Papers by Stephen Schaeffer
Genetics, Sep 1, 1987
The alcohol dehydrogenase (Adh) locus (ADH; alcohol: NAD+ oxidoreductase, EC 1.1.1.1) of Drosophi... more The alcohol dehydrogenase (Adh) locus (ADH; alcohol: NAD+ oxidoreductase, EC 1.1.1.1) of Drosophila pseudoobscura was cloned and sequenced. Forty-five percent of the "effectively silent sites" have changed between Adh in D. pseudoobscura of the obscura species group and the homologous DNA sequence in D. mauritiana, the latter representing the melanogaster species group. The untranslated leader sequence of the adult transcript of D. pseudoobscura has two deletions relative to the D. mauritiana message. The ADH protein sequences of D. pseudoobscura is missing the third and fourth amino acids at the N-terminus relative to the D. mauritiana enzyme. Of the remaining 254 amino acid positions, 27 (1 0.64%) differ between the two species. Amino acid replacements are randomly distributed into hydrophilic and hydrophobic domains of ADH. However, replacement substitutions are distributed nonrandomly across the three exons among D. pseudoobscura and members of the melanogaster subgroup, suggesting that functional constraints across the exons are different. Surprisingly, silent substitutions are also nonrandomly distributed with the third exon being the most divergent. This pattern suggests possible selective constraints on supposedly neutral silent substitutions and/or variation in underlying mutation rates across the gene. The presence of transcriptional and translational signals at the beginning and end of conserved sequences 3' to Adh implies the existence of a previously undescribed gene. Codon usage and patterns of nucleotide divergence are consistent with a protein coding function for this gene. In addition, conservation of nucleotide and amino acid sequence and similarity in hydropathy plots suggests that the gene 3' to Adh represents an ancient duplication of the Adh gene.
bioRxiv (Cold Spring Harbor Laboratory), Aug 15, 2022
When adaptive phenotypic variation maps within an inverted segment of a chromosome, researchers o... more When adaptive phenotypic variation maps within an inverted segment of a chromosome, researchers often despair because it is thought that the suppression of crossing over will prevent the discovery of selective target genes through fine scale genetic mapping. If an inversion polymorphism is old enough, then the accumulation of gene conversion tracts offers the promise that QTLs or selected loci within inversions can be identified. This study uses the inversion polymorphism of Drosophila pseudoobscura as a model system to determine if gene conversion analysis can be a useful tool for mapping adaptive loci within inversions. D. pseudoobscura has over 30 different chromosomal arrangements on the third chromosome (Muller C) in natural populations and their frequencies vary with changes in environmental habitats. Statistical tests identified outlier genes within inverted regions based on local clusters of fixed SNP differences. These outlier genes also had potentially selectable variation, either fixed amino acid differences or differential expression patterns among arrangements. Here, we use genome sequences of the inverted third chromosome (Muller C) to infer 98,443 gene conversion tracts for a total coverage of 142 Mb. We tested whether the frequency of gene conversion tracts in outlier versus non-outlier genes were equal. Gene conversion tracts occur less frequently in outlier versus non-outlier genes suggesting that selection removes exchanged DNA from multiple outlier genes. These data support the hypothesis that these inversions captured adaptive alleles and that strong epistatic selection removes recombinants generated through gene conversion. The pattern and organization of genetic diversity in the third chromosome in D. pseudoobscura is consistent with the capture of locally adapted combinations of alleles prior to inversion mutation events. .
Conservation Genetics Resources, Dec 4, 2012
ABSTRACT
PLOS ONE, Jun 13, 2007
Drosophila pseudoobscura harbors a rich gene arrangement polymorphism on the third chromosome gen... more Drosophila pseudoobscura harbors a rich gene arrangement polymorphism on the third chromosome generated by a series of overlapping paracentric inversions. The arrangements suppress recombination in heterokaryotypic individuals, which allows for the selective maintenance of coadapted gene complexes. Previous mapping experiments used to determine the degree to which recombination is suppressed in gene arrangement heterozygotes produced non-recombinant progeny in non-Mendelian ratios. The deviations from Mendelian expectations could be the result of viability differences between wild and mutant chromosomes, meiotic drive because of achiasmate pairing of homologues in heterokaryotypic females during meiosis, or a combination of both mechanisms. The possibility that the frequencies of the chromosomal arrangements in natural populations are affected by mechanisms other than adaptive selection led us to consider these hypotheses. We performed reciprocal crosses involving both heterozygous males and females to determine if the frequency of the non-recombinant progeny deviates significantly from Mendelian expectations and if the frequencies deviate between reciprocal crosses. We failed to observe non-Mendelian ratios in multiple crosses, and the frequency of the non-recombinant classes differed in only one of five pairs of reciprocal crosses despite sufficient power to detect these differences in all crosses. Our results indicate that deviations from Mendelian expectations in recombination experiments involving the D. pseudoobscura inversion system are most likely due to fitness differences of gene arrangement karyotypes in different environments.
