Morten Skage

The genome sequence of Atlantic cod reveals a unique immune system

Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.

A taxonomic reappraisal of the European Daphnia longispina complex (Crustacea, Cladocera, Anomopoda)

The Daphnia longispina complex contains some of the most common water flea species in the northern hemisphere, and has been a model organism for many ecological and evolutionary studies. Nevertheless, the systematics and nomenclature of this group, in particular its Palaearctic members, have been in flux for the past 150 years; this hinders the correct interpretation of scientific results and promotes the erroneous use of species names. We revise the systematics of this species complex based on mitochondrial sequence variation (12S rDNA and COI) of representative populations across Europe, with a special focus on samples from type localities of the respective taxa. Combining genetic evidence and morphological assignments of analysed individuals, we propose a comprehensive revision of the European members of the D. longispina complex. We show that D. hyalina and D. rosea morphotypes have evolved several times independently, and we find no evidence to maintain these morphotypes as distinct biological species. Alpine individuals described as D. zschokkei are conspecific with the above‐mentioned lineage. We suggest that this morphologically and ecologically plastic but genetically uniform hyalina–rosea–zschokkei clade should be identified as D. longispina (O. F. Müller, 1776). The valid name of Fennoscandian individuals labelled D. longispina sensu stricto in the recent literature is D. lacustris G. O. Sars, 1862. Additionally, we discovered another divergent lineage of this group, likely an undescribed species, in southern Norway. Our results present a solution for several prevailing taxonomic problems in the genus Daphnia, and have broad implications for interpretation of biogeographical patterns, and ecological and evolutionary studies.

Origin of Fucus serratus (Heterokontophyta; Fucaceae) populations in Iceland and the Faroes : a microsatellite-based assessment

The common intertidal seaweed Fucus serratus was almost certainly introduced to Iceland and the Faroes by humans from Europe, as previous genetic studies have confirmed that life-history constraints preclude long-distance dispersal. Introduction must have occurred sometime in the 1,000 years between arrival of the first Icelandic settlers c. 900 AD and when the species was first noted in a phycological survey in 1900. We genotyped 19 populations from throughout northern Europe, Iceland, and the Faroes with seven microsatellite loci in order to identify the source or sources of the Icelandic/Faroese populations. Assignment tests indicated that the Småskjaer area of the Oslofjorden in Norway was the source for the Icelandic populations and the Hafnarfjörður area of Iceland was the likely source for the single Faroese population. The time of introduction to Iceland was probably during the 19th century, whereas introduction to the Faroes occurred during the late 20th century. Additionally, molecular data verified hybridization between the introduced F. serratus and the native F. evanescens.

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

BackgroundThe first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.ResultsBy combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual.ConclusionsThe inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

Restoring Daphnia lacustris G.O. Sars, 1862 (Crustacea, Anomopoda): a cryptic species in the Daphnia longispina group

While molecular markers have revealed several distinct species within the Daphnia longispina group, there is a need to reconcile these species with traditional nomenclature. Here we show that one such species, called D. longispina in recent literature based on molecular markers, can reliably be associated with the described taxon Daphnia lacustris G.O. Sars, 1862. Both mitochondrial and nuclear molecular markers readily distinguish this species from others in the D. longispina group. D. lacustris is absent in the region from which D. longispina was first described (Denmark), and the designation D. longispina must be reserved for another widespread species represented by Danish lineages. While the diagnosis of D. lacustris (and other species of the D. longispina group) by molecular markers is unequivocal, distinguishing it morphologically from other species is still problematic. The presently known distribution range of D. lacustris includes most of Norway, northern Finland and a single lake in the Polish Tatra Mountains. Its typical habitat is oligotrophic lakes without intense fish predation.

Molecular analysis of predation by carabid beetles (Carabidae) on the invasive Iberian slug Arion lusitanicus.

