scholarly journals Nucleotide variation and balancing selection at theCkmagene in Atlantic cod: analysis with multiple merger coalescent models

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e786 ◽  
Author(s):  
Einar Árnason ◽  
Katrín Halldórsdóttir
Keyword(s):  
Atlantic Cod ◽  
Balancing Selection ◽  
Nucleotide Variation

scholarly journals Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: Analysis with multiple merger coalescent models

2014 ◽  
Author(s):  
Einar Árnason ◽  
Katrín Halldórsdóttir
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Time Scales ◽  
High Frequency ◽  
Atlantic Cod ◽  
Balancing Selection ◽  
Reproductive Capacity ◽  
Parameter Estimates ◽  
Nucleotide Variation ◽  
High Fecundity

A high-fecundity organisms, such as Atlantic cod, can withstand substantial natural selection and can at any time simultaneously replace alleles at a number of loci due to their excess reproductive capacity. High-fecundity organisms may reproduce by sweepstakes leading to highly skewed heavy-tailed offspring distribution. Under such reproduction the Kingman coalescent of binary mergers breaks down and models of multiple merger coalescent are more appropriate. Here we study nucleotide variation at the Ckma (Creatine Kinase Muscle type A) gene in Atlantic cod. The gene shows extreme differentiation between the North (Canada, Greenland, Iceland, Norway, Barents Sea) and the South (Faroe Islands, North-, Baltic-, Celtic-, and Irish Seas) with a between regions FST > 0.8 whereas neutral loci show no differentiation. This is evidence for natural selection. The protein sequence is conserved by purifying selection whereas silent and non-coding sites show extreme differentiation. Relative to outgroup the site-frequency spectrum has three modes, a mode at singleton sites and two high frequency modes at opposite frequencies representing divergent branches of the gene genealogy that is evidence for balancing selection. Analysis with multiple-merger coalescent models can account for the high frequency of singleton sites and indicate reproductive sweepstakes. Coalescent time scales with population size and with the inverse of variance in offspring number. Parameter estimates using multiple-merger coalescent models show fast time-scales. Time-scales of mitochondrial DNA are about square root of the effective population size and time-scales of nuclear genes are much faster.

scholarly journals Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: Analysis with multiple merger coalescent models

2014 ◽  
Author(s):  
Einar Árnason ◽  
Katrín Halldórsdóttir
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Time Scales ◽  
High Frequency ◽  
Atlantic Cod ◽  
Balancing Selection ◽  
Reproductive Capacity ◽  
Parameter Estimates ◽  
Nucleotide Variation ◽  
High Fecundity

A high-fecundity organisms, such as Atlantic cod, can withstand substantial natural selection and can at any time simultaneously replace alleles at a number of loci due to their excess reproductive capacity. High-fecundity organisms may reproduce by sweepstakes leading to highly skewed heavy-tailed offspring distribution. Under such reproduction the Kingman coalescent of binary mergers breaks down and models of multiple merger coalescent are more appropriate. Here we study nucleotide variation at the Ckma (Creatine Kinase Muscle type A) gene in Atlantic cod. The gene shows extreme differentiation between the North (Canada, Greenland, Iceland, Norway, Barents Sea) and the South (Faroe Islands, North-, Baltic-, Celtic-, and Irish Seas) with a between regions FST > 0.8 whereas neutral loci show no differentiation. This is evidence for natural selection. The protein sequence is conserved by purifying selection whereas silent and non-coding sites show extreme differentiation. Relative to outgroup the site-frequency spectrum has three modes, a mode at singleton sites and two high frequency modes at opposite frequencies representing divergent branches of the gene genealogy that is evidence for balancing selection. Analysis with multiple-merger coalescent models can account for the high frequency of singleton sites and indicate reproductive sweepstakes. Coalescent time scales with population size and with the inverse of variance in offspring number. Parameter estimates using multiple-merger coalescent models show fast time-scales. Time-scales of mitochondrial DNA are about square root of the effective population size and time-scales of nuclear genes are much faster.

scholarly journals Living in each other’s pockets: Nucleotide variation inside a genomic island harboring Pan I and its neighbors in Atlantic cod

2015 ◽  
Author(s):  
Ubaldo Benitez Hernandez ◽  
Einar Árnason
Keyword(s):  
Frequency Spectrum ◽  
High Frequency ◽  
Genomic Island ◽  
Atlantic Cod ◽  
Balancing Selection ◽  
Genomic Region ◽  
Parameter Estimates ◽  
Nucleotide Variation ◽  
Site Frequency Spectrum ◽  
High Frequency Modes

