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 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 Effects of linked selective sweeps on demographic inference and model selection

2016 ◽  
Author(s):  
Daniel R. Schrider ◽  
Alexander G. Shanku ◽  
Andrew D. Kern
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Positive Selection ◽  
Population Size ◽  
Natural Populations ◽  
Parameter Estimates ◽  
Selective Sweeps ◽  
Recent Positive Selection ◽  
Demographic Inference ◽  
The Impact

AbstractThe availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of datasets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models—often severely. Moreover, we find that selection can lead to incorrect inferences of population size changes when none have occurred. We argue that the amount of recent positive selection required to skew inferences may often be acting in natural populations. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.

scholarly journals Mitochondrial Cytochrome b DNA Variation in the High-Fecundity Atlantic Cod: Trans-Atlantic Clines and Shallow Gene Genealogy

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1871-1885 ◽  
Author(s):  
Einar Árnason
Keyword(s):  
Natural Selection ◽  
Cytochrome B ◽  
Atlantic Cod ◽  
Clinal Variation ◽  
Mitochondrial Cytochrome ◽  
High Fecundity ◽  
Gene Genealogy ◽  
Local Selection ◽  
Mitochondrial Cytochrome B ◽  
The Baltic

Abstract An analysis of sequence variation of 250 bp of the mitochondrial cytochrome b gene of 1278 Atlantic cod Gadus morhua ranging from Newfoundland to the Baltic shows four high-frequency (>8%) haplotypes and a number of rare and singleton haplotypes. Variation is primarily synonymous mutations. Natural selection acting directly on these variants is either absent or very weak. Common haplotypes show regular trans-Atlantic clines in frequencies and each of them reaches its highest frequency in a particular country. A shallow multifurcating constellation gene genealogy implies young age and recent turnover of polymorphism. Haplotypes characterizing populations at opposite ends of the geographic distribution in Newfoundland and the Baltic are mutationally closest together. The haplotypes are young and have risen rapidly in frequency. Observed differentiation among countries is due primarily to clinal variation. Hypotheses of historical isolation and polymorphisms balanced by local selection and gene flow are unlikely. Instead the results are explained by demic selection of mitochondria carried by highly fit females winning reproductive sweepstakes. By inference the Atlantic cod, a very high-fecundity vertebrate, is characterized by a high variance of offspring number and strong natural selection that leads to very low effective to actual population sizes.

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.

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