The invasive Iberian slug, Arion lusitanicus, is spreading through Europe and poses a major threat to horticulture and agriculture. Natural enemies, capable of killing A. lusitanicus, may be important to our understanding of its population dynamics in recently invaded regions. We used polymerase chain reaction (PCR) to study predation on A. lusitanicus by carabid beetles in the field. A first multiplex PCR was developed, incorporating species-specific primers, and optimised in order to amplify parts of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of large Arion slugs, including A. lusitanicus from the gut contents of the predators. A second multiplex PCR, targeting 12S rRNA mtDNA, detected predation on smaller Arion species and the field slug Deroceras reticulatum. Feeding trials were conducted to measure the effects of digestion time on amplicon detectability. The median detection times (the time at which 50% of samples tested positive) for A. lusitanicus and D. reticulatum DNA in the foreguts of Carabus nemoralis were 22 h and 20 h, respectively. Beetle activity-densities were monitored using pitfall traps, and slug densities were estimated using quadrats. Predation rates on slugs in the field by C. nemoralis in spring ranged from 16-39% (beetles positive for slug DNA) and were density dependent, with numbers of beetles testing positive being positively correlated with densities of the respective slug species. Carabus nemoralis was shown to be a potentially important predator of the alien A. lusitanicus in spring and may contribute to conservation biological control.

Daphnia galeata · D. longispina hybrids in western Norway

We describe the occurrence of D. galeata×longispina hybrids in two lakes of western Norway. Parental species and interspecific hybrids were characterised by both nuclear and mitochondrial molecular markers. In one of the populations, hybrids were shown to dominate the population over several years. A few individuals in both populations were probably not F1 hybrids, but possibly backcrosses or F2 hybrids. Most (possibly all) F1 hybrids were of D. galeata maternal origin. In addition, interspecific hybrids could be identified based on morphological characters, which were intermediate between the parental species. Interspecific hybridisation between these two species is remarkable, since they are distantly related.

DNA from formalin-fixed tissue: extraction or repair? That is the question

Abstract Establishing effective DNA-based protocols for use on archival material fixed in formaldehyde (formalin) is a particularly challenging task. Formalin fixation induces cross-linking with nucleic acids and proteins, thereby reducing the amount and quality of the extracted DNA. Previous attempts have primarily focused on optimizing DNA extraction protocols. Here we focus on the use of enzymes capable of in vitro repair of DNA extracts prior to amplification of the nucleic acids by the polymerase chain reaction (PCR). The amplification success of mitochondrial DNA was greater using the repair enzyme assay (56%) than with the regular PCR assay (20%), and even more convincing results were obtained with the amplified nuclear ribosomal region (91% versus 21%). These results indicate that in vitro repair of DNA damage (depurinated sites, strand nicks and base modifications) increases the number of samples that amplify, amplify to a greater extent and amplify fewer ancillary bands and that DNA repair has been overlooked as a way of improving the efficiency of molecular methods used on formalin-fixed samples. Fidelity has not been specifically investigated, but preliminary results indicate that misincorporation is not a major problem.

Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA.

Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting of reverse complementary sequence at the 5′ and 3′-ends of sequencing reads. The palindromic sequences themselves have specific properties – the bases at the 5′-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3′-end. The terminal 3′ bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA), which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3′-end of DNA strands, with the 5′-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA) datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias.

Introgression and Differentiation of the Invasive Slug Arion vulgaris from Native A. ater

ABSTRACT The large arionid slug Arion vulgaris is an invasive pest dispersing through large parts of Europe and causing considerable damage in gardens, horticulture and agriculture. It is also possible that this so-called “Iberian slug” has an impact on Norwegian ecosystems, displacing or hybridizing with the native black slug Arion ater. The taxonomy of the large arionids is complex and confusing, encompassing different anatomical forms and colour varieties. The present study integrates, for the first time, coloration, ligula morphology, genital morphometry, nuclear and mitochondrial DNA in order to differentiate the large arionids found in Norway, A. vulgaris, A. ater and A. rufus. These data revealed a clear separation between A. vulgaris and A. ater based on the morphology of the genitalia and mtDNA. However, introgression with the red slug A. rufus was apparent in approximately half of the A. ater specimens analysed, evidenced by ligula morphology, mitochondrial and nuclear DNA. In addition, the mitochondrial COI gene and the nuclear ITS1 gene suggested introgression between A. ater and A. vulgaris. Phylogenetic analyses that included A. vulgaris, A. ater and A. rufus from other parts of Europe, together with A. flagellus, A. fuscus, A. lusitanicus and A. nobrei suggest that A. vulgaris is more closely related to A. ater and A. rufus than to A. lusitanicus. This study confirms the uncertainty of identification based solely on coloration and stresses the importance of integrating several approaches to differentiate these large arionids, allowing a better appreciation of their invasive potential, ecological impact and current distribution.