The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses

Webb, Andrew E.; Knoblauch, Jared; Sabankar, Nitesh; Kallur, Apeksha Sukesh; Hey, Jody; Sethuraman, Arun

doi:10.1093/molbev/msab113

Cited by 14 publications

(11 citation statements)

References 27 publications

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“…To test for potential significant differences in genome-wide heterozygosity between the three cohorts, an ANOVA test was conducted. A fSFS was generated using the “ vcf_to_sfs ” tool distributed within the popgen pipeline platform ( Webb et al 2021 ).…”

Section: Methodsmentioning

confidence: 99%

“…Afterwards, demographic changes were applied as depicted in supplementary figure S3 A – H , Supplementary Material online and a number of individuals were sampled equal to the number of fin whale individuals. fSFS were extracted from the resulting vcf files using the “ vcf_to_sfs ” tool as described above ( Webb et al 2021 ). Eventually, we compared different demographic simulations by calculating log-likelihoods of observing the empirical fSFS given one of the simulated fSFS using the R base function “ dmultinom ” ( supplementary table S4, Supplementary Material online).…”

Section: Methodsmentioning

confidence: 99%

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Genomic Impact of Whaling in North Atlantic Fin Whales

Wolf

Jong

Halldórsson

et al. 2022

Molecular Biology and Evolution

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It is generally recognized that large-scale whaling in the 19th and 20th century led to a substantial reduction of the size of many cetacean populations, particularly those of the baleen whales (Mysticeti). The impact of these operations on genomic diversity of one of the most hunted whales, the fin whale (Balaenoptera physalus), has remained largely unaddressed, because of the paucity of adequate samples and the limitation of applicable techniques. Here, we have examined the effect of whaling on the North Atlantic fin whale based on genomes of 51 individuals from Icelandic waters, representing three temporally separated intervals, 1989, 2009 and 2018 and provide a reference genome for the species. Demographic models suggest a noticeable drop of the effective population size of the North Atlantic fin whale around a century ago. The present results suggest that the genome-wide heterozygosity is not markedly reduced and has remained comparable to other baleen whale species. Similarly, there are no signs of apparent inbreeding, as measured by the proportion of long runs of homozygosity, or of a distinctively increased mutational load, as measured by the amount of putative deleterious mutations. Compared to other baleen whales, the North Atlantic fin whale appears to be less affected by anthropogenic influences than other whales such as the North Atlantic right whale, consistent with the presence of long runs of homozygosity and higher levels of mutational load in an otherwise more heterozygous genome. Thus, genome-wide assessments of other species and populations are essential for future, more specific, conservation efforts.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genomic Impact of Whaling in North Atlantic Fin Whales

Wolf

Jong

Halldórsson

et al. 2022

Molecular Biology and Evolution

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“…Prior to population genomic analyses, further filtering was applied using BCFtools v.1.11 to remove (a) the sites that were not in Hardy–Weinberg equilibrium ( P < 10 −4 ) for analyses of population structure, genetic diversity, and estimates of contemporary and historic migration and (b) the sites in linkage disequilibrium ( R 2 > 0.6 in 1000 sites) that were filtered for F ST outlier analyses. All population genomics analyses were performed with the PPP pipeline [ 94 ] using the BCFtools v.1.11 ( https://samtools.github.io/bcftools/bcftools.html ).…”

Section: Methodsmentioning

confidence: 99%

Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird

Yan

Wang

et al. 2023

BMC Biol

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Background The harlequin ladybird Harmonia axyridis (Coleoptera: Coccinellidae), native to Asia, has been introduced to other major continents where it has caused serious negative impacts on local biodiversity. Though notable advances to understand its invasion success have been made during the past decade, especially with then newer molecular tools, the conclusions reached remain to be confirmed with more advanced genomic analyses and especially using more samples from larger geographical regions across the native range. Furthermore, although H. axyridis is one of the best studied invasive insect species with respect to life history traits (often comparing invasive and native populations), the traits responsible for its colonization success in non-native areas warrant more research. Results Our analyses of genome-wide nuclear population structure indicated that an eastern Chinese population could be the source of all non-native populations and revealed several putatively adaptive candidate genomic loci involved in body color variation, visual perception, and hemolymph synthesis. Our estimates of evolutionary history indicate (1) asymmetric migration with varying population sizes across its native and non-native range, (2) a recent admixture between eastern Chinese and American populations in Europe, (3) signatures of a large progressive, historical bottleneck in the common ancestors of both populations and smaller effective sizes of the non-native population, and (4) the southwest origin and subsequent dispersal routes within its native range in China. In addition, we found that while two mitochondrial haplotypes-Hap1 and Hap2 were dominant in the native range, Hap1 was the only dominant haplotype in the non-native range. Our laboratory observations in both China and USA found statistical yet slight differences between Hap1 and Hap2 in some of life history traits. Conclusions Our study on H. axyridis provides new insights into its invasion processes into other major continents from its native Asian range, reconstructs a geographic range evolution across its native region China, and tentatively suggests that its invasiveness may differ between mitochondrial haplotypes.

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“…The reads that aligned to mitochondrial (MT) genome-extracted from the WGS dataset using the Paleomix pipeline (see above for details)-were used in haplotype and variant calling (GATK v. Phylogenetic analyses were made in order to look at clustering of maternal linages. To reconstruct the phylogeny of mitochondrial protein coding genes (PCGs), fasta sequences were extracted from the VCF using PPP v0.1.12 (Webb et al, 2021). PCGs were extracted using BLASTN (Camacho et al, 2009), aligned with MAFFT v7.480 (Katoh & Standley, 2013), manually corrected for length, and ND6 was reverse complemented as it is encoded on the light strand.…”

Section: Mt Genome Analysesmentioning

confidence: 99%

Evidence of hybridization between genetically distinct Baltic cod stocks during peak population abundance(s)

Helmerson

Weist

Brieuc

et al. 2023

Evolutionary Applications

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Range expansions can lead to increased contact of divergent populations, thus increasing the potential of hybridization events. Whether viable hybrids are produced will most likely depend on the level of genomic divergence and associated genomic incompatibilities between the different entities as well as environmental conditions. By taking advantage of historical Baltic cod (Gadus morhua) otolith samples combined with genotyping and whole genome sequencing, we here investigate the genetic impact of the increased spawning stock biomass of the eastern Baltic cod stock in the mid 1980s. The eastern Baltic cod is genetically highly differentiated from the adjacent western Baltic cod and locally adapted to the brackish environmental conditions in the deeper Eastern basins of the Baltic Sea unsuitable for its marine counterparts. Our genotyping results show an increased proportion of eastern Baltic cod in western Baltic areas (Mecklenburg Bay and Arkona Basin)—indicative of a range expansion westwards—during the peak population abundance in the 1980s. Additionally, we detect high frequencies of potential hybrids (including F1, F2 and backcrosses), verified by whole genome sequencing data for a subset of individuals. Analysis of mitochondrial genomes further indicates directional gene flow from eastern Baltic cod males to western Baltic cod females. Our findings unravel that increased overlap in distribution can promote hybridization between highly divergent populations and that the hybrids can be viable and survive under specific and favourable environmental conditions. However, the observed hybridization had seemingly no long‐lasting impact on the continuous separation and genetic differentiation between the unique Baltic cod stocks.

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The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses

Cited by 14 publications

References 27 publications

Genomic Impact of Whaling in North Atlantic Fin Whales

Genomic Impact of Whaling in North Atlantic Fin Whales

Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird

Evidence of hybridization between genetically distinct Baltic cod stocks during peak population abundance(s)

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