Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids

Introgressive hybridization creates networks of genetic relationships across species. Among marine fish of the Gadidae family, Pacific cod and walleye pollock are separate invasions of an Atlantic cod ancestor into the Pacific. Cods are ecological success stories, and their ecologies allow them to support the largest fisheries of the world. The enigmatic walleye pollock differs morphologically, behaviorally, and ecologically from its relatives, representing a niche shift. Here, we apply whole-genome sequencing to Pacific, Arctic, and Atlantic gadids and reveal extensive introgression among them with the ABBA-BABA test and pseudolikelihood phylogenetic network analysis. We propose that walleye pollock resulted from extensive adaptive introgression or homoploid hybrid speciation. The path of evolution of these taxa is more web than a tree. Their ability to invade and expand into new habitats and become ecologically successful may depend on genes acquired through adaptive introgression or hybrid speciation.

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Whole-genome sequencing uncovers cryptic and hybrid species among Atlantic and Pacific cod-fish

10.1101/034926 ◽

2015 ◽

Cited By ~ 7

Author(s):

Katrín Halldórsdóttir ◽

Einar Árnason

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Atlantic Cod ◽

Walleye Pollock ◽

Evolutionary Status ◽

Whole Genome ◽

Hybrid Speciation ◽

Hybrid Species ◽

The Pacific ◽

Starting Point

Speciation often involves the splitting of a lineage and the adaptation of daughter lineages to different environments. It may also involve the merging of divergent lineages, thus creating a stable homoploid hybrid species1that constructs a new ecological niche by transgressing2the ecology of the parental types. Hybrid speciation may also contribute to enigmatic and cryptic biodiversity in the sea.3,4The enigmatic walleye pollock, which is not a pollock at all but an Atlantic cod that invaded the Pacific 3.8 Mya,5differs considerably from its presumed closest relatives, the Pacific and Atlantic cod. Among the Atlantic cod, shallow-water coastal and deep-water migratory frontal ecotypes are associated with highly divergent genomic islands;6,7however, intermediates remain an enigma.8Here, we performed whole-genome sequencing of over 200 individuals using up to 33 million SNPs based on genotype likelihoods9and showed that the evolutionary status of walleye pollock is a hybrid species: it is a hybrid between Arctic cod and Atlantic cod that transgresses the ecology of its parents. For the first time, we provide decisive evidence that the Atlantic cod coastal and frontal ecotypes are separate species that hybridized, leading to a true-breeding hybrid species that differs ecologically from its parents. We refute monophyly and dichotomous branching of these taxa, and stress the importance of looking beyond branching trees at admixture and hybridity. Our study demonstrates the power of whole-genome sequencing and population genomics in providing deep insights into fundamental processes of speciation. Our study was a starting point for further work aimed at examining the criteria of hybrid speciation,10selection, sterility and structural chromosomal variation11among cod-fish, which are among the most important fish stocks in the world. The hybrid nature of both the walleye pollock and Atlantic cod raises the question concerning the extent to which very profitable fisheries12,13depend on hybrid vigour. Our results have implications for management of marine resources in times of rapid climate change.14,15

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Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L.

Plants ◽

10.3390/plants10112514 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2514

Author(s):

