Research Interests

Research Interests

Evolutionary geneticists have studied species of Drosophila, especially D. melanogaster, throughout most of the 20^th century (see Progress and Prospects in Evolutionary Biology: The Drosophila Model, by JR Powell, 1997, Oxford Univ. Press). A vast amount of information has been obtained regarding evolutionary relationships and comparative genomics among Drosophila species. This knowledge assists our research in several ways. It is known which taxa have specific types of chromosomal changes and the polarity (ancestral vs. derived) of these rearrangements can be easily inferred. Studies have demonstrated that conservation of gene content within chromosomes is a general rule in Drosophila, although the linear arrangement of genes is often disrupted by inversions and different chromosomes commonly join together at the centromere through fusions. We can use information that is known about gene content within the sequenced D. melanogaster genome in order to develop tools to analyze specific regions in the genome of other species. These tools will become even more powerful as the genome sequences of additional Drosophila species are obtained.

Our research is currently focused on genetic analyses of the fly species, Drosophila americana. This species is a member of the virilis group of Drosophila, which is distantly related to the common laboratory fruit fly, D. melanogaster. The phylogenetic tree depicted in Figure 1 illustrates the relationships among a few members of the virilis species group and the estimated divergence times for a few lineages within the genus Drosophila.

Several members of the virilis species group are native to North America and have wide distributions throughout the United States. The range of D. americana spans the central and eastern US. All flies in the virilis species group are found natively in riparian habitats, and their larvae feed on decaying willows, poplars and alders. We study natural populations of D. americana and routinely make collections of flies.

Chromosomal Evolution and Speciation

Chromosomal change is common. Numerous cytogenetic studies have revealed differences in genome organization upon comparisons of karyotypes of closely related taxa. Chromosome painting studies in representative mammalian taxa reveal an extensive number of rearrangements among mammals (see Science Vol. 286, No. 5439). Chromosomal rearrangements have been implicated as playing important roles in adaptation and speciation; however, little supporting evidence has been obtained for this assertion. One of the active projects in the lab is examining the role of a chromosomal rearrangement in mediating adaptation in a natural population.

A chromosomal polymorphism is present throughout the range of D. americana (Figure 2). The two chromosomal types were previously recognized as the subspecies, D. a. americana and D. a. texana, although genetic differentiation between these two taxa has only been observed for the chromosomal rearrangement and linked loci (McAllister 2002; Vieira et al. 2001). The derived chromosomal arrangement (D. a. americana) is comprised of the X chromosome being fused to an autosome (chromosome 4). This autosomal pair is freely segregating in other species in the virilis group of Drosophila, including what is recognized as D. a. texana.

The range of D. americana includes most of the United States east of the Rocky Mountains. The distribution of the derived arrangement is throughout the northern part of this range, with populations in the Great Plains, Midwest and Northeast having nearly all X chromosomes fused with chromosome 4. Populations of D. americana in the south-central to southeast US lack the X-4 fusion arrangement. Throughout a region from Arkansas/Missouri eastward to North Carolina/Virginia, populations exhibit both chromosomal arrangements. The best classic summary of the distributions of these subspecies is found in the book by Patterson and Stone (1952), Evolution in the Genus Drosophila. We have sampled flies at many localities throughout the range of D. americana in an attempt to better understand the distribution of these alternative chromosomal forms. Our lab currently maintains a number of iso-female lines from these collections. Straightforward assays have been developed for determining chromosomal organization within wild-collected flies (McAllister 2001; 2002), and we are willing to assist others in collecting and analyzing natural populations of D. americana.

We are actively analyzing the genetic structure of populations of D. americana that are polymorphic for the chromosomal arrangement. During the summer of 1999, flies were collected at five localities just west of the Mississippi River along a latitudinal transect. Genetic analyses were performed to determine the arrangement of the X chromosome (fused to 4, or unfused) in these samples. As expected, the X-4 fusion is common in the northern part of the transect (west of St. Louis, MO) and rare in the southern part (southeast of Pine Bluff, AR). It was demonstrated (McAllister 2002) that the frequencies of the alternative chromosomal arrangements are tightly correlated with latitude in this geographic region (Figure 3). Nucleotide variation assayed at three different nuclear genes showed little evidence of geographic structure among these samples; a result that is consistent with previous studies (for an example, see McAllister and McVean 2000).

