scholarly journals Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic

2021 ◽  
Vol 118 (15) ◽  
pp. e2025453118
Author(s):  
Malin L. Pinsky ◽  
Anne Maria Eikeset ◽  
Cecilia Helmerson ◽  
Ian R. Bradbury ◽  
Paul Bentzen ◽  
...  
Keyword(s):  
Atlantic Cod ◽  
Sequence Data ◽  
Genomic Variation ◽  
Whole Genome Sequence ◽  
Phenotypic Change ◽  
Rapid Decline ◽  
Effective Population ◽  
Genomic Change ◽  
Early 21St Century ◽  
Intensive Exploitation

The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

scholarly journals Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation

2021 ◽  
Vol 288 (1961) ◽  
Author(s):  
Anna Brüniche-Olsen ◽  
Kenneth F. Kellner ◽  
Jerrold L. Belant ◽  
J. Andrew DeWoody
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Management Practices ◽  
Sequence Data ◽  
Extinction Risk ◽  
Conservation Status ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Habitat Availability

More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes ( N e ) and current genomic variability ( H ), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that N e and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.

scholarly journals An accurate assignment test for extremely low-coverage whole-genome sequence data

2021 ◽  
Author(s):  
Giada Ferrari ◽  
Lane M Atmore ◽  
Sissel Jentoft ◽  
Kjetill S Jakobsen ◽  
Daniel Makowiecki ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Atlantic Cod ◽  
Sequence Data ◽  
Biological Characteristics ◽  
Assignment Test ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Assignment Tests ◽  
Low Coverage

Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. In ancient DNA research, such characters can provide further information on population continuity, evolution, climate change, species migration, or trade, depending on archaeological context. Yet, assignment tests often rely on moderate- to high-coverage sequence data, which can be difficult to obtain for many ancient specimens and in ecological studies, which often use sequencing techniques such as ddRAD to bypass the need for costly whole-genome sequencing. We have developed a novel approach that efficiently assigns biologically relevant information (such as population identity or structural variants) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic Single Nucleotide Polymorphisms (SNPs) associated with a biological characteristic. Low coverage alignment files from ancient specimens are subsequently compared to these databases to ascertain allelic state yielding a joint probability for each association. To assess the efficacy of this approach, we assigned inversion haplotypes and population identity in several species including Heliconius butterflies, Atlantic herring, and Atlantic cod. We used both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage (e.g. 0.0001x fold) based on genome-wide SNPs. This approach will therefore increase the number of ancient samples in ecological and bioarchaeological research for which relevant biological information can be obtained.

scholarly journals Distinguishing gene flow between malaria parasite populations

2021 ◽  
Author(s):  
Tyler Steven Brown ◽  
Aimee R. Taylor ◽  
Olufunmilayo Arogbokun ◽  
Caroline O. Buckee ◽  
Hsiao-Han Chang
Keyword(s):  
Gene Flow ◽  
Malaria Parasite ◽  
Sequence Data ◽  
Simulated Data ◽  
Whole Genome Sequence ◽  
Effective Population ◽  
Migration Rates ◽  
Population Sizes ◽  
And Migration ◽  
Parasite Populations

Measuring gene flow between malaria parasite populations in different geographic locations can provide strategic information for malaria control interventions. Multiple important questions pertaining to the design of such studies remain unanswered, limiting efforts to operationalize genomic surveillance tools for routine public health use. This report evaluates numerically the ability to distinguish different levels of gene flow between malaria populations, using different amounts of real and simulated data, where data are simulated using parameters that approximate different epidemiological conditions. Specifically, using Plasmodium falciparum  whole genome sequence data and sequence data simulated for a metapopulation with different migration rates and effective population sizes, we compare two estimators of gene flow, explore the number of genetic markers and number of individuals required to reliably rank highly connected locations, and describe how these thresholds change given different effective population sizes and migration rates. Our results have implications for the design and implementation of malaria genomic surveillance efforts.

scholarly journals Fine-scale population structure in five rural populations from the Spanish Eastern Pyrenees using high-coverage whole-genome sequence data

2021 ◽  
Author(s):  
Iago Maceda ◽  
Miguel Martín Álvarez ◽  
Georgios Athanasiadis ◽  
Raúl Tonda ◽  
Jordi Camps ◽  
...  
Keyword(s):  
Rural Areas ◽  
Sequence Data ◽  
Population Substructure ◽  
Whole Genome Sequence ◽  
Effective Population ◽  
High Coverage ◽  
Demographic Modeling ◽  
Eastern Pyrenees ◽  
Scale Population ◽  
Population Sizes