James Friel ◽

Aureliano Bombarely ◽

Carmen Dorca Fornell ◽

Francisco Luque ◽

Ana Maria Fernández-Ocaña

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Olea Europaea ◽

Genetic Relationships ◽

Germplasm Collection ◽

Whole Genome ◽

Population Genetic Analysis ◽

Olea Europaea L ◽

The World ◽

Olea Europaéa

Olive, Olea europaea L., is a tree of great economic and cultural importance in the Mediterranean basin. Thousands of cultivars have been described, of which around 1200 are conserved in the different olive germplasm banks. The genetic characterisation of these cultivars can be performed in different ways. Whole-genome sequencing (WGS) provides more information than the reduced representation methods such as genotype by sequencing (GBS), but at a much higher cost. This may change as the cost of sequencing continues to drop, but, currently, genotyping hundreds of cultivars using WGS is not a realistic goal for most research groups. Our aim is to systematically compare both methodologies applied to olive genotyping and summarise any possible recommendations for the geneticists and molecular breeders of the olive scientific community. In this work, we used a selection of 24 cultivars from an olive core collection from the World Olive Germplasm Collection of the Andalusian Institute of Agricultural and Fisheries Research and Training (WOGBC), which represent the most of the cultivars present in cultivated fields over the world. Our results show that both methodologies deliver similar results in the context of phylogenetic analysis and popular population genetic analysis methods such as clustering. Furthermore, WGS and GBS datasets from different experiments can be merged in a single dataset to perform these analytical methodologies with proper filtering. We also tested the influence of the different olive reference genomes in this type of analysis, finding that they have almost no effect when estimating genetic relationships. This work represents the first comparative study between both sequencing techniques in olive. Our results demonstrate that the use of GBS is a perfectly viable option for replacing WGS and reducing research costs when the goal of the experiment is to characterise the genetic relationship between different accessions. Besides this, we show that it is possible to combine variants from GBS and WGS datasets, allowing the reuse of publicly available data.

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Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod ( Gadus morhua , Linnaeus 1758)

Ecology and Evolution ◽

10.1002/ece3.7878 ◽

2021 ◽

Author(s):

Timothy P. O’Donnell ◽

Timothy J. Sullivan

Keyword(s):

Molecular Markers ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Gadus Morhua ◽

Gulf Of Maine ◽

Atlantic Cod ◽

Sex Identification ◽

Spawning Season ◽

Whole Genome ◽

Low Coverage

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Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing

Evolutionary Applications ◽

10.1111/eva.12861 ◽

2019 ◽

Vol 12 (10) ◽

pp. 1971-1987 ◽

Cited By ~ 6

Author(s):

Gemma V. Clucas ◽

R. Nicolas Lou ◽

Nina O. Therkildsen ◽

Adrienne I. Kovach

Keyword(s):

Genetic Variation ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Atlantic Cod ◽

Whole Genome ◽

Adaptive Genetic Variation

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Whole-genome Sequencing Reveals the Genetic Relationships and Selection Signatures of the Min Pig

Pakistan Journal of Zoology ◽

10.17582/journal.pjz/20200709040722 ◽

2021 ◽

Author(s):

Zhang Dong-jie

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Relationships ◽

Whole Genome ◽

Selection Signatures

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Use of whole-genome sequencing in the epidemiology of Campylobacter jejuni infections: state-of-knowledge

10.1101/078550 ◽

2016 ◽

Cited By ~ 2

Author(s):

Ann-Katrin Llarena ◽

Mirko Rossi

Keyword(s):

Public Health ◽

Whole Genome Sequencing ◽

Campylobacter Jejuni ◽

Genome Sequencing ◽

Genetic Relationships ◽

Outbreak Detection ◽

Epidemiological Methods ◽

Whole Genome ◽

Ample Evidence ◽

Outbreak Investigations

High-throughput whole-genome sequencing (WGS) is a revolutionary tool in public health microbiology and is gradually substituting classical typing methods in surveillance of infectious diseases. In combination with epidemiological methods, WGS is able to identify both sources and transmission-pathways during disease outbreak investigations. This review provides the current state of knowledge on the application of WGS in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the European Union. We describe how WGS has improved surveillance and outbreak detection of C. jejuni infections and how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen. However, the full implementation of this methodology in real-time is still hampered by a few hurdles. The limited insight into the genetic diversity of different lineages of C. jejuni impedes the validity of assumed genetic relationships. Furthermore, efforts are needed to reach a consensus on which analytic pipeline to use and how to define the strains cut-off value for epidemiological association while taking the needs and realities of public health microbiology in consideration. Even so, we claim that ample evidence is available to support the benefit of integrating WGS in the monitoring of C. jejuni infections and outbreak investigations.