The Pan I locus in Atlantic cod lies in a genomic island of divergence extending over a large genomic region. The locus has two divergent alleles, defined by a single DraI restriction site, that have been related to behavioral differences of habitat selection by depth and temperature. The Pan I locus is known to be under an unusual mix of balancing selection and selective sweeps within the functional types. Here we study nucleotide variation in a 12.5 kb region inside the genomic island harboring Pan I and neighboring loci for sortilin 1 (Sort1) and ataxin 7-like 2 (Atxn7l2) which we partially covered. Variation of the 31 gene copies throughout the region falls into two divergent haplogroups that correlate with the 25 copies of A and six copies of B alleles of Pan I. The unfolded site frequency spectrum for the part with Pacific cod used as the outgroup is trimodal with a mode at singletons and two high frequency modes at 6/31 and 25/31 representing the two genealogical lineages. The folded site frequency spectrum for the entire region similarly has a high frequency mode of mutations that have accumulated on the two lineages. The high frequency of singletons is accounted for by multiple merger coalescent models. Parameter estimates using these models indicate sweepstakes reproduction. The high frequency modes of the spectrum is evidence for balancing selection. Analysis of non-synonymous changes shows that Pan I is at least one focus of selection within the genomic island. There may be multiple sites of selection and epistatic interactions. There is extensive linkage disequilibrium throughout the region. We suggest that the genomic island of divergence is a supergene of co-adapted complexes possibly locked together by structural variation.

scholarly journals Living in each other’s pockets: Nucleotide variation inside a genomic island harboring Pan I and its neighbors in Atlantic cod

2015 ◽  
Author(s):  
Ubaldo Benitez Hernandez ◽  
Einar Árnason
Keyword(s):  
Frequency Spectrum ◽  
High Frequency ◽  
Genomic Island ◽  
Atlantic Cod ◽  
Balancing Selection ◽  
Genomic Region ◽  
Parameter Estimates ◽  
Nucleotide Variation ◽  
Site Frequency Spectrum ◽  
High Frequency Modes

The Pan I locus in Atlantic cod lies in a genomic island of divergence extending over a large genomic region. The locus has two divergent alleles, defined by a single DraI restriction site, that have been related to behavioral differences of habitat selection by depth and temperature. The Pan I locus is known to be under an unusual mix of balancing selection and selective sweeps within the functional types. Here we study nucleotide variation in a 12.5 kb region inside the genomic island harboring Pan I and neighboring loci for sortilin 1 (Sort1) and ataxin 7-like 2 (Atxn7l2) which we partially covered. Variation of the 31 gene copies throughout the region falls into two divergent haplogroups that correlate with the 25 copies of A and six copies of B alleles of Pan I. The unfolded site frequency spectrum for the part with Pacific cod used as the outgroup is trimodal with a mode at singletons and two high frequency modes at 6/31 and 25/31 representing the two genealogical lineages. The folded site frequency spectrum for the entire region similarly has a high frequency mode of mutations that have accumulated on the two lineages. The high frequency of singletons is accounted for by multiple merger coalescent models. Parameter estimates using these models indicate sweepstakes reproduction. The high frequency modes of the spectrum is evidence for balancing selection. Analysis of non-synonymous changes shows that Pan I is at least one focus of selection within the genomic island. There may be multiple sites of selection and epistatic interactions. There is extensive linkage disequilibrium throughout the region. We suggest that the genomic island of divergence is a supergene of co-adapted complexes possibly locked together by structural variation.

scholarly journals Balancing Selection on Electrophoretic Variation of Phosphoglucose Isomerase in Two Species of Field Cricket: Gryllus veletis and G. pennsylvanicus

Genetics ◽  
1997 ◽  
Vol 147 (2) ◽  
pp. 609-621
Author(s):  
Laura A Katz ◽  
Richard G Harrison
Keyword(s):  
Balancing Selection ◽  
Emergent Property ◽  
Phosphoglucose Isomerase ◽  
Field Cricket ◽  
Nucleotide Variation ◽  
Eastern United States ◽  
Electrophoretic Variation ◽  
Sympatric Populations ◽  
Field Crickets ◽  
Gryllus Veletis

