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The fungal mitochondrial small subunit (mtSSU) ribosomal DNA is one of the most commonly used loci for phylogenetic analysis of lichen-forming fungi, but their primer specificity to mycobionts has not been evaluated. The current study aimed to design mycobiont-specific mtSSU primers and highlights their utility with an example from the saxicolous lichen-forming fungal genus Melanelia Essl. in Iceland. The study found a 12.5% success rate (3 out of 24 specimens with good-quality mycobiont mtSSU sequences) using universal primers (i.e. mrSSU1 and mrSSU3R), not including off-target amplification of environmental fungi, e.g. Cladophialophora carrionii and Lichenothelia convexa . New mycobiont-specific primers (mt-SSU-581-5’ and mt-SSU-1345-3’) were designed by targeting mycobiont-specific nucleotide sites in comparison with environmental fungal sequences, and assessed for mycobiont primer specificity using in silico PCR. The new mycobiont-specific mtSSU primers had a success rate of 91.7% (22 out of 24 specimens with good-quality mycobiont mtSSU sequences) on the studied Melanelia specimens. Additional testing confirmed the specificity and yielded amplicons from 79 specimens of other Parmeliaceae mycobiont lineages. This study highlights the effectiveness of designing mycobiont-specific primers for studies on lichen identification, barcoding and phylogenetics.

Mountain birch (Betula pubescens subsp. tortuosa (Ledeb.) Nyman) is the only indigenous forest-forming tree species in Iceland, and conservation of the remaining native birch forests is a recognized priority. In the last 30 years, a glacial outwash plain at Skeiðarársandur, southeast Iceland, has been colonized by birch which has now been established on an area > 35 km2. Genotyping by sequencing was used to determine the origin of the birch plants in the new population by assessing the genetic variation of its first generation and assessing its relatedness with the three neighboring but geographically isolated woodlands/forests closest to the outwash plain (Núpsstaðarskógar, Bæjarstaðarskógur, and Skaftafellsheiði). In total, 135K single-nucleotide polymorphisms (SNPs) were obtained, and 26K SNPs with the lower allele frequency (MAF) > 5% in 20,562 contigs. The new population on Skeiðarársandur most likely originated from Bæjarstaðarskógur and has slightly less variation than the established forests. Comparisons of the three established forests show that the adjacent forest Bæjarstaðarskógur and Skaftafellsheiði are more similar to each other than to Núpsstaðarskógar.

The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were 33605, 394, and 4265 bp, respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes).

The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were, 33605, 394, and 4265 bp respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan and its unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe and serve as a reference genome for the species in the family Phasianidae (order Galliformes).Competing Interest StatementThe authors have declared no competing interest.Footnotes* Significant revisions to wording and contents, approval of all authors for the updated text. This is a major update before submission to peer-reviewed jounrals.

Gene promoter and enhancer sequences are bound by transcription factors and are depleted of methylated CpG sites (cytosines preceding guanines in DNA). The absence of methylated CpGs in these sequences typically correlates with increased gene expression, indicating a regulatory role for methylation. We used nanopore sequencing to determine haplotype-specific methylation rates of 15.3 million CpG units in 7,179 whole-blood genomes. We identified 189,178 methylation depleted sequences where three or more proximal CpGs were unmethylated on at least one haplotype. A total of 77,789 methylation depleted sequences (~41%) associated with 80,503 cis -acting sequence variants, which we termed allele-specific methylation quantitative trait loci (ASM-QTLs). RNA sequencing of 896 samples from the same blood draws used to perform nanopore sequencing showed that the ASM-QTL, that is, DNA sequence variability, drives most of the correlation found between gene expression and CpG methylation. ASM-QTLs were enriched 40.2-fold (95% confidence interval 32.2, 49.9) among sequence variants associating with hematological traits, demonstrating that ASM-QTLs are important functional units in the noncoding genome. Allele-specific DNA methylation data in whole blood from 7,179 individuals sequenced by Nanopore, and gene expression profiles from 896 samples, show that DNA sequence variability accounts for most of the correlation between CpG methylation and gene expression.

The coexistence of four morphs of arctic charr in Thingvallavatn, Iceland, was demonstrated by investigations of morphology, habitat use, diet, endoparasitic fauna, life history, time and place of spawning, early ontogeny, and population genetics. Head morphology in embryos, juveniles and adults revealed the presence of two charr morphotypes, each including two morphs: (1) a benthic morphotype including large benthivorous (LB-) and small benthivorous (SB-) charr, featuring overshot mouth and relatively large pectoral fins, and (2) a pelagic morphotype including planktivorous (PL-) and piscivorous (PI-) charr, featuring terminal mouth and relatively small pectoral fins. SB-charr mature sexually (50%) at 2 (males) and 4 yr (females); asymptotic length is 133 mm. LB-charr mature sexually at 8 yr; asymptotic length is 553 mm. PL-charr mature sexually at 4 (males) and 5 yr (females); asymptotic length is 205 mm. PI-charr mature sexually at 6 yr; asymptotic length is 302 mm. SB- and LB-charr both live in the littoral zone, but they segregate in microhabitat: LB-charr live epibenthically, whereas SB-charr live mainly in the interstitial spaces of the stony substrate. Their diet, however, is similar (Schoener's D = 0.34 - 0.89). Both feed mainly on the snail Lymnaea peregra. PI-charr live mainly epibenthically, feeding on sticklebacks and juvenile charr. PL-charr is the most numerous morph in the lake. It lives both in the pelagic and in the epibenthic zone, feeding on crustacean zooplankton and chironomid pupae. The young of the year of all morphs live in the littoral zone where they feed on chironomid larvae. All morphs spawn in the littoral zone, LB-charr spawn in July-August, PL- and PI-charr spawn in September-November, whereas SB-charr spawn during August to November. Genetically, the morphs are very similar; Nei's genetic distances were between 0.00004 to 0.00126. The only significant difference found was between SB-charr and the other three morphs combined. The four morphs are conspecifics, although they may be reproductively segregated to some extent.