Quinten Bafort

The immediate effects of plant polyploidization are well characterized and it is generally accepted that these morphological, physiological, developmental, and phenological changes contribute to polyploid establishment. Studies on the environmental dependence of the immediate effects of whole-genome duplication (WGD) are, however, scarce but suggest that these immediate effects are altered by stressful conditions. As polyploid establishment seems to be associated with environmental disturbance, the relationship between ploidy-induced phenotypical changes and environmental conditions is highly relevant. Here, we use a common garden experiment on the greater duckweed Spirodela polyrhiza to test whether the immediate effects of WGD can facilitate the establishment of tetraploid duckweed along gradients of two environmental stressors. Because successful polyploid establishment often depends on recurrent polyploidization events, we include four genetically diverse strains and assess whether these immediate effects are strain-specific. We find evidence that WGD can indeed confer a fitness advantage under stressful conditions and that the environment affects ploidy-induced changes in fitness and trait reaction norms in a strain-specific way.

The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there is growing evidence that polyploidization can help overcome environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete or outlive nonpolyploids at times of environmental upheaval remain elusive, especially for autopolyploids, in which heterosis effects are limited. On the longer term, WGD might increase both mutational and environmental robustness due to redundancy and increased genetic variation, but on the short—or even immediate—term, selective advantages of WGDs are harder to explain. Here, by duplicating artificially generated Gene Regulatory Networks (GRNs), we show that duplicated GRNs—and thus duplicated genomes—show higher signal output variation than nonduplicated GRNs. This increased variation leads to niche expansion and can provide polyploid populations with substantial advantages to survive environmental turmoil. In contrast, under stable environments, GRNs might be maladaptive to changes, a phenomenon that is exacerbated in duplicated GRNs. We believe that these results provide insights into how genome duplication and (auto)polyploidy might help organisms to adapt quickly to novel conditions and to survive ecological uproar or even cataclysmic events.

In this chapter, we present the use of Spirodela polyrhiza in experiments designed to study the evolutionary impact of whole-genome duplication (WGD). We shortly introduce this duckweed species and explain why it is a suitable model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related duckweed experiment. These steps include strain selection, ploidy determination, different methods of making polyploid duckweeds, replication, culturing conditions, preservation, and the ways to quantify phenotypic and transcriptomic change.

In this chapter, we present the use of Chlamydomonas reinhardtii in experiments designed to study the evolutionary impacts of whole genome duplication. We shortly introduce the algal species and depict why it is an excellent model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related Chlamydomonas experiment. These steps include strain selection, ploidy determination, different methods of making diplo- and polyploid Chlamydomonas cells, replication, culturing conditions, preservation, and the ways to quantify phenotypic and genotypic change.

Effective monitoring of non-indigenous seaweeds and combatting their effects relies on a solid confirmation of the non-indigenous status of the respective species. We critically analysed the status of presumed non-indigenous seaweed species reported from the Mediterranean Sea, the Northeast Atlantic Ocean and Macaronesia, resulting in a list of 140 species whose non-indigenous nature is undisputed. For an additional 87 species it is unclear if they are native or non-indigenous (cryptogenic species) or their identity requires confirmation (data deficient species). We discuss the factors underlying both taxonomic and biogeographic uncertainties and outline recommendations to reduce uncertainty about the non-indigenous status of seaweeds. Our dataset consisted of over 19,000 distribution records, half of which can be attributed to only five species (Sargassum muticum, Bonnemaisonia hamifera, Asparagopsis armata, Caulerpa cylindracea and Colpomenia peregrina), while 56 species (40%) are recorded no more than once or twice. In addition, our analyses revealed considerable variation in the diversity of non-indigenous species between the geographic regions. The Eastern Mediterranean Sea is home to the largest fraction of non-indigenous seaweed species, the majority of which have a Red Sea or Indo-Pacific origin and have entered the Mediterranean Sea mostly via the Suez Canal. Non-indigenous seaweeds with native ranges situated in the Northwest Pacific make up a large fraction of the total in the Western Mediterranean Sea, Lusitania and Northern Europe, followed by non-indigenous species with a presumed Australasian origin. Uncertainty remains, however, regarding the native range of a substantial fraction of non-indigenous seaweeds in the study area. In so far as analyses of first detections can serve as a proxy for the introduction rate of non-indigenous seaweeds, these do not reveal a decrease in the introduction rate, indicating that the current measures and policies are insufficient to battle the introduction and spread of non-indigenous species in the study area.

