Epigenetic diversity of genes with copy number variations among natural populations of the three-spined stickleback.

Duplicated genes provide the opportunity for evolutionary novelty and adaptive divergence. In many cases, having more gene copies increases gene expression, which might facilitate adaptation to stressful or novel environments. Conversely, overexpression or misexpression of duplicated genes can be detrimental and subject to negative selection.

Heteroplasmy Is Rare in Plant Mitochondria Compared with Plastids despite Similar Mutation Rates.

Plant cells harbor two membrane-bound organelles containing their own genetic material-plastids and mitochondria. Although the two organelles coexist and coevolve within the same plant cells, they differ in genome copy number, intracellular organization, and mode of segregation. How these attributes affect the time to fixation or, conversely, loss of neutral alleles is currently unresolved.

A somatic genetic clock for clonal species.

Age and longevity are key parameters for demography and life-history evolution of organisms. In clonal species, a widespread life history among animals, plants, macroalgae and fungi, the sexually produced offspring (genet) grows indeterminately by producing iterative modules, or ramets, and so obscure their age. Here we present a novel molecular clock based on the accumulation of fixed somatic genetic variation that segregates among ramets.

The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions.

Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life.

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment.

We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C.

An evolutionary epigenetic clock in plants.

Molecular clocks are the basis for dating the divergence between lineages over macroevolutionary timescales (~10 to 10 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes display a clocklike behavior.

Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant.

Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination.

Population genetic differentiation of the ubiquitous brooding coral Pocillopora acuta along Phuket Island reefs in the Andaman Sea, Thailand.

Background: The widespread Indo-Pacific coral species Pocillopora acuta Lamarck, 1816 displays varying levels of asexual versus sexual reproduction, with strong repercussions on genetic diversity, connectivity and genetic structuring within and among populations. For many geographic regions, baseline information on genetic diversity is still lacking, particularly in the Andaman Sea. The region suffered a massive heat-induced bleaching event in 2010 with high coral cover loss of branching coral species such as P.

Origin matters: Using a local reference genome improves measures in population genomics.

Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data.

A trait-based framework for seagrass ecology: Trends and prospects.

In the last three decades, quantitative approaches that rely on organism traits instead of taxonomy have advanced different fields of ecological research through establishing the mechanistic links between environmental drivers, functional traits, and ecosystem functions. A research subfield where trait-based approaches have been frequently used but poorly synthesized is the ecology of seagrasses; marine angiosperms that colonized the ocean 100M YA and today make up productive yet threatened coastal ecosystems globally. Here, we compiled a comprehensive trait-based response-effect framework (TBF) which builds on previous concepts and ideas, including the use of traits for the study of community assembly processes, from dispersal and response to abiotic and biotic factors, to ecosystem function and service provision.

An evolutionary epigenetic clock in plants.

Molecular clocks are the basis for dating the divergence between lineages over macro-evolutionary timescales (~10 -10 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes possess a clock-like behavior.

Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index.

Clonal reproduction, the formation of nearly identical individuals via mitosis in the absence of genetic recombination, is a very common reproductive mode across plants, fungi and animals. To detect clonal genetic structure, genetic similarity indices based on shared alleles are widely used, such as the Jaccard index, or identity by state. Here we propose a new pairwise genetic similarity index, the SH index, based on segregating genetic marker loci (typically single nucleotide polymorphisms) that are identically heterozygous for pairs of samples (N ).

Effects of changing environmental conditions on plastic ingestion and feeding ecology of a benthopelagic fish (Gadus morhua) in the Southwest Baltic Sea.

This study documents how the abundance of microplastics (<5 mm) in the Atlantic cod, Gadus morhua, relates to the changes of the fish diet during years with contrasting levels of anoxia for example following years of low or high major Baltic inflows (MBI). A MultiNet Maxi trawl and CTD were deployed annually to collect microplastic samples alongside oxygen, temperature, and salinity conditions. Microplastics were homogenously distributed both within the water column and across years.

Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader.

Invasion rates have increased in the past 100 y irrespective of international conventions. What characterizes a successful invasion event? And how does genetic diversity translate into invasion success? Employing a whole-genome perspective using one of the most successful marine invasive species world-wide as a model, we resolve temporal invasion dynamics during independent invasion events in Eurasia. We reveal complex regionally independent invasion histories including cases of recurrent translocations, time-limited translocations, and stepping-stone range expansions with severe bottlenecks within the same species.

Improved chromosome-level genome assembly and annotation of the seagrass, (eelgrass).