Natural selection along this north-south gradient apparently maintains the polymorphism for these alternative chromosomal arrangements. One hypothesis for the form of selection acting on the chromosomes is that alleles near the centromere of the X-4 fusion are favored in northern regions, whereas alleles on the unfused chromosomes are favored in southern regions. Genetic variation in the centromeric region of the X and 4^th chromosomes is currently being analyzed to test this hypothesis. Genotype data are used to examine the degree of genetic isolation among samples and chromosomal populations, and to detect regions of observed relative to expected linkage disequilibrium along these chromosomes. Effects of chromosomal arrangements on phenotypes related to temperature are also being examined. Ultimately, the goal is to reveal regions on the X and/or 4^th chromosomes that are targets of natural selection.

Sex Chromosome Evolution

Sex chromosomes are the basis of gender determination in many organisms. In the type of chromosomal sex determination present in Drosophila and humans, presence of two X chromosomes specifies development of a female, and presence of single X and Y chromosomes specifies development of a male. Males transmit a single sex chromosome (either X or Y) to each sperm, and upon fertilization of an egg already containing a single X from a female, gender is determined. The genetic content and structure of X and Y chromosomes is very different. Many genes are specific to the X chromosome and not present on the Y, but the reverse is rare. A long-standing hypothesis is that X and Y chromosomes are derived from identical chromosomal pairs, but upon isolation of Y chromosomes in males, genes on this chromosome loose their functions (Figure 4). This hypothesis has gained strong support from analysis of the X and Y chromosome in humans (Lahn and Page 1999, Science 286:964).

In the northern range of D. americana, X chromosomes are fused with 4^th chromosomes. In these populations, this chromosomal arrangement transforms autosomal pair 4 into neo-sex chromosomes (i.e., this autosomal pair segregates as sex chromosomes). The X chromosome is fused with a 4^th chromosome, and male flies have an unfused 4^th chromosome that segregates with the primary Y chromosome (as seen in the male with the X-4 fusion in Figure 1 above). These unfused 4^th chromosomes of D. americana are male-limited, and are isolated from recombination due to the absence of crossing over in male Drosophila, thus the unfused 4^th chromosomes represent neo-Y chromosomes. We are using this system as a model to study sex chromosome evolution, which is the genetic and morphologic differentiation of X and Y chromosomes (Figure 4).

Important aspects on the state of this system have been revealed. The neo-sex chromosomes in D. americana are very young, and neo-Y chromosomes are not completely isolated from recombination (McAllister and Charlesworth, 1999). Fixation of the fusion between the X and 4^th chromosomes is responsible for creating the neo-sex chromosomes, and only the most northern populations of D. americana are fixed. Also, active gene flow of unfused 4^th chromosomes apparently occurs from southern populations, where these chromosomes are present in females, into the northern neo-Y chromosomal population. Because only a short period of time has been available for differentiation of the neo-X and neo-Y chromosomes, coupled with opportunities for exchange between neo-X and neo-Y chromosomes, this system is ideal for studying the earliest events in sex-chromosome evolution.

We recently analyzed sequence differentiation between the neo-X, neo-Y and autosomal 4^th chromosomes in several samples of D. americana (McAllister 2003). Sequence variation in the big brain (bib) gene was found to be strongly differentiated for a subset of neo-X chromosomes. These neo-X chromosomes exhibit a set of closely related sequences (a haplogroup) at bib, and the pattern of sequence variation among chromosomes is also consistent with bib being influenced by hitchhiking resulting from directional selection on a nearby variant. Furthermore, we identified the complete association between variation in bib and a nearby paracentric inversion (Figure 5). The derived bib haplogroup and the derived inversion are specific to the neo-X chromosome. The finding of the inversion is interesting in regard to the evolution of sex chromosomes, because direct measurements indicate that recombination is suppressed in females between neo-X chromosomes with In(4)ab and unfused 4^th chromosomes with the standard arrangement. Thus, the inversion appears to be serving as a suppressor of recombination between neo-X and neo-Y chromosomes.

The X-4 chromosomal fusion has created a gradient of reduced recombination on unfused 4^th chromosomes. We are also using this system to test for the predicted effects of background selection on patterns of sequence variation on the neo-Y chromosome of D. americana. We are characterizing sequence variation at loci throughout unfused 4^th chromosomes. Specific regions of this chromosome are being targeted based on their availability within a physically mapped library of large-fragment containing clones of the D. virilis genome. Variation among neo-Y chromosomes is being examined through sequence analyses of these regions. This study will generate a powerful data set for testing the background selection model.

Acknowledgements

This material is based upon work supported by the National Science Foundation under the following Grant Nos.