Proceedings of the National Academy of Sciences of the United States of America, 1991
The amylase region of the third chromosome of Drosophila pseudoobseura has been cloned and locali... more The amylase region of the third chromosome of Drosophila pseudoobseura has been cloned and localized to cytological band 73A. It is contained within a series of highly polymorphic inversions and serves as a convenient tool for a molecular evolutionary analysis of the inverted gene arrangements. Amylase in D. pseudoobscura is a family of three genes, and some chromosomes have deletions for one or two of them. Two overlapping clones covering 26 kilobases were isolated and used as probes to survey DNA restriction map polymorphism among 28 lines, representing five of the major inversion types
Heredity, Oct 1, 1995
S-allele diversity in Solanum carolinense was surveyed in two natural populations, located in Ten... more S-allele diversity in Solanum carolinense was surveyed in two natural populations, located in Tennessee and North Carolina, with a molecular assay to determine the genotype of individual plants. A total of 13 different S-alleles were identified and sequenced. There is high overlap between the two populations sampled, with 10 alleles shared in common, one allele found only in Tennessee, and two found only in North Carolina. The number of alleles in this species appears to be extremely low compared with other species with gametophytic self-incompatibility. Sequence comparisons show that most alleles are extremely different one from another in their primary sequence and a phylogenetic analysis indicates extensive trans-specific evolution of S-lineages. In addition, some alleles appear to be derived much more recently. The implications of these observations are discussed in the light of recent theoretical results on S-allele population diversity and persistence.
The evolution of complex traits in heterogeneous environments may shape the order of genes within... more The evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with > 10 inversions with appreciable frequencies and wide geographic distributions. This study analyzes the genomic sequences of 54 strains of Drosophila pseudoobscura that carry one of six different chromosomal arrangements to test whether (1) genetic drift, (2) hitchhiking with an adaptive allele, (3) direct effects of inversions to create gene disruptions caused by breakpoints, or (4) indirect effects of inversions in limiting the formation of recombinant gametes are responsible for the establishment of new gene arrangements. We found that the inversion events do not disrupt the structure of protein coding genes at the breakpoints. Population genetic analyses of 2,669 protein coding genes identified 277 outlier loci harboring elevated frequencies of arrangement-specific derived alleles. Significant linkage disequilibrium occurs among distant loci interspersed between regions with low levels of association indicating that distant allelic combinations are held together despite shared polymorphism among arrangements. Outlier genes showing evidence of genetic differentiation between arrangements are enriched for sensory perception and detoxification genes. The data presented here support the indirect effect of inversion hypothesis where chromosomal inversions are favored because they maintain linked associations among multi-locus allelic combinations among different arrangements.
PeerJ, Aug 23, 2016
Background. Vestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea c... more Background. Vestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM) seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed for Escarpia spp. could be amplified in the GoM seep tubeworm, Seepiophila jonesi. Additionally, we determine if cross-amplified loci can reliably uncover the same signatures of high gene flow seen in a previous investigation of S. jonesi. Methods. Seventy-seven S. jonesi individuals were collected from eight seep sites across the upper Louisiana slope (<1,000 m) in the GoM. Forty-eight microsatellite loci that were originally developed for Escarpia laminata (18 loci) and Escarpia southwardae (30 loci) were tested to determine if they were homologous and polymorphic in S. jonesi. Loci found to be both polymorphic and of high quality were used to test for significant population structuring in S. jonesi. Results. Microsatellite pre-screening identified 13 (27%) of the Escarpia loci were homologous and polymorphic in S. jonesi, revealing that microsatellites can be amplified within the escarpiid clade of vestimentiferans. Our findings uncovered low levels of heterozygosity and a lack of genetic differentiation amongst S. jonesi from various sites and regions, in line with previous investigations that employed species-specific polymorphic loci on S. jonesi individuals retrieved from both the same and different seep sites. The lack of genetic structure identified from these populations supports the presence of significant gene flow via larval dispersal in mixed oceanic currents. Discussion. The ability to develop ''universal'' microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show that S. jonesi collected from various How to cite this article Huang et al. (2016), Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae) using cross-amplified microsatellite loci. PeerJ 4:e2366; DOI 10.7717/peerj.2366 localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen in Escarpia spp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species.