In this study we explore the introduction of the brown alga Dictyota acutiloba in the Mediterranean Sea and provide a substantive update on the geographic distribution of this species, which was long thought to be confined to the Pacific Ocean. A critical assessment of published distribution records and additional identifications based on cox1, psbA and rbcL genetic markers confirm the presence of D. acutiloba at a number of locations in the Indo-Pacific as well as three locations along the Israeli coastline in the south-eastern Mediterranean Sea. The close genetic affinity between introduced specimens and those from a population in Hurghada (Red Sea) strongly suggests an introduction via the Suez Canal. The occurrence of D. acutiloba in these regions is further supported by predictions made by correlative ecological niche models (ENMs), which show high suitability values in the northern Red Sea and the Levantine Basin. In contrast, environmental conditions in the western Mediterranean and parts of the north-eastern Mediterranean are currently less favourable, as evidenced by the lower predicted probability of occurrence. Under future scenarios, the suitability of these regions increases. The further spread of D. acutiloba in the eastern Mediterranean seems imminent, and the species may even extend its range to the western Mediterranean Sea, depending on the climate change scenario considered. While D. acutiloba can be relatively easily distinguished from the majority of Mediterranean Dictyota species, it remains difficult to differentiate this species from narrow growth forms of D. dichotoma. Therefore, we recommend the use of molecular markers such as cox1, psbA and rbcL, to unequivocally identify this species and monitor its further spread.

Aim: Historical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora and Padina, are exceptionally diverse. Specifically, we test whether the evolutionary processes that shaped the latitudinal diversity patterns in these clades are in line with the tropical conservatism, out-of-the-tropics or diversification rate hypotheses. Location: Global coastal benthic marine environments. Taxon: Dictyotales (Phaeophyceae). Methods: Species diversity was inferred using DNA-based species delineation, addressing cryptic diversity and circumventing taxonomic problems. A six-gene time-calibrated phylogeny, distribution data of 3,755 specimens and probabilistic modelling of geographical range evolution were used to infer historical biogeographical patterns. The phylogeny was tested against different trait-dependent models to compare diversification rates for different geographical units as well as different thermal affinities. Results: Our results indicate that Dictyotales originated in the Middle Jurassic and reach a current peak of species diversity in the Central Indo-Pacific. Ancestral range estimation points to a southern hemisphere origin of Dictyotales corresponding to the tropical southern Tethys Sea. Our results demonstrate that diversification rates were generally higher in tropical regions, but increased diversification rates in different clades are driven by different processes. Our results suggest that three major clades underwent a major diversification burst in the early Cenozoic, with Dictyota and Padina expanding their distribution into temperate regions while Lobophora retained a predominantly tropical niche. Main conclusions: Our results are consistent with both the tropical conservatism hypothesis, in which clades originate and remain in the tropics (Lobophora), and the out-of-the-tropics scenario, where taxa originate and expand towards the temperate regions while preserving their presence in the tropics (Dictyota, Padina).

Here, we report for the first time the presence of Dictyota cyanoloma in southern California. Dictyota cyanoloma is conspicuous in harbors and bays by its distinctive bright blue-iridescent margins. This species was originally described from Europe, but subsequent studies have revealed that it represented an introduction from Australia. The current distribution of D. cyanoloma comprises southern Australia and the North East Atlantic, including the Mediterranean Sea and the Macaronesian islands. The presence of D. cyanoloma in southern California is supported by molecular cox1 and psbA gene sequences. A reconstruction of the invasive history based on nine polymorphic microsatellite markers reveals a close affinity of the Californian specimens with European populations. Dictyota cyanoloma in the United States appears to be (so far) restricted to the Californian coast from San Diego Bay in the south to Santa Catalina Island and Long Beach Harbor in the north. A correlative species distribution model suggests gradually declining habitat suitability north of the Southern Californian Bight and high suitability in Baja California, including the Gulf of California. Finally, its widespread abundance in bays and harbors suggests shipping is a likely transport mechanism.

Milkcaps form a diverse group of widely consumed ectomycorrhizal fungi. Despite their popularity and ubiquity, large gaps still exist in our knowledge of the milkcap genera. This paper summarizes our current state of knowledge of both Lactarius and Lactifluus. Lacunas in our knowledge are indicated, and an overview of their culinary uses is given.