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

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

Science Advances ◽

10.1126/sciadv.aat8788 ◽

2019 ◽

Vol 5 (3) ◽

pp. eaat8788 ◽

Cited By ~ 3

Author(s):

Einar Árnason ◽

Katrín Halldórsdóttir

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Atlantic Cod ◽

Genetic Relationships ◽

Phylogenetic Network ◽

Walleye Pollock ◽

Niche Shift ◽

Whole Genome ◽

Hybrid Speciation ◽

Adaptive Introgression

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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Short Communication: The emergence and rise of indigenous thermophilic bacteria exploration from hot springs in Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d211156 ◽

2020 ◽

Vol 21 (11) ◽

Author(s):

Kenny Lischer ◽

ANANDA BAGUS RICHKY DIGDAYA PUTRA ◽

Brian Wirawan Guslianto ◽

Forbes Avila ◽

Sarah Grace Sitorus ◽

...

Keyword(s):

High Temperature ◽

16S Rrna ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Short Communication ◽

Hot Springs ◽

Thermophilic Bacteria ◽

Whole Genome ◽

Thermostable Enzymes ◽

The Pacific

Abstract. Lischer K, Putra ABRD, Guslianto BW, Avilla F, Sitorus SG, Nugraha Y, Sarmoko. 2020. Short Communication: The emergence and rise of indigenous thermophilic bacteria exploration from hot springs in Indonesia. Biodiversitas 21: 5474-5481. Indonesia is an archipelagic country located in the pacific ring of fire, and is estimated to cause numerous hot springs spread across the country. In addition, small living microbes have been explored in these locations since 1985. These microbes possess the ability to survive in areas with high temperature (more than 40oC-90oC), and are therefore termed thermophiles. Hence, massive explorations have been conducted on Java island and other unexplored areas at Sumatra to Papua in New Guinea islands. Moreover, a total of 71 hot springs characterized by the presence of thermophilic bacteria have been explored in Indonesia. These investigations ensue with various approaches, including through conventional and microbiological, 16S rRNA, as well as whole-genome sequencing methods. In addition to species exploration, the application of thermophiles has become a topic of interest from 1999, especially based on thermostable enzymes with the capacity to maintain activity at high-temperature conditions. These include amylase, protease, lipase, xylanase, esterase, and cellulase as the most common isolated form, which indicates the existence of significant extractable potentials. Hence, there is a need for further research in terms of both exploration and application purposes.

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Candidate Predisposition Variants in Kaposi Sarcoma as Detected by Whole-Genome Sequencing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz337 ◽

2019 ◽

Vol 6 (10) ◽

Author(s):

Sanni J Rinne ◽

Lauri J Sipilä ◽

Päivi Sulo ◽

Emmanuelle Jouanguy ◽

Vivien Béziat ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Kaposi Sarcoma ◽

The Other ◽

Whole Genome ◽

Genome Wide ◽

Starting Point ◽

Familial Clustering ◽

Iranian Family ◽

Classic Kaposi Sarcoma

Abstract Familial clustering of classic Kaposi sarcoma (CKS) is rare with, approximately 100 families reported to date. We studied 2 consanguineous families, 1 Iranian and 1 Israeli, with multiple cases of adult CKS and without overt underlying immunodeficiency. We performed genome-wide linkage analysis and whole-genome sequencing to discover the putative genetic cause for predisposition. A 9-kb homozygous intronic deletion in RP11-259O2.1 in the Iranian family and 2 homozygous variants, 1 in SCUBE2 and the other in CDHR5, in the Israeli family were identified as possible candidates. The presented variants provide a robust starting point for validation in independent samples.

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A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis

Gene ◽

10.1016/j.gene.2015.10.023 ◽

2016 ◽

Vol 576 (2) ◽

pp. 603-609 ◽

Cited By ~ 5

Author(s):

Motoshige Yasuike ◽

Atushi Fujiwara ◽

Yoji Nakamura ◽

Yuki Iwasaki ◽

Issei Nishiki ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Transcriptome Analysis ◽

Bluefin Tuna ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Pacific Bluefin Tuna ◽

Sequencing Data ◽

The Pacific ◽

Global Transcriptome

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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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Using Whole Genome Sequencing to Characterize Clinically Significant Blood Groups Among Healthy Older Australians

10.1101/2021.04.18.21255241 ◽

2021 ◽

Author(s):