Journal of Heredity, Nov 1, 2003
Two Drosophila pseudoobscura genomic clones have sequence similarity to the Drosophila melanogast... more Two Drosophila pseudoobscura genomic clones have sequence similarity to the Drosophila melanogaster amylase region that maps to the 53CD region on the D. melanogaster cytogenetic map. The two clones with similarity to amylase map to sections 73A and 78C of the D. pseudoobscura third chromosome cytogenetic map. The complete sequences of both the 73A and 78C regions were compared to the D. melanogaster genome to determine if the coding region for amylase is present in both regions and to determine the evolutionary mechanism responsible for the observed distribution of the amylase gene or genes. The D. pseudoobscura 73A and 78C linkage groups are conserved with the D. melanogaster 41E and 53CD regions, respectively. The amylase gene, however, has not maintained its conserved linkage between the two species. These data indicate that amylase has moved via a transposition event in the D. melanogaster or D. pseudoobscura lineage. The predicted genes within the 73A and 78C regions show patterns of molecular evolution in synonymous and nonsynonymous sites that are consistent with previous studies of these two species.
bioRxiv (Cold Spring Harbor Laboratory), Oct 31, 2017
Philosophical Transactions of the Royal Society B, Jun 13, 2022
DNA within chromosomes in the nucleus is non-randomly organized into chromosome territories, comp... more DNA within chromosomes in the nucleus is non-randomly organized into chromosome territories, compartments and topologically associated domains (TADs). Chromosomal rearrangements have the potential to alter chromatin organization and modify gene expression leading to selection against these structural variants. Drosophila pseudoobscura has a wealth of naturally occurring gene arrangements that were generated by overlapping inversion mutations caused by two chromosomal breaks that rejoin the central region in reverse order. Unlike humans, Drosophila inversion heterozygotes do not have negative effects associated with crossing over during meiosis because males use achiasmate mechanisms for proper segregation, and aberrant recombinant meiotic products generated in females are lost in polar bodies. As a result, Drosophila populations are found to harbour extensive inversion polymorphisms. It is not clear, however, whether chromatin architecture constrains which inversions breakpoints persist in populations. We mapped the breakpoints of seven inversions in D. pseudoobscura to the TAD map to determine if persisting inversion breakpoints are more likely to occur at boundaries between TADs. Our results show that breakpoints occur at TAD boundaries more than expected by chance. Some breakpoints may alter gene expression within TADs supporting the hypothesis that position effects contribute to inversion establishment. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
Genetics, Sep 1, 2020
Sex-Ratio (SR) chromosomes are selfish X-chromosomes that distort Mendelian segregation and are c... more Sex-Ratio (SR) chromosomes are selfish X-chromosomes that distort Mendelian segregation and are commonly associated with inversions. These chromosomal rearrangements suppress recombination with Standard (ST) X-chromosomes and are hypothesized to maintain multiple alleles important for distortion in a single large haplotype. Here, we conduct a multifaceted study of the multiply inverted Drosophila pseudoobscura SR chromosome to understand the evolutionary history, genetic architecture, and present-day dynamics that shape this enigmatic selfish chromosome. The D. pseudoobscura SR chromosome has three nonoverlapping inversions of the right arm of the metacentric X-chromosome: basal, medial, and terminal. We find that 23 of 29 Mb of the D. pseudoobscura X-chromosome right arm is highly differentiated between the Standard and SR arrangements, including a 6.6 Mb collinear region between the medial and terminal inversions. Although crossing-over is heavily suppressed on this chromosome arm, we discover it is not completely eliminated, with measured rates indicating recombination suppression alone cannot explain patterns of differentiation or the near-perfect association of the three SR chromosome inversions in nature. We then demonstrate the ancient basal and medial inversions of the SR chromosome contain genes sufficient to cause weak distortion. In contrast, the younger terminal inversion cannot distort by itself, but contains at least one modifier gene necessary for full manifestation of strong sex chromosome distortion. By parameterizing population genetic models for chromosome-wide linkage disequilibrium with our experimental results, we infer that strong selection acts to maintain the near-perfect association of SR chromosome inversions in present-day populations. Based on comparative genomic analyses, direct recombination experiments, segregation distortion assays, and population genetic modeling, we conclude the combined action of suppressed recombination and strong, ongoing, epistatic selection shape the D. pseudoobscura SR arrangement into a highly differentiated chromosome. KEYWORDS meiotic drive; chromosomal inversions; recombination; selfish genetic elements S EX-Ratio (SR) chromosomes are selfish X-chromosomes that distort Mendelian segregation in their own favor by decreasing Y-bearing sperm (Policansky and Ellison 1970;
