Population Genomics of Marine Zooplankton

Abstract

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 closelyrelated 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.

Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

“…The statistical strength from analysing many genomic loci overcomes the limitation of an incomplete sampling of the metapopulation [74] and increases the capacity to detect even subtle patterns in population structure. This is especially relevant in widespread marine zooplankton where there is likely to be cryptic diversity and undiscovered species [12,20], which is essential information for species that are proposed as indicators of ocean change.…”

“…For Limacina helicina, the Arctic and Antarctic populations were discovered to be separate species through differences in the COI gene [16,17]. However, the use of a few molecular markers has often been insufficient to detect subtle patterns of population structure expected in high gene flow species such as marine fish and zooplankton [18][19][20]. In order to identify potential barriers to dispersal, we need to sample a large number of loci across the genome, which is possible due to recent developments in next-generation sequencing (NGS) technologies [21,22].…”

“…Here, we chose a genome reduced-representation method to characterise genome-wide variation in pteropods because of their potentially large genome sizes and small amount of input DNA per individual. In species with large genomes, as reported for several zooplankton groups [20], whole genome sequencing may not be feasible for population-level studies. Reduced-representation methods can overcome the difficulty of sequencing numerous large genomes.…”

Towards population genomics in non-model species with large genomes: a case study of the marine zooplanktonCalanus finmarchicus

“…However, this task may be challenging, as gene flow can be high in zooplankton species and often results in subtle patterns of genetic structure not necessarily detectable with only a few markers [61,62], thus requiring a genomic approach [63]. So far, technical difficulties linked to the large genome sizes of many of these organisms, particularly in the Arthropoda phylum, have hampered population genomics studies (reviewed by [64]). In the present study, our aim was to identify an efficient genome reduction method to obtain a sufficiently large number of SNPs to conduct robust population structure studies on Calanus finmarchicus .…”

Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)

“…Particularly, marine species populations belonging to plankton face a large panel of physico-chemical changes in open ocean, (Guinder & Molinero, 2013;Pelejero, Calvo, & Hoegh-Guldberg, 2010) and gene expression variations have been observed in several studies (Lauritano, Procaccini, & Ianora, 2012;Salazar et al 2019). However, taxonomic identification (Cepeda, Sabatini, Scioscia, Ramírez, & Viñas, 2016), DNA and mRNA extraction of small marine eukaryote species due to their complex genomes (Bucklin et al, 2018) still constitute an obstacle to conduct proper studies focusing on gene expression and selection in natural populations.…”