Sudhir S Jadhao ◽

Candice Davison ◽

Eileen V. Roulis ◽

Simon Lee ◽

Paul Lacaze ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Blood Group ◽

Genome Sequencing ◽

Rare Variants ◽

Blood Group System ◽

Blood Group Antigens ◽

Whole Genome ◽

Group System ◽

Starting Point ◽

Clinically Significant

There have been no comprehensive studies of a full range of blood group polymorphisms within the Australian population. The problem is compounded by the absence of any databases carrying genomic information on chronically transfused patients and low frequency blood group antigens in Australia. Here, we use RBCeq, a web server-based blood group genotyping software, to identify unique blood group variants among Australians and compare the variation detected versus global data. Whole genome sequencing data was analysed from for 2796 healthy older Australians from the Medical Genome Reference Bank and compared with data from 1000G phase 3 (1KGP3) databases comprising 661 African, 347 American, 503 European, 504 East Asian, and 489 South Asian participants. There were 688 rare variants detected in this Australian sample population, including nine variants that had clinical associations. Notably, we identified 149 variants that were computationally predicted to be novel and deleterious. No clinically significant rare or novel variants were found associated with the genetically complex ABO blood group system. For the Rh blood group system one novel and 16 rare variants were found. Our detailed blood group profiling results provide a starting point for the creation of an Australian blood group variant database.

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Highly Recombinant VGII Cryptococcus gattii Population Develops Clonal Outbreak Clusters through both Sexual Macroevolution and Asexual Microevolution

mBio ◽

10.1128/mbio.01494-14 ◽

2014 ◽

Vol 5 (4) ◽

Cited By ~ 56

Author(s):

R. Blake Billmyre ◽

Daniel Croll ◽

Wenjun Li ◽

Piotr Mieczkowski ◽

Dee A. Carter ◽

...

Keyword(s):

United States ◽

Sexual Reproduction ◽

Whole Genome Sequencing ◽

Pacific Northwest ◽

Genome Sequencing ◽

The United States ◽

Cryptococcus Gattii ◽

Whole Genome ◽

Content Type ◽

The Pacific

ABSTRACT An outbreak of the fungal pathogen Cryptococcus gattii began in the Pacific Northwest (PNW) in the late 1990s. This outbreak consists of three clonal subpopulations: VGIIa/major, VGIIb/minor, and VGIIc/novel. Both VGIIa and VGIIc are unique to the PNW and exhibit increased virulence. In this study, we sequenced the genomes of isolates from these three groups, as well as global isolates, and analyzed a total of 53 isolates. We found that VGIIa/b/c populations show evidence of clonal expansion in the PNW. Whole-genome sequencing provided evidence that VGIIb originated in Australia, while VGIIa may have originated in South America, and these were likely independently introduced. Additionally, the VGIIa outbreak lineage may have arisen from a less virulent clade that contained a mutation in the MSH2 ortholog, but this appears to have reverted in the VGIIa outbreak strains, suggesting that a transient mutator phenotype may have contributed to adaptation and evolution of virulence in the PNW outbreak. PNW outbreak isolates share genomic islands, both between the clonal lineages and with global isolates, indicative of sexual recombination. This suggests that VGII C. gattii has undergone sexual reproduction, either bisexual or unisexual, in multiple locales contributing to the production of novel, virulent subtypes. We also found that the genomes of two basal VGII isolates from HIV+ patients contain an introgression tract spanning three genes. Introgression substantially contributed to intra-VGII polymorphism and likely occurred through sexual reproduction with VGI. More broadly, these findings illustrate how both microevolution and sexual reproduction play central roles in the development of infectious outbreaks from avirulent or less virulent progenitors. IMPORTANCE Cryptococcus gattii is the causative agent responsible for ongoing infections in the Pacific Northwest of the United States and western Canada. The incidence of these infections increased dramatically in the 1990s and remains elevated. These infections are attributable to three clonal lineages of C. gattii, VGIIa, VGIIb, and VGIIc, with only VGIIa identified once previously in the Pacific Northwest prior to the start of the outbreak, albeit in a less virulent form. This study addresses the origin and emergence of this outbreak, using whole-genome sequencing and comparison of both outbreak and global isolates. We show that VGIIa arose mitotically from a less virulent clonal group, possibly via the action of a mutator phenotype, while VGIIb was likely introduced from Australia, and VGIIc appears to have emerged in the United States or in an undersampled locale via sexual reproduction. This work shows that multiple processes can contribute to the emergence of an outbreak.

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