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Whole Genome Sequencing and Phylogenetic Analysis of Rabies Viruses from Bats in Connecticut, USA, 2018–2019

Viruses ◽

10.3390/v13122500 ◽

2021 ◽

Vol 13 (12) ◽

pp. 2500

Author(s):

Ji-Yeon Hyeon ◽

Guillermo R. Risatti ◽

Zeinab H. Helal ◽

Holly McGinnis ◽

Maureen Sims ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Relationships ◽

Fluorescent Antibody ◽

Antibody Test ◽

Whole Genome ◽

Diagnostic Laboratory ◽

Big Brown Bats ◽

Hoary Bat

We performed whole genome sequencing and genetic characterization of rabies viruses (RABV) detected in bats submitted to the Connecticut Veterinary Medical Diagnostic Laboratory (CVMDL) during 2018-2019. Among 88 bats submitted to CVMDL, six brain samples (6.8%, 95% confidence interval: 1.6% to 12.1%) tested positive by direct fluorescent antibody test. RABVs were detected in big brown bats (Eptesicus fuscus, n = 4), a hoary bat (Lasiurus cinereus, n = 1), and an unidentified bat species (n = 1). Complete coding sequences of four out of six detected RABVs were obtained. In phylogenetic analysis, the RABVs (18-62, 18-4347, and 19-2274) from big brown bats belong to the bats EF-E1 clade, clustering with RABVs detected from the same bat species in Pennsylvania and New Jersey. The bat RABV (19-2898) detected from the migratory hoary bat belongs to the bats LC clade, clustering with the eleven viruses detected from the same species in Arizona, Washington, Idaho, and Tennessee. The approach used in this study generated novel data regarding genetic relationships of RABV variants, including their reservoirs, and their spatial origin and it would be useful as reference data for future investigations on RABV in North America. Continued surveillance and genome sequencing of bat RABV would be needed to monitor virus evolution and transmission, and to assess the emergence of genetic mutations that may be relevant for public health.

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Analysis of bovine tuberculosis transmission in Jalisco, Mexico through whole-genome sequencing

Journal of Veterinary Research ◽

10.2478/jvetres-2020-0010 ◽

2020 ◽

Vol 64 (1) ◽

pp. 51-61

Author(s):

Dulce Anahy Verdugo Escárcega ◽

Claudia Angélica Perea Razo ◽

Sara González Ruíz ◽

Susana Lucia Sosa Gallegos ◽

Feliciano Milián Suazo ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Bovine Tuberculosis ◽

Genetic Relationships ◽

Whole Genome ◽

Tuberculosis Transmission ◽

Source Of Infection ◽

El Alto ◽

Diversity Sampling ◽

Unique Source

AbstractIntroductionBovine tuberculosis, caused by M. bovis, is endemic in Mexico and has had a big impact on public health. Jalisco is considered to be an important dairy region in the country, accounting for approximately 19% of the total milk production. Within Jalisco, the region of Altos Sur holds the largest proportion of the cattle inventory of the state.Material and MethodsTo determine the frequency of bovine tuberculosis in Altos Sur, Jalisco, as well as M. bovis genetic diversity, sampling of tissue (lymph nodes, lungs, and liver) from Holstein cattle was performed in four abattoirs belonging to three municipalities of this region (Tepatitlán de Morelos, San Miguel el Alto, and Arandas). Spoligotyping and whole-genome sequencing were carried out to assess the genetic relationships of M. bovis strains circulating in this area, as well as a comparison to isolates from other places in Mexico.ResultsPrevalence was 15.06%, and distribution similar among the three municipalities. The most frequent spoligotypes were SB0673, SB121, and SB0145. Whole-genome sequencing revealed three main clades (I, II, III), but isolates did not show clustering by region.ConclusionPhylogenetic analysis suggested ongoing transmission between herds of the different regions, and no unique source of infection was determined. This hinders efforts under the national program for the control and eradication of the disease, so serious attention must be paid to rural regions such as Altos Sur in order to improve its success.

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