Irina Smolina

Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers to efficiently identify parental species and hybrids. Using next‐generation sequencing analysis of both the genome and transcriptome from two sibling species, Calanus finmarchicus and Calanus glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species‐specific amplicon length. Furthermore, most of the markers were successfully amplified in other Calanus species, allowing the molecular identification of Calanus helgolandicus, Calanus hyperboreus and Calanus marshallae.

Genetics redraws pelagic biogeography of Calanus

Planktonic copepods of the genus Calanus play a central role in North Atlantic/Arctic marine food webs. Here, using molecular markers, we redrew the distributional ranges of Calanus species inhabiting the North Atlantic and Arctic Oceans and revealed much wider and more broadly overlapping distributions than previously described. The Arctic shelf species, C. glacialis, dominated the zooplankton assemblage of many Norwegian fjords, where only C. finmarchicus has been reported previously. In these fjords, high occurrences of the Arctic species C. hyperboreus were also found. Molecular markers revealed that the most common method of species identification, prosome length, cannot reliably discriminate the species in Norwegian fjords. Differences in degree of genetic differentiation among fjord populations of the two species suggested that C. glacialis is a more permanent resident of the fjords than C. finmarchicus. We found no evidence of hybridization between the species. Our results indicate a critical need for the wider use of molecular markers to reliably identify and discriminate these morphologically similar copepod species, which serve as important indicators of climate responses.

Variation in thermal stress response in two populations of the brown seaweed, Fucus distichus, from the Arctic and subarctic intertidal

It is unclear whether intertidal organisms are ‘preadapted’ to cope with the increase of temperature and temperature variability or if they are currently at their thermal tolerance limits. To address the dichotomy, we focused on an important ecosystem engineer of the Arctic intertidal rocky shores, the seaweed Fucus distichus and investigated thermal stress responses of two populations from different temperature regimes (Svalbard and Kirkenes, Norway). Thermal stress responses at 20°C, 24°C and 28°C were assessed by measuring photosynthetic performance and expression of heat shock protein (HSP) genes (shsp, hsp90 and hsp70). We detected population-specific responses between the two populations of F. distichus, as the Svalbard population revealed a smaller decrease in photosynthesis performance but a greater activation of molecular defence mechanisms (indicated by a wider repertoire of HSP genes and their stronger upregulation) compared with the Kirkenes population. Although the temperatures used in our study exceed temperatures encountered by F. distichus at the study sites, we believe response to these temperatures may serve as a proxy for the species’ potential to respond to climate-related stresses.

Low cost sequencing of mitogenomes from museum samples using baits capture and Ion Torrent

Abstract The development of various target enrichment methods in combination with next generation sequencing techniques has greatly facilitated the use of partially degraded DNA samples in genetic studies. We employed the MYbaits target enrichment system in combination with Ion Torrent sequencing on a broad range of DNA quality, extracted from tissues obtained from both natural history archives and through various opportunistic sampling methods, to sequence the mitogenome of 11 mobulid rays and two closely related species. Mobulids are large, elusive pelagic filter feeders, for which conservation concerns have recently be raised in connection to their vulnerable life histories and increasing fishing pressure. We show that the MYbaits target enrichment method can be used to effectively sequence large parts of the mitogenome from heavily degraded DNA samples, and provide a time and cost effective alternative for genetic studies of rare and/or difficult to sample species.

Population genomics of marine zooplankton

The exceptionally large population size and cosmopolitan biogeographic distribution that distinguish many – but not all – marine zooplankton species generate similarly exceptional patterns of population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has slowed the application of population genomic approaches, due to lack of genomic resources for closely related species and diversity of genomic architecture, including highly replicated genomes of many crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is transforming our ability to analyze population genetics and connectivity of marine zooplankton, and providing new understanding and different answers than earlier analyses, which typically used mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that, despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are critically needed to allow further examination of micro-evolution and local adaptation, including identification of genes that show evidence of selection. These new tools will also enable further examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to discriminate genetic “noise” in large and patchy populations from local adaptation to environmental conditions and change.