Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change

The Arctic is experiencingthe fastest rates of globalwarming,leadingto shiftsin the distributionof its biotaandincreasingthe potentialfor hybridization. However, genomicevidenceof recenthybridization events in theArctic remainsunexpectedlyrare. Here, we use whole-genomesequencingof contemporary and 122-year-oldhistoricalspecimensto investigate the originof an Arctic hybridpopulation of Atlanticpuffins(Fr aterculaarctica)on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodiedsubspeciesF. a. naumanniand the temperate, smaller-sizedsubspeciesF. a. arcticabeganas recentlyas six generationsagodue to an unexpectedsouthward rangeexpansionofF. a. naumanni.Moreover, we find a significanttemporalloss of geneticdiversityacross Arctic and temperate puffinpopulations.Our observationsprovide compellinggenomicevidenceof the impacts of recentdistributionalshiftsand loss of diversityin Arctic communitiesduringthe 20th century.publishedVersio

De novo assembly and comparative genomics of teleosts

During the last 20 years, genome sequencing and assembly projects have changed from requiring large international collaborations to a task that a handful of people can plan and conduct. This has been driven by improvements in sequencing technology and computational methods. More and more sequencing and assembly projects are being conducted, with older assemblies being updated and improved, resulting in deeper understanding of the biology of a large and steadily growing number of species. The projects described in this thesis focus on genome assemblies created from species of the order Gadiformes, an order containing commercially and ecologically important fishes. Here, these assemblies are investigated in detail and compared to other teleost genome assemblies, with special attention to immune genes and short tandem repeats. We have updated and substantially improved the Atlantic cod (Gadus morhua) genome assembly with the use of different sequencing technologies and computational approaches. A major finding was that the presence of short tandem repeats (STRs) is the main factor that led to the fragmentation of the previous assembly. STRs are hypermutating loci that occur at high frequency (loci/Mbp) and high density (bp/Mbp) in the cod genome, surpassing that of other published genome assemblies. The STRs likely contribute to substantial genetic variation in natural cod populations. The Atlantic cod lacks genes involved in the major histocompatibility complex (MHC) II pathway, which is the pathway that normally detects and initiates a response against bacterial pathogens and thus is a crucial part of the adaptive immune system. To infer when in the ancestry of cod these genes were lost, we sequenced and assembled the genomes of 66 teleost species. We found that the loss is shared by all species in the order Gadiformes, and that there is an expanded repertoire of MHCI genes in the Gadiformes, which is likely connected with the large number of species in this order. Since the 66 new teleost (including gadiform) genome assemblies are fragmented, the properties of STRs and multi-copy immune genes are not easily investigated. To further elucidate their role in Gadiformes, we sequenced and assembled the genome of haddock (Melanogrammus aeglefinus), a relative of cod. Our result shows that the high density and frequency of STRs is a feature likely shared by all codfishes (a family inside Gadiformes), and possibly all Gadiformes. Cod and haddock share a similar repertoire of the innate immune Toll-like receptor (TLR) genes, with both losses and expansions. The expansions might be part of a compensatory mechanism for the absence of MHCII. Another class of genes, the NOD-like receptors (NLRs) has been reported in large numbers in species without an adaptive immune system. We find that cod and haddock as well as most other teleosts generally have a high number of NLRs, with a likely expansion at the root of this clade. Thus, a high number of NLRs in teleosts does not seem to be connected with the presence or absence of MHCII. This thesis shows what kind of questions genome assemblies created for different purposes can answer. Ideally, genome assemblies for all kinds of species should be created, upgraded and updated based on the best available technologies. But this is costly. With the right planning and set-up, assemblies based on low-coverage sequencing can be very powerful with regards to topics such as the presence/absence of genes and for phylogeny. Also, even with moderate amounts of long-read PacBio sequencing, it is possible to create highly contiguous genome assemblies addressing issues that are impossible to elucidate with fragmented assemblies, such as the amount of multi-copy immune genes

Programmerbar ADC med robust lager og GPS

Forsvarets forskningsinstitutt har en miljølab der de tester ut sine og andres proenkter under ekstreme forhold (slag/risting, temperatur og luftfuktighet) for å se om de klarer de belastninger proenktet blir utsatt for i løpet av sin levetid. For å få mest mulig virkelighetsnære simuleringer trenger de å vite hvordan omgivelsene der proenktet skal være oppfører seg. For å finne ut dette plasseres sensorer ut i omgivelsene og dataen lagres. Etter som det er nødvendig å teste proenktet i ekstreme situasjoner er dermed omgivelsene ekstreme og dette kan være veldig fysisk krevende for de personene som er tilstede for å overvåke disse målingene. Et eksempel på ekstreme omgivelser er en MTB i høy sjø. Derfor er det ønskelig å slippe å faktisk måtte være til stede under innsamlingen av data. Her kommer vårt prosjekt inn med at det er datalogger som lagrer dataene slik at de kan leses ut når testene er over. Det er også muligens ønskelig å bruke dem i forskningsraketter og der er det ikke plass til at noen er med og tar opp dataene