 Seagrasses (Alismatales) are the only fully marine angiosperms.  (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change.

Evolution via somatic genetic variation in modular species.

Somatic genetic variation (SoGV) may play a consequential yet underappreciated role in long-lived, modular species among plants, animals, and fungi. Recent genomic data identified two levels of genetic heterogeneity, between cell lines and between modules, that are subject to multilevel selection. Because SoGV can transfer into gametes when germlines are sequestered late in ontogeny (plants, algae, and fungi and some basal animals), sexual and asexual processes provide interdependent routes of mutational input and impact the accumulation of genetic load and molecular evolution rates of the integrated asexual/sexual life cycle.

Phenotypic plasticity under rapid global changes: The intrinsic force for future seagrasses survival.

Coastal oceans are particularly affected by rapid and extreme environmental changes with dramatic consequences for the entire ecosystem. Seagrasses are key ecosystem engineering or foundation species supporting diverse and productive ecosystems along the coastline that are particularly susceptible to fast environmental changes. In this context, the analysis of phenotypic plasticity could reveal important insights into seagrasses persistence, as it represents an individual property that allows species' phenotypes to accommodate and react to fast environmental changes and stress.

A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region.

Cephalopods are pivotal components of marine food webs, but biodiversity studies are hampered by challenges to sample these agile marine molluscs. Metabarcoding of environmental DNA (eDNA) is a potentially powerful technique to study oceanic cephalopod biodiversity and distribution but has not been applied thus far. We present a novel universal primer pair for metabarcoding cephalopods from eDNA, (Forward: 5'-CGC GGC GCT ACA TAT TAG AC-3', Reverse: 5'-GCA CTT AAC CGA CCG TCG AC-3').

Deep-sea predator niche segregation revealed by combined cetacean biologging and eDNA analysis of cephalopod prey.

Fundamental insight on predator-prey dynamics in the deep sea is hampered by a lack of combined data on hunting behavior and prey spectra. Deep-sea niche segregation may evolve when predators target specific prey communities, but this hypothesis remains untested. We combined environmental DNA (eDNA) metabarcoding with biologging to assess cephalopod community composition in the deep-sea foraging habitat of two top predator cetaceans.

The Native Microbiome is Crucial for Offspring Generation and Fitness of .

All multicellular organisms are associated with microbial communities, ultimately forming a metaorganism. Several studies conducted on well-established model organisms point to immunological, metabolic, and behavioral benefits of the associated microbiota for the host. Consequently, a microbiome can influence the physiology of a host; moreover, microbial community shifts can affect host health and fitness.

From ecosystems to socio-economic benefits: A systematic review of coastal ecosystem services in the Baltic Sea.

Seagrass meadows, algal forests and mussel beds are widely regarded as foundation species that support communities providing valuable ecosystem services in many coastal regions; however, quantitative evidence of the relationship is scarce. Using the Baltic Sea as a case study, a region of significant socio-economic importance in the northern hemisphere, we systematically synthesized the primary literature and summarized the current knowledge on ecosystem services derived from seagrass, macroalgae, and mussels (see animated video summary of the manuscript: Video abstract). We found 1740 individual ecosystem service records (ESR), 61% of which were related to macroalgae, 26% to mussel beds and 13% to seagrass meadows.

Modeling eelgrass spatial response to nutrient abatement measures in a changing climate.

For many coastal areas including the Baltic Sea, ambitious nutrient abatement goals have been set to curb eutrophication, but benefits of such measures were normally not studied in light of anticipated climate change. To project the likely responses of nutrient abatement on eelgrass (Zostera marina), we coupled a species distribution model with a biogeochemical model, obtaining future water turbidity, and a wave model for predicting the future hydrodynamics in the coastal area. Using this, eelgrass distribution was modeled for different combinations of nutrient scenarios and future wind fields.

Cultivable microbiota associated with Aurelia aurita and Mnemiopsis leidyi.

The associated microbiota of marine invertebrates plays an important role to the host in relation to fitness, health, and homeostasis. Cooperative and competitive interactions between bacteria, due to release of, for example, antibacterial substances and quorum sensing (QS)/quorum quenching (QQ) molecules, ultimately affect the establishment and dynamics of the associated microbial community. Aiming to address interspecies competition of cultivable microbes associated with emerging model species of the basal animal phyla Cnidaria (Aurelia aurita) and Ctenophora (Mnemiopsis leidyi), we performed a classical isolation approach.