Biology subjects

Laine, V.

Publications and source records attributed to Laine, V..

4 recordsLinked to original sources

bioRxiv2026

DEADMON: A protocol for long-term monitoring of deadwood-associated species

Dead wood has a vital role in maintaining biodiversity and ecosystem processes in boreal forests. A large proportion of deadwood-dependent species are threatened by habitat loss and degradation resulting from intensive forest management practices. In Finland, approximately 25% of all forest-dwelling species, around 5,000 species, are dependent on deadwood, of which 596 are red-listed. Currently, there is no large-scale, long-term monitoring programme for saproxylic species in Finland, and the tools required to implement such monitoring remain underdeveloped. Here, we develop, test and report a DNA-based monitoring method for dead wood associated organisms including fungi, lichens, bryophytes, and insects. Three study sites were selected for the research, one from each boreal vegetation zone. From each study site, 16 study logs were selected and permanently marked for long-term monitoring. Our results show that the method is applicable to all studied species groups. However, especially fungi and lichens show considerable difference between species detected morphologically and those detected using DNA-based methods. We conclude that two partly contrasting strategies emerge for implementing long-term monitoring of deadwood -associated boreal species. The first strategy emphasizes as comprehensive geographical sampling of habitat types and tree species as possible. The second approach focuses on long-term monitoring of individual deadwood units across their full decomposition trajectory. We recommend that solutions for unifying the currently fragmented monitoring research on deadwood-associated organisms would be sought together with potential coordinating institutions.

ecology↗

bioRxiv2026

The road to nowhere: geolocation-by-genotype traces large-scale yellow-browed warbler vagrancy to central Siberia

Vagrant animals - individuals found far outside their normal range - offer powerful natural experiments for understanding migratory mechanisms. The yellow-browed warbler (Phylloscopus inornatus) provides perhaps the best-yet example, typically migrating from Siberia to South/Southeast Asia yet found in increasingly large numbers in Western Europe. This represents a strikingly unresolved evolutionary puzzle: why do so many migrants consistently move in almost the complete wrong direction? A critical first step toward solving this enigma is determining where these birds come from. If vagrants came from the proximal western range edge this would imply simple disorientation, whilst a more easterly origin could imply large-scale reverse misorientation. Here, we develop a geolocation-by-genotype algorithm for low-coverage whole-genome resequencing data collected from feathers. Our method identifies spatially informative SNPs; clusters them to account for covariance in allele frequency through space; and employs a bootstrapped maximum-likelihood framework to estimate spatial origin with uncertainty. Applied to more than 80 European-caught birds, our results place their origin in central Siberia (118{degrees}E; 89-134{degrees}E [95% CI]); over 2000km east of the western range edge. These results suggest mass misorientation in a near-reverse direction, and highlight the yellow-browed warbler as an exceptional system for probing the mechanism, ontogeny and evolution of migration.

animal behavior and cognition↗

bioRxiv2020

Does arsenic contamination affect DNA methylation patterns in a wild bird population? An experimental approach

Pollutants, such as toxic metals, negatively influence organismal health and performance, even leading to population collapses. Studies in model organisms have shown that epigenetic marks, such as DNA methylation, can be modulated by various environmental factors, including pollutants, influencing gene expression and various organismal traits. Yet experimental data on the effects of pollution on DNA methylation from wild animal populations is largely lacking. We here experimentally investigated for the first time the effects of early-life exposure to environmentally relevant levels of a key pollutant, arsenic (As), on genome-wide DNA methylation in a wild bird population. We experimentally exposed nestlings of great tits (Parus major) to arsenic during their post-natal developmental period (3 to 14 days post-hatching) and compared their erythrocyte DNA methylation levels to those of respective controls. In contrast to predictions, we found no overall hypomethylation in the arsenic group. We found evidence for loci to be differentially methylated between the treatment groups, but for five CpG sites only. Three of the sites were located in gene bodies of zinc finger and BTB domain containing 47 (ZBTB47), HIVEP zinc finger 3 (HIVEP3) and insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1). Further studies are needed to evaluate whether epigenetic dysregulation is a commonly observed phenomena in polluted populations, and what the consequences are for organism functioning and for population dynamics.

ecology↗

bioRxiv2018

Exploring the unmapped DNA and RNA reads in a songbird genome

BackgroundA widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. A significant percentage of reads, however, frequently remain unmapped despite improvements in the methods and hardware, which have enhanced the efficiency and accuracy of alignments. Usually unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from this data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies. The generated sequence contigs were then aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence.\n\nResultsMany of the aligned contigs showed sequence similarity to sequences from different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma.\n\nConclusionsOur analyses revealed that meaningful biological information can be found when further exploring unmapped reads. It is possible to discover sequences that are either absent or misassembled in the reference genome and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.

genomics↗