DEB-0420399 Genome Arrangement and Adaptive Evolution, 9/1/04-8/31-08
DEB-0075295 /0228832 Causes of Y-Chromosome Degeneration, 8/1/00-7/31/03
BIR-9626084, Molecular Evolution of Sex Chromosomes, NSF/Sloan Postdoctoral Fellowship, 10/1/96-9/30/98

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

Iowa • FLYowa • Biological Sciences • Genetics • CCG • McAllister Lab

Evolutionary geneticists have studied species of Drosophila, especially D. melanogaster, throughout most of the 20^th century (see Progress and Prospects in Evolutionary Biology: The Drosophila Model, by JR Powell, 1997, Oxford Univ. Press). A vast amount of information has been obtained regarding evolutionary relationships and comparative genomics among Drosophila species. This knowledge assists our research in several ways. It is known which taxa have specific types of chromosomal changes and the polarity (ancestral vs. derived) of these rearrangements can be easily inferred. Studies have demonstrated that conservation of gene content within chromosomes is a general rule in Drosophila, although the linear arrangement of genes is often disrupted by inversions and different chromosomes commonly join together at the centromere through fusions. We can use information that is known about gene content within the sequenced D. melanogaster genome in order to develop tools to analyze specific regions in the genome of other species. These tools will become even more powerful as the genome sequences of additional Drosophila species are obtained.
Our research is currently focused on genetic analyses of the fly species, Drosophila americana. This species is a member of the virilis group of Drosophila, which is distantly related to the common laboratory fruit fly, D. melanogaster. The phylogenetic tree depicted in Figure 1 illustrates the relationships among a few members of the virilis species group and the estimated divergence times for a few lineages within the genus Drosophila. Several members of the virilis species group are native to North America and have wide distributions throughout the United States. The range of D. americana spans the central and eastern US. All flies in the virilis species group are found natively in riparian habitats, and their larvae feed on decaying willows, poplars and alders. We study natural populations of D. americana and routinely make collections of flies.
Chromosomal Evolution and Speciation
Chromosomal change is common. Numerous cytogenetic studies have revealed differences in genome organization upon comparisons of karyotypes of closely related taxa. Chromosome painting studies in representative mammalian taxa reveal an extensive number of rearrangements among mammals (see Science Vol. 286, No. 5439). Chromosomal rearrangements have been implicated as playing important roles in adaptation and speciation; however, little supporting evidence has been obtained for this assertion. One of the active projects in the lab is examining the role of a chromosomal rearrangement in mediating adaptation in a natural population.
A chromosomal polymorphism is present throughout the range of D. americana (Figure 2). The two chromosomal types were previously recognized as the subspecies, D. a. americana and D. a. texana, although genetic differentiation between these two taxa has only been observed for the chromosomal rearrangement and linked loci (McAllister 2002; Vieira et al. 2001). The derived chromosomal arrangement (D. a. americana) is comprised of the X chromosome being fused to an autosome (chromosome 4). This autosomal pair is freely segregating in other species in the virilis group of Drosophila, including what is recognized as D. a. texana.
The range of D. americana includes most of the United States east of the Rocky Mountains. The distribution of the derived arrangement is throughout the northern part of this range, with populations in the Great Plains, Midwest and Northeast having nearly all X chromosomes fused with chromosome 4. Populations of D. americana in the south-central to southeast US lack the X-4 fusion arrangement. Throughout a region from Arkansas/Missouri eastward to North Carolina/Virginia, populations exhibit both chromosomal arrangements. The best classic summary of the distributions of these subspecies is found in the book by Patterson and Stone (1952), Evolution in the Genus Drosophila. We have sampled flies at many localities throughout the range of D. americana in an attempt to better understand the distribution of these alternative chromosomal forms. Our lab currently maintains a number of iso-female lines from these collections. Straightforward assays have been developed for determining chromosomal organization within wild-collected flies (McAllister 2001; 2002), and we are willing to assist others in collecting and analyzing natural populations of D. americana.
We are actively analyzing the genetic structure of populations of D. americana that are polymorphic for the chromosomal arrangement. During the summer of 1999, flies were collected at five localities just west of the Mississippi River along a latitudinal transect. Genetic analyses were performed to determine the arrangement of the X chromosome (fused to 4, or unfused) in these samples. As expected, the X-4 fusion is common in the northern part of the transect (west of St. Louis, MO) and rare in the southern part (southeast of Pine Bluff, AR). It was demonstrated (McAllister 2002) that the frequencies of the alternative chromosomal arrangements are tightly correlated with latitude in this geographic region (Figure 3). Nucleotide variation assayed at three different nuclear genes showed little evidence of geographic structure among these samples; a result that is consistent with previous studies (for an example, see McAllister and McVean 2000).
