scholarly journals Selective Constraint Dominates the Evolution of Genes Expressed in a Novel Reproductive Gland

2014 ◽  
Vol 31 (12) ◽  
pp. 3266-3281 ◽  
Author(s):  
Findley R. Finseth ◽  
Eliana Bondra ◽  
Richard G. Harrison
Keyword(s):  
Selective Constraint ◽  
Reproductive Gland

scholarly journals Molecular Evolution at the decapentaplegic Locus in Drosophila

Genetics ◽  
1997 ◽  
Vol 145 (2) ◽  
pp. 297-309 ◽  
Author(s):  
Stuart J Newfeld ◽  
Richard W Padgett ◽  
Seth D Findley ◽  
Brent G Richter ◽  
Michele Sanicola ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Transforming Growth Factor ◽  
Transforming Growth Factor Β ◽  
Selective Constraint ◽  
Amino Acid Sequences ◽  
Regulatory Sequences ◽  
Protein Coding ◽  
Terminal Ligand ◽  
Cdna Sequences ◽  
Interspecific Comparisons

Using an elaborate set of cis-regulatory sequences, the decapentaplegic (dpp) gene displays a dynamic pattern of gene expression during development. The C-terminal portion of the DPP protein is processed to generate a secreted signaling molecule belonging to the transforming growth factor-β (TGF-β) family. This signal, the DPP ligand, is able to influence the developmental fates of responsive cells in a concentration-dependent fashion. Here we examine the sequence level organization of a significant portion of the dpp locus in Drosophila melanogaster and use interspecific comparisons with D. simulans, D. pseudoobscura and D.virilis to explore the molecular evolution of the gene. Our interspecific analysis identified significant selective constraint on both the nucleotide and amino acid sequences. As expected, interspecific comparison of protein coding sequences shows that the C-terminal ligand region is highly conserved. However, the central portion of the protein is also conserved, while the N-terminal third is quite variable. Comparison of noncoding regions reveals significant stretches of nucleotide identity in the 3′ untranslated portion of exon 3 and in the intron between exons 2 and 3. An examination of cDNA sequences representing five classes of dpp transcripts indicates that these transcripts encode the same polypeptide.

scholarly journals Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 667-677
Author(s):  
Hitoshi Araki ◽  
Nobuyuki Inomata ◽  
Tsuneyuki Yamazaki
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Natural Populations ◽  
Sliding Window ◽  
Selective Constraint ◽  
Proximal Region ◽  
Coding Regions ◽  
Asian Populations ◽  
Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

scholarly journals Recombination and Selection at Brassica Self-Incompatibility Loci

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 413-425 ◽  
Author(s):  
Philip Awadalla ◽  
Deborah Charlesworth
Keyword(s):  
Linkage Disequilibrium ◽  
Balancing Selection ◽  
Brassica Species ◽  
Selective Constraint ◽  
Intragenic Recombination ◽  
Self Incompatibility ◽  
History Of ◽  
Unknown Gene ◽  
Slg Gene ◽  
High Diversity

Abstract In Brassica species, self-incompatibility is controlled genetically by haplotypes involving two known genes, SLG and SRK, and possibly an as yet unknown gene controlling pollen incompatibility types. Alleles at the incompatibility loci are maintained by frequency-dependent selection, and diversity at SLG and SRK appears to be very ancient, with high diversity at silent and replacement sites, particularly in certain “hypervariable portions of the genes. It is important to test whether recombination occurs in these genes before inferences about function of different parts of the genes can be made from patterns of diversity within their sequences. In addition, it has been suggested that, to maintain the relationship between alleles within a given S-haplotype, recombination is suppressed in the S-locus region. The high diversity makes many population genetic measures of recombination inapplicable. We have analyzed linkage disequilibrium within the SLG gene of two Brassica species, using published coding sequences. The results suggest that intragenic recombination has occurred in the evolutionary history of these alleles. This is supported by patterns of synonymous nucleotide diversity within both the SLG and SRK genes, and between domains of the SRK gene. Finally, clusters of linkage disequilibrium within the SLG gene suggest that hypervariable regions are under balancing selection, and are not merely regions of relaxed selective constraint.

scholarly journals Vampire bats exhibit evolutionary reduction of bitter taste receptor genes common to other bats

2014 ◽  
Vol 281 (1788) ◽  
pp. 20141079 ◽  
Author(s):  
Wei Hong ◽  
Huabin Zhao
Keyword(s):  
Bitter Taste ◽  
Food Selection ◽  
Taste Receptor ◽  
Selective Constraint ◽  
Behavioural Response ◽  
Bitter Taste Receptor ◽  
Pathway Gene ◽  
Vampire Bats ◽  
Vampire Bat ◽  
Strong Functional Constraint

The bitter taste serves as an important natural defence against the ingestion of poisonous foods and is thus believed to be indispensable in animals. However, vampire bats are obligate blood feeders that show a reduced behavioural response towards bitter-tasting compounds. To test whether bitter taste receptor genes ( T2R s) have been relaxed from selective constraint in vampire bats, we sampled all three vampire bat species and 11 non-vampire bats, and sequenced nine one-to-one orthologous T2R s that are assumed to be functionally conserved in all bats. We generated 85 T2R sequences and found that vampire bats have a significantly greater percentage of pseudogenes than other bats. These results strongly suggest a relaxation of selective constraint and a reduction of bitter taste function in vampire bats. We also found that vampire bats retain many intact T2R s, and that the taste signalling pathway gene Calhm1 remains complete and intact with strong functional constraint. These results suggest the presence of some bitter taste function in vampire bats, although it is not likely to play a major role in food selection. Together, our study suggests that the evolutionary reduction of bitter taste function in animals is more pervasive than previously believed, and highlights the importance of extra-oral functions of taste receptor genes.

scholarly journals Selective constraint and adaptive potential of West Nile virus within and among naturally infected avian hosts and mosquito vectors

2018 ◽  
Vol 4 (1) ◽  
Author(s):  
Chase W Nelson ◽  
Samuel D Sibley ◽  
Sergios-Orestis Kolokotronis ◽  
Gabriel L Hamer ◽  
Christina M Newman ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Selective Constraint ◽  
Mosquito Vectors ◽  
Adaptive Potential ◽  
West Nile

scholarly journals Inferring the frequency spectrum of derived variants to quantify adaptive molecular evolution in protein-coding genes of Drosophila melanogaster

2016 ◽  
Author(s):  
Peter D. Keightley ◽  
Jose Campos ◽  
Tom Booker ◽  
Brian Charlesworth
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Frequency Spectrum ◽  
Population Genomics ◽  
Selective Constraint ◽  
Accurate Estimation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Adaptive Molecular Evolution ◽  
Amino Acid Mutations

Many approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high copy number elements of the SFS is difficult, however, because of misassignment of alleles as derived versus ancestral. This is a known problem with parsimony using outgroup species. Here, we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups, which attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites of protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites from Phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations, and estimate that ~50% of amino acid substitutions are positively selected, but that less than 0.5% of new amino acid mutations are beneficial, with a scaled selection strength of Nes ≈ 12.

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