis was explored in a large linkage mapping population of F2 plants (n = 465) to provide an accurate estimate of the number and magnitude of effect of quantitative trait loci (QTLs) governing each character. Between one and six QTLs were identified for each trait. Most (9/12) traits appear to be controlled in part by at least one major QTL explaining 25% of the total phenotypic variance. This implies that either single genes of individually large effect or linked clusters of genes with a large cumulative effect can play a role in the evolution of reproductive isolation and speciation.