Hydrobiologia, May 16, 2014
Lamellibrachia vestimentiferan tubeworms form aggregations at hydrocarbon cold seeps in the deep ... more Lamellibrachia vestimentiferan tubeworms form aggregations at hydrocarbon cold seeps in the deep Gulf of Mexico (GoM), creating structures that provide living space for other fauna. In the GoM, three Lamellibrachia taxa vary in morphology and depth ranges: Lamellibrachia luymesi (300-950 m), Lamellibrachia sp. 1 (950-2,604 m), and Lamellibrachia sp. 2 (1,175-3,304 m). While Lamellibrachia sp. 2 is consistently identified as a separate species, L. luymesi and sp. 1 cannot be discriminated using barcoding markers cytochrome oxidase subunit 1 (COI) and large ribosomal subunit rDNA (16S). To determine if limited gene flow was a factor in the formation of these taxa, we employed more quickly evolving markers, including mitochondrial cytochrome B (CYTB), hemoglobin subunit B2 intron (HbB2i), and six polymorphic microsatellites; microsatellites were amplified across 45 L. luymesi and sp. 1 individuals. Additionally, we used microsatellites to ask whether populations of Lamellibrachia sp. 1 and sp. 2 show evidence of significant structure. Despite a lack of resolution seen with CYTB and HbB2i, L. luymesi and sp. 1 form genetically differentiated clusters at the cross-amplified microsatellites. Furthermore, we find no evidence for population structure for either Lamellibrachia sp. 1 or sp. 2 across the GoM.
Genetics, Apr 1, 1994
The transformer locus (tra) produces an RNA processing protein that alternatively splices the dou... more The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Comparisons of the tra coding region among Drosophila species have revealed an unusually high degree of divergence in synonymous and nonsynonymous sites. In this study, we tested the hypothesis that the tra gene will be polymorphic in synonymous and nonsynonymous sites within species by investigating nucleotide sequence variation in eleven tra alleles within D. melanogaster. Of the 1063 nucleotides examined, two synonymous sites were polymorphic and no amino acid variation was detected. Three statistical tests were used to detect departures from an equilibrium neutral model. Two tests failed to reject a neutral model of molecular evolution because of low statisitical power associated with low levels of genetic variation (Tajima/Fu and Li). The Hudson, Kreitman, and Aguade test rejected a neutral model when the tra region was compared to the 5"flanking region of alcohol dehydrogenase (A d h). The lack of variability in the tra gene is consistent with a recent selective sweep of a beneficial allele in or near the tra locus.
Molecular Biology and Evolution, May 1, 1987
A 32-kb region including the Adh structural gene was analyzed with six restriction endonucleases ... more A 32-kb region including the Adh structural gene was analyzed with six restriction endonucleases in 20 lines of Drosophila pseudoobscura, one line of D. persimilis, and one line of D. miranda. Nineteen lines of D. pseudoobscura from a single population were estimated to be polymorphic at one in every 15 nucleotides (p = 0.066). Any two homologous chromosomes chosen at random were heterozygous at one in 48 (H = 0.02 1) nucleotides. Two small insertions of 50 and 200 bp were found-7 kb upstream from the Adh transcript. High haplotype diversity and low linkage disequilibrium suggest that the polymorphic restriction sites around Adh have segregated almost randomly during the history of this D. pseudoobscura population and that the effects of inbreeding and periodic reduction of population size have been negligible. The restriction-endonuclease analysis for the Adh region of D. pseudoobscura stands in sharp contrast to the strong linkage disequilibrium, high levels of insertion/deletion polymorphism, and lower estimates of nucleotide polymorphism found for this same region in D. melanogaster. A phylogeny for the Adh haplotypes is consistent with an early divergence of D. miranda, while D. persimiks falls within the cluster of D. pseudoobscura haplotypes.