Natural selection along this north-south gradient apparently maintains the polymorphism for these alternative chromosomal arrangements. One hypothesis for the form of selection acting on the chromosomes is that alleles near the centromere of the X-4 fusion are favored in northern regions, whereas alleles on the unfused chromosomes are favored in southern regions. Genetic variation in the centromeric region of the X and 4^th chromosomes is currently being analyzed to test this hypothesis. Genotype data are used to examine the degree of genetic isolation among samples and chromosomal populations, and to detect regions of observed relative to expected linkage disequilibrium along these chromosomes. Effects of chromosomal arrangements on phenotypes related to temperature are also being examined. Ultimately, the goal is to reveal regions on the X and/or 4^th chromosomes that are targets of natural selection.
Sex Chromosome Evolution
Sex chromosomes are the basis of gender determination in many organisms. In the type of chromosomal sex determination present in Drosophila and humans, presence of two X chromosomes specifies development of a female, and presence of single X and Y chromosomes specifies development of a male. Males transmit a single sex chromosome (either X or Y) to each sperm, and upon fertilization of an egg already containing a single X from a female, gender is determined. The genetic content and structure of X and Y chromosomes is very different. Many genes are specific to the X chromosome and not present on the Y, but the reverse is rare. A long-standing hypothesis is that X and Y chromosomes are derived from identical chromosomal pairs, but upon isolation of Y chromosomes in males, genes on this chromosome loose their functions (Figure 4). This hypothesis has gained strong support from analysis of the X and Y chromosome in humans (Lahn and Page 1999, Science 286:964).
In the northern range of D. americana, X chromosomes are fused with 4^th chromosomes. In these populations, this chromosomal arrangement transforms autosomal pair 4 into neo-sex chromosomes (i.e., this autosomal pair segregates as sex chromosomes). The X chromosome is fused with a 4^th chromosome, and male flies have an unfused 4^th chromosome that segregates with the primary Y chromosome (as seen in the male with the X-4 fusion in Figure 1 above). These unfused 4^th chromosomes of D. americana are male-limited, and are isolated from recombination due to the absence of crossing over in male Drosophila, thus the unfused 4^th chromosomes represent neo-Y chromosomes. We are using this system as a model to study sex chromosome evolution, which is the genetic and morphologic differentiation of X and Y chromosomes (Figure 4).
Important aspects on the state of this system have been revealed. The neo-sex chromosomes in D. americana are very young, and neo-Y chromosomes are not completely isolated from recombination (McAllister and Charlesworth, 1999). Fixation of the fusion between the X and 4^th chromosomes is responsible for creating the neo-sex chromosomes, and only the most northern populations of D. americana are fixed. Also, active gene flow of unfused 4^th chromosomes apparently occurs from southern populations, where these chromosomes are present in females, into the northern neo-Y chromosomal population. Because only a short period of time has been available for differentiation of the neo-X and neo-Y chromosomes, coupled with opportunities for exchange between neo-X and neo-Y chromosomes, this system is ideal for studying the earliest events in sex-chromosome evolution.
We recently analyzed sequence differentiation between the neo-X, neo-Y and autosomal 4^th chromosomes in several samples of D. americana (McAllister 2003). Sequence variation in the big brain (bib) gene was found to be strongly differentiated for a subset of neo-X chromosomes. These neo-X chromosomes exhibit a set of closely related sequences (a haplogroup) at bib, and the pattern of sequence variation among chromosomes is also consistent with bib being influenced by hitchhiking resulting from directional selection on a nearby variant. Furthermore, we identified the complete association between variation in bib and a nearby paracentric inversion (Figure 5). The derived bib haplogroup and the derived inversion are specific to the neo-X chromosome. The finding of the inversion is interesting in regard to the evolution of sex chromosomes, because direct measurements indicate that recombination is suppressed in females between neo-X chromosomes with In(4)ab and unfused 4^th chromosomes with the standard arrangement. Thus, the inversion appears to be serving as a suppressor of recombination between neo-X and neo-Y chromosomes.
The X-4 chromosomal fusion has created a gradient of reduced recombination on unfused 4^th chromosomes. We are also using this system to test for the predicted effects of background selection on patterns of sequence variation on the neo-Y chromosome of D. americana. We are characterizing sequence variation at loci throughout unfused 4^th chromosomes. Specific regions of this chromosome are being targeted based on their availability within a physically mapped library of large-fragment containing clones of the D. virilis genome. Variation among neo-Y chromosomes is being examined through sequence analyses of these regions. This study will generate a powerful data set for testing the background selection model.