Genomic characterization of the Atlantic cod sex-locus

A variety of sex determination mechanisms can be observed in evolutionary divergent teleosts. Sex determination is genetic in Atlantic cod (Gadus morhua), however the genomic location or size of its sex-locus is unknown. Here, we characterize the sex-locus of Atlantic cod using whole genome sequence (WGS) data of 227 wild-caught specimens. Analyzing more than 55 million polymorphic loci, we identify 166 loci that are associated with sex. These loci are located in six distinct regions on five different linkage groups (LG) in the genome. The largest of these regions, an approximately 55 Kb region on LG11, contains the majority of genotypes that segregate closely according to a XX-XY system. Genotypes in this region can be used genetically determine sex, whereas those in the other regions are inconsistently sex-linked. The identified region on LG11 and its surrounding genes have no clear sequence homology with genes or regulatory elements associated with sex-determination or differentiation in other species. The functionality of this sex-locus therefore remains unknown. The WGS strategy used here proved adequate for detecting the small regions associated with sex in this species. Our results highlight the evolutionary flexibility in genomic architecture underlying teleost sex-determination and allow practical applications to genetically sex Atlantic cod

The genomic mosaicism of hybrid speciation

publishedVersio

De novo gene evolution of antifreeze glycoproteins in codfishes revealed by whole genome sequence data

New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown. Here, we demonstrate that afgps in codfishes have evolved de novo from non-coding DNA 13–18 Ma, coinciding with the cooling of the Northern Hemisphere. Using whole-genome sequence data from several codfishes and notothenioids, we find higher copy number of afgp in species exposed to more severe freezing suggesting a gene dosage effect. Notably, antifreeze function is lost in one lineage of codfishes analogous to the afgp losses in non-Antarctic notothenioids. This indicates that selection can eliminate the antifreeze function when freezing is no longer imminent. In addition, we show that evolution of afgp-assisting antifreeze potentiating protein genes (afpps) in notothenioids coincides with origin and lineage-specific losses of afgp. The origin of afgps in codfishes is one of the first examples of an essential gene born from non-coding DNA in a non-model species. Our study underlines the power of comparative genomics to uncover past molecular signatures of genome evolution, and further highlights the impact of de novo gene origin in response to a changing selection regime

Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions

Genome sequencing of the teleost Atlantic cod demonstrated loss of the Major Histocompatibility Complex (MHC) class II, an extreme gene expansion of MHC class I and gene expansions and losses in the innate pattern recognition receptor (PRR) family of Toll-like receptors (TLR). In a comparative genomic setting, using an improved version of the genome, we characterize PRRs in Atlantic cod with emphasis on TLRs demonstrating the loss of TLR1/6, TLR2 and TLR5 and expansion of TLR7, TLR8, TLR9, TLR22 and TLR25. We find that Atlantic cod TLR expansions are strongly influenced by diversifying selection likely to increase the detectable ligand repertoire through neo- and subfunctionalization. Using RNAseq we find that Atlantic cod TLRs display likely tissue or developmental stage-specific expression patterns. In a broader perspective, a comprehensive vertebrate TLR phylogeny reveals that the Atlantic cod TLR repertoire is extreme with regards to losses and expansions compared to other teleosts. In addition we identify a substantial shift in TLR repertoires following the evolutionary transition from an aquatic vertebrate (fish) to a terrestrial (tetrapod) life style. Collectively, our findings provide new insight into the function and evolution of TLRs in Atlantic cod as well as the evolutionary history of vertebrate innate immunity

Towards correction-free assembly of raw PacBio reads

<p>Poster presented at the 15th annual Advances in Genome Biology and Technology (AGBT) February 12-15, 2014. Poster number 211.</p

Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth

Understanding the genetic basis of adaptation is one of the main enigmas of evolutionary biology. Among vertebrates, hemoglobin has been well documented as a key trait for adaptation to different environments. Here, we investigate the role of hemoglobins in adaptation to ocean depth in the diverse teleost order Gadiformes, with species distributed at a wide range of depths varying in temperature, hydrostatic pressure and oxygen levels. Using genomic data we characterized the full hemoglobin (Hb) gene repertoire for subset of species within this lineage. We discovered a correlation between expanded numbers of Hb genes and ocean depth, with the highest numbers in species occupying shallower, epipelagic regions. Moreover, we demonstrate that the Hb genes have functionally diverged through diversifying selection. Our results suggest that the more variable environment in shallower water has led to selection for a larger Hb gene repertoire and that Hbs have a key role in adaptive processes in marine environments

Selection on gene duplicates following whole genome duplication: Insights from salmonid genomes

Poster presented at the Biology Of Genomes meeting 201