Two species of crickets, Gryllus veletis and G. pennsylvanicus, share six electrophoretic mobility classes for the enzyme phosphoglucose isomerase (PGI), despite evidence from other genetic markers that the two species are not closely related within eastern North American field crickets. Moreover, the frequencies of the two most common PGI electrophoretic classes (PGI-100 and PGI-65) covary in sympatric populations of these species in the eastern United States, suggesting that PGI may be subject to trans-specific balancing selection. To determine the molecular basis of the electrophoretic variation, we characterized the DNA sequence of the Pgi gene from 29 crickets (15 G. veletis and 14 G. pennsylvanicus). Amino acid substitutions that distinguish the electrophoretic classes are not the same in the two species, and there is no evidence that specific replacement substitutions represent trans-specific polymorphism. In particular, the amino acids that diagnose the PGI-65 allele relative to the PGI-100 allele differ both between G. veletis and G. pennsylvanicus and within G. pennsylvanicus. The heterogeneity among electrophoretic classes that covary in sympatric populations coupled with analysis of patterns of nucleotide variation suggest that Pgi is not evolving neutrally. Instead, the data are consistent with balancing selection operating on an emergent property of the PGI protein.

scholarly journals Nucleotide Variation at theCHALCONE ISOMERASELocus inArabidopsis thaliana

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 863-872 ◽  
Author(s):  
Helmi Kuittinen ◽  
Montserrat Aguadé
Keyword(s):  
Nucleotide Diversity ◽  
Direct Relationship ◽  
Selective Sweep ◽  
Balancing Selection ◽  
Neutral Theory ◽  
Low Frequency ◽  
The Other ◽  
Nucleotide Variation ◽  
Rapid Population Growth ◽  
History Of

AbstractAn ~1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity (θTOTAL = 0.004, θSIL = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

scholarly journals Historical DNA reveals the demographic history of Atlantic cod ( Gadus morhua ) in medieval and early modern Iceland

2014 ◽  
Vol 281 (1777) ◽  
pp. 20132976 ◽  
Author(s):  
Guðbjörg Ásta Ólafsdóttir ◽  
Kristen M. Westfall ◽  
Ragnar Edvardsson ◽  
Snæbjörn Pálsson
Keyword(s):  
Early Modern ◽  
Population Size ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Demographic History ◽  
Ecosystem Change ◽  
Nucleotide Variation ◽  
Modern Times ◽  
History Of ◽  
Early Modern Times

Atlantic cod ( Gadus morhua ) vertebrae from archaeological sites were used to study the history of the Icelandic Atlantic cod population in the time period of 1500–1990. Specifically, we used coalescence modelling to estimate population size and fluctuations from the sequence diversity at the cytochrome b ( cytb ) and Pantophysin I ( Pan I) loci. The models are consistent with an expanding population during the warm medieval period, large historical effective population size ( N E ), a marked bottleneck event at 1400–1500 and a decrease in N E in early modern times. The model results are corroborated by the reduction of haplotype and nucleotide variation over time and pairwise population distance as a significant portion of nucleotide variation partitioned across the 1550 time mark. The mean age of the historical fished stock is high in medieval times with a truncation in age in early modern times. The population size crash coincides with a period of known cooling in the North Atlantic, and we conclude that the collapse may be related to climate or climate-induced ecosystem change.

scholarly journals Polymorphism Patterns in Two Tightly Linked Developmental Genes, Idgf1 and Idgf3, of Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 177-188 ◽  
Author(s):  
Martina Z˘urovcová ◽  
Francisco J Ayala
Keyword(s):  
Balancing Selection ◽  
Nucleotide Variation ◽  
Neutral Model ◽  
Developmental Gene ◽  
Distinctive Features ◽  
Cell Lineages ◽  
Close Physical Proximity ◽  
Tests Of Neutrality ◽  
Excellent Candidate ◽  
Cytological Localization

Abstract A new developmental gene family, recently identified in D. melanogaster, has been called imaginal disc growth factors (IDGF) because the proteins promote growth of cell lineages derived from imaginal discs. These are the first genes reported that encode polypeptide factors with mitotic activity in invertebrates. Characteristics such as similar arrangement of introns and exons, small size, and different cytological localization make this family an excellent candidate for evolutionary studies. We focus on the loci Idgf1 and Idgf3, two genes that possess the most distinctive features. We examine the pattern of intra- and interspecific nucleotide variation in the sequences from 20 isogenic lines of D. melanogaster and sequences from D. simulans and D. yakuba. While MK, HKA, and Tajima’s tests of neutrality fail to reject a neutral model of molecular evolution, Fu and Li’s test with outgroup and McDonald’s test suggest that balancing selection is modulating the evolution of the Idgf1 locus. The rate of recombination between the two loci is high enough to uncouple any linkage disequilibrium arising between Idgf1 and Idgf3, despite their close physical proximity.

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