Genetics, Sep 1, 1997
The larval cuticle protein (Lcp) cluster in Drosophila melunoguster contains four functional gene... more The larval cuticle protein (Lcp) cluster in Drosophila melunoguster contains four functional genes and a closely related pseudogene. A 630-bp fragment including the larval cuticle pseudogene locus (L c N) was nucleotide sequenced in 10 strains of D. melanogaster and a 458-bp L c N fragment from D. simulans was also sequenced. We used these data to test the hypotheses that the rates of synonymous and nonsynonymous substitution are equal, that the absolute levels of variation are higher than in functional genes, and that intraspecific polymorphism is correlated with interspecific divergence. As predicted, synonymous and nonsynonymous substitution rates were equivalent, and overall nucleotide divergence between D. melanogusterand D. simulans Uukes-Cantor distance = 0.149 ? 0.150) was extremely high. However, within-species DNA sequence comparisons at Lcplr revealed lower levels of polymorphism (0 = 0.001 2 0.001) than at many functional loci in D. melanoguster. Using the HUDSON, KREITMAN, and AGUADE (HKA) test, we show that the level of polymorphism in Lcpllr within D. melanogasteris lower than expected given the amount of divergence between D. melanogaster and D. simulans when the pseudogene data are compared to the Adh 5' flanking region. Because the LC@ lies in a region of relatively infrequent recombination, we suggest that the low level of within-species polymorphism is the result of background selection.
Molecular Ecology, Nov 15, 2017
The evolution of complex traits in heterogeneous environments may shape the order of genes within... more The evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with > 10 inversions with appreciable frequencies and wide geographic distributions. This study analyzes the genomic sequences of 54 strains of Drosophila pseudoobscura that carry one of six different chromosomal arrangements to test whether (1) genetic drift, (2) hitchhiking with an adaptive allele, (3) direct effects of inversions to create gene disruptions caused by breakpoints, or (4) indirect effects of inversions in limiting the formation of recombinant gametes are responsible for the establishment of new gene arrangements. We found that the inversion events do not disrupt the structure of protein coding genes at the breakpoints. Population genetic analyses of 2,669 protein coding genes identified 277 outlier loci harboring elevated frequencies of arrangement-specific derived alleles. Significant linkage disequilibrium occurs among distant loci interspersed between regions with low levels of association indicating that distant allelic combinations are held together despite shared polymorphism among arrangements. Outlier genes showing evidence of genetic differentiation between arrangements are enriched for sensory perception and detoxification genes. The data presented here support the indirect effect of inversion hypothesis where chromosomal inversions are favored because they maintain linked associations among multi-locus allelic combinations among different arrangements.
Lecture Notes in Computer Science, 2014
In this paper, we designed a distance metric as DCJ-Indel-Exemplar distance to estimate the dissi... more In this paper, we designed a distance metric as DCJ-Indel-Exemplar distance to estimate the dissimilarity between two genomes with unequal contents (with gene insertions/deletions (Indels) and duplications). Based on the aforementioned distance metric, we proposed the DCJ-Indel-Exemplar median problem, to find a median genome that minimize the DCJ-Indel-Exemplar distance between this genome and the given three genomes. We adapted Lin-Kernighan (LK) heuristic to calculate the median quickly by utilizing the features of adequate subgraph decomposition and search space reduction technologies. Experimental results on simulated gene order data indicate that our distance estimator can closely estimate the real number of rearrangement events; while compared with the exact solver using equal content genomes, our median solver can get very accurate results as well. More importantly, our median solver can deal with Indels and duplications and generates results very close to the synthetic cumulative number of evolutionary events.
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Papers by Stephen Schaeffer