AbstractThe area of the Spanish Pyrenees is particularly interesting for studying the demographic dynamics of European rural areas given its orography, the main traditional rural condition of its population and the reported higher patterns of consanguinity of the region. Previous genetic studies suggest a gradient of genetic continuity of the area in the West to East axis. However, it has been shown that micro-population substructure can be detected when considering high-quality NGS data and using spatial explicit methods. In this work, we have analyzed the genome of 30 individuals sequenced at 40× from five different valleys in the Spanish Eastern Pyrenees (SEP) separated by less than 140 km along a west to east axis. Using haplotype-based methods and spatial analyses, we have been able to detect micro-population substructure within SEP not seen in previous studies. Linkage disequilibrium and autozygosity analyses suggest that the SEP populations show diverse demographic histories. In agreement with these results, demographic modeling by means of ABC-DL identify heterogeneity in their effective population sizes despite of their close geographic proximity, and suggests that the population substructure within SEP could have appeared around 2500 years ago. Overall, these results suggest that each rural population of the Pyrenees could represent a unique entity.

scholarly journals Diverse demographic histories in a guild of hymenopteran parasitoids

2019 ◽  
Author(s):  
William Walton ◽  
Graham N Stone ◽  
Konrad Lohse
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Demographic History ◽  
Whole Genome Sequence ◽  
Parasitoid Wasps ◽  
Effective Population ◽  
Glacial Cycles ◽  
Genome Wide ◽  
History Of ◽  
Hymenopteran Parasitoids

AbstractSignatures of changes in population size have been detected in genome-wide variation in many species. However, the causes of such changes and the extent to which they are shared across co-distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles have been widely studied, little is known about the demographic history of refugial populations, and the extent and causes of demographic variation among codistributed species. We used whole genome sequence data to reconstruct and compare demographic histories during the Quaternary for Iberian refuge populations in a single ecological guild (seven species of chalcid parasitoid wasps associated with oak cynipid galls). We find support for large changes in effective population size (Ne) through the Pleistocene that coincide with major climate change events. However, there is little evidence that the timing, direction and magnitude of demographic change are shared across species, suggesting that demographic histories are largely idiosyncratic. Our results are compatible with the idea that specialist parasitoids attacking a narrow range of hosts experience greater fluctuations in Ne than generalists.

scholarly journals An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree

Heredity ◽  
2020 ◽  
Author(s):  
Setegn Worku Alemu ◽  
Naveen Kumar Kadri ◽  
Chad Harland ◽  
Pierre Faux ◽  
Carole Charlier ◽  
...  
Keyword(s):  
Sequence Data ◽  
Intermediate Frequency ◽  
Whole Genome Sequence ◽  
Heterozygote Advantage ◽  
Whole Genome ◽  
Effective Population ◽  
Deleterious Alleles ◽  
Genomic Relationships ◽  
Excess Homozygosity ◽  
Small Effective Population Size

Abstract The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (FUNI) or on the genomic relationships (FGRM) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (FHOM), homozygous-by-descent segments (FHBD), runs-of-homozygosity (FROH) or on the known genealogy (FPED) was better at capturing whole-genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies (0.10 < . < 0.25). The results indicate that FUNI and FGRM might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus-specific inbreeding measures or at low marker density, the ranking of the methods can also change as FHBD makes better use of the information from neighboring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, FPED was uncorrelated with locus-specific homozygosity.

scholarly journals Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
John A Lees ◽  
Nicholas J Croucher ◽  
David Goldblatt ◽  
François Nosten ◽  
Julian Parkhill ◽  
...  
Keyword(s):  
Low Income ◽  
Genome Wide Association Study ◽  
Sequence Data ◽  
Theoretical Models ◽  
Invasive Disease ◽  
Genomic Variation ◽  
Whole Genome Sequence ◽  
Pneumococcal Carriage ◽  
Genome Wide ◽  
Significant Locus

Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). A pan-genome-wide association study identified prophage sequences as being associated with decreased carriage duration independent of serotype, potentially by disruption of the competence mechanism. These findings support theoretical models of pneumococcal competition and antibiotic resistance.

scholarly journals A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

2018 ◽  
Author(s):  
Tony Kess ◽  
Paul Bentzen ◽  
Sarah J. Lehnert ◽  
Emma V.A. Sylvester ◽  
Sigbjørn Lien ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Phenotypic Variation ◽  
Chromosomal Rearrangement ◽  
Atlantic Cod ◽  
Marine Species ◽  
Genomic Variation ◽  
Fine Scale ◽  
Effective Population ◽  
Northern Cod

AbstractIntraspecific phenotypic diversity is integral to ecological resilience and the provision of ecosystem services1. Chromosome structural variation may underpin intraspecific diversity and complex phenotypes2 by reducing recombination within supergenes containing linked, co-adapted alleles. Connecting ecologically-relevant phenotypes to genomic variation can enable more precise conservation of exploited marine species by protecting important genetic diversity3,4. Here, using genome-wide association analysis of a 12K single nucleotide polymorphism (SNP) array we confirm that an ancient, derived chromosomal rearrangement consisting of two adjacent inversions is strongly associated with migratory phenotype and individual-level genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. The presence of all identified migration-associated loci within this rearrangement indicates that pervasive variation in migration phenotype is in part controlled by a recombination-resistant supergene, facilitating fine-scale individual phenotypic variation within Northern cod. Furthermore, we reconstruct trends in effective population size over the last century, and find genomic signatures of population collapse, and different patterns of population expansion and decline among individuals based on supergene alleles. We demonstrate declines in effective population size consistent with the onset of industrialized harvest (post 1950) and substantially reduced effective size of individuals homozygous for the derived chromosomal rearrangement relative to heterozygous individuals or those homozygous for the ancestral version of this chromosomal region. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic and phenotypic variation in a highly connected marine species, and suggest a loss of biocomplexity from a migration-associated supergene within Northern cod by overfishing.

scholarly journals Extensive genome-wide duplications in the eastern oyster ( Crassostrea virginica )

2021 ◽  
Vol 376 (1825) ◽  
Author(s):  
Tejashree H. Modak ◽  
Robert Literman ◽  
Jonathan B. Puritz ◽  
Kevin M. Johnson ◽  
Erin M. Roberts ◽  
...  
Keyword(s):  
Crassostrea Virginica ◽  
Structural Variation ◽  
Structural Changes ◽  
Sequence Data ◽  
Phenotypic Diversity ◽  
Critical Role ◽  
Eastern Oyster ◽  
Genomic Variation ◽  
Interindividual Variation ◽  
Whole Genome Sequence

Genomic structural variation is an important source of genetic and phenotypic diversity, playing a critical role in evolution. The recent availability of a high-quality reference genome for the eastern oyster, Crassostrea virginica , and whole-genome sequence data of samples from across the species range in the USA, provides an opportunity to explore structural variation across the genome of this species. Our analysis shows significantly greater individual-level duplications of regions across the genome than that of most model vertebrate species. Duplications are widespread across all ten chromosomes with variation in frequency per chromosome. The eastern oyster shows a large interindividual variation in duplications as well as particular chromosomal regions with a higher density of duplications. A high percentage of duplications seen in C. virginica lie completely within genes and exons, suggesting the potential for impacts on gene function. These results support the hypothesis that structural changes may play a significant role in standing genetic variation in C. virginica , and potentially have a role in their adaptive and evolutionary success. Altogether, these results suggest that copy number variation plays an important role in the genomic variation of C. virginica . This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

scholarly journals Benchmarking phasing software with a whole-genome sequenced cattle pedigree

2021 ◽  
Author(s):  
Claire Oget-Ebrad ◽  
Naveen Kumar Kadri ◽  
Gabriel Costa Monteiro Moreira ◽  
Latifa Karim ◽  
Wouter Coppieters ◽  
...  
Keyword(s):  
Haplotype Block ◽  
Population Genomics ◽  
Sequence Data ◽  
Population Based ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Haplotype Reconstruction ◽  
Effective Population ◽  
Mendelian Segregation ◽  
Livestock Population

Background: Accurate haplotype reconstruction is required in many applications in quantitative and population genomics. Different phasing methods are available but their accuracy must be evaluated for samples with different properties (population structure, marker density, etc.). We herein took advantage of whole-genome sequence data available for a Holstein cattle pedigree containing 264 individuals, including 98 trios, to evaluate several population-based phasing methods. This data represents a typical example of a livestock population, with low effective population size, high levels of relatedness and long-range linkage disequilibrium. Results: After stringent filtering of our sequence data, we evaluated several population-based phasing programs including one or more versions of AlphaPhase, ShapeIT, Beagle, Eagle and FImpute. To that end we used 98 individuals having both parents sequenced for validation. Their haplotypes reconstructed based on Mendelian segregation rules were considered the gold standard to assess the performance of population-based methods in two scenarios. In the first one, only these 98 individuals were phased, while in the second one, all the 264 sequenced individuals were phased simultaneously, ignoring the pedigree relationships. We assessed phasing accuracy based on switch error counts (SEC) and rates (SER), lengths of correctly phased haplotypes and pairwise SNP phasing accuracies (the probability that a pair of SNPs is correctly phased as a function of their distance). For most evaluated metrics or scenarios, the best software was either ShapeIT4.1 or Beagle5.2, both methods resulting in particularly high phasing accuracies. For instance, ShapeIT4.1 achieved a median SEC of 50 per individual and a mean haplotype block length of 24.1 Mb in the second scenario. These statistics are remarkable since the methods were evaluated with a map of 8,400,000 SNPs, and this corresponds to only one switch error every 40,000 phased informative markers. When more relatives were included in the data, FImpute3.0 reconstructed extremely long segments without errors. Conclusions: We report extremely high phasing accuracies in a typical livestock sample of 100 sequenced individuals. ShapeIT4.1 and Beagle5.2 proved to be the most accurate, particularly for phasing long segments. Nevertheless, most tools achieved high accuracy at short distances and would be suitable for applications requiring only local haplotypes.

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