Oceanic dispersal barriers in a holoplanktonic gastropod

Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterize the species' population structure, demographic history and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasizes how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.

The impact of aragonite saturation variability on shelled pteropods: An attribution study in the California Current System

Observations from the California Current System (CalCS) indicate that the long-term trend in ocean acidification (OA) and the naturally occurring corrosive conditions for the CaCO3 mineral aragonite (saturation state Ω < 1) have a damaging effect on shelled pteropods, a keystone group of calcifying organisms in the CalCS. Concern is heightened by recent findings suggesting that shell formation and developmental progress are already impacted when Ω falls below 1.5. Here, we quantify the impact of low Ω conditions on pteropods using an individual-based model (IBM) with life-stage-specific mortality, growth, and behavior in a high-resolution regional hindcast simulation of the CalCS between 1984 and 2019. Special attention is paid to attributing this impact to different processes that lead to such low Ω conditions, namely natural variability, long-term trend, and extreme events. We find that much of the observed damage in the CalCS, and specifically >70% of the shell CaCO3 loss, is due to the pteropods' exposure to naturally occurring low Ω conditions as a result of their diel vertical migration (DVM). Over the hindcast period, their exposure to damaging waters (Ω < 1.5) increases from 9% to 49%, doubling their shell CaCO3 loss, and increasing their mortality by ~40%. Most of this increased exposure is due to the shoaling of low Ω waters driven by the long-term trend in OA. Extreme OA events amplify this increase by ~40%. Our approach can quantify the health of pteropod populations under shifting environmental conditions, and attribute changes in fitness or population structure to changes in the stressor landscape across hierarchical time scales.

Historical climate change and vicariance events contributed to the intercontinental disjunct distribution pattern of ash species (Fraxinus, Oleaceae)

The Northern Hemisphere temperate forests exhibit a disjunct distributional pattern in Europe, North America, and East Asia. Here, to reveal the promoter of intercontinental disjunct distribution, Fraxinus was used as a model organism to integrate abundant fossil evidence with high-resolution phylogenies in a phytogeographic analysis. We constructed a robust phylogenetic tree using genomic data, reconstructed the geographic ancestral areas, and evaluated the effect of incorporating fossil information on the reconstructed biogeographic history. The phylogenetic relationships of Fraxinus were highly resolved and divided into seven clades. Fraxinus originated in western North America during Eocene, and six intercontinental dispersal events and five intercontinental vicariance events were occured. Results suggest that climate change and vicariance contributed to the intercontinental disjunct distribution pattern of Fraxinus. Moreover, results highlight the necessity of integrating phylogenetic relationship and fossil to improve the reliability of inferred biogeographic events and our understanding of the processes underlying disjunct distributions.

Global diversity patterns of larger benthic foraminifera under future climate change

Global warming threatens the viability of tropical coral reefs and associated marine calcifiers, including symbiont-bearing larger benthic foraminifera (LBF). The impacts of current climate change on LBF are debated because they were particularly diverse and abundant during past warm periods. Studies on the responses of selected LBF species to changing environmental conditions reveal varying results. Based on a comprehensive review of the scientific literature on LBF species occurrences, we applied species distribution modeling using Maxent to estimate present-day and future species richness patterns on a global scale for the time periods 2040-2050 and 2090-2100. For our future projections, we focus on Representative Concentration Pathway 6.0 from the Intergovernmental Panel on Climate Change, which projects mean surface temperature changes of +2.2°C by the year 2100. Our results suggest that species richness in the Central Indo-Pacific is two to three times higher than in the Bahamian ecoregion, which we have identified as the present-day center of LBF diversity in the Atlantic. Our future predictions project a dramatic temperature-driven decline in low-latitude species richness and an increasing widening bimodal latitudinal pattern of species diversity. While the central Indo-Pacific, now the stronghold of LBF diversity, is expected to be most pushed outside of the currently realized niches of most species, refugia may be largely preserved in the Atlantic. LBF species will face large-scale non-analogous climatic conditions compared to currently realized climate space in the near future, as reflected in the extensive areas of extrapolation, particularly in the Indo-Pacific. Our study supports hypotheses that species richness and biogeographic patterns of LBF will fundamentally change under future climate conditions, possibly initiating a faunal turnover by the late 21st century.

Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

Speciation in marine environments: Diving under the surface

Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model-based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.

Oceanic dispersal barriers in a holoplanktonic gastropod

Pteropods, a group of holoplanktonic gastropods, are regarded as bioindicators of the effects of ocean acidification on open ocean ecosystems, because their thin aragonitic shells are susceptible to dissolution. While there have been recent efforts to address their capacity for physiological acclimation, it is also important to gain predictive understanding of their ability to adapt to future ocean conditions. However, little is known about the levels of genetic variation and large-scale population structuring of pteropods, key characteristics enabling local adaptation. We examined the spatial distribution of genetic diversity in the mitochondrial cytochrome c oxidase I (COI) and nuclear 28S gene fragments, as well as shell shape variation, across a latitudinal transect in the Atlantic Ocean (35°N-36°S) for the pteropod Limacina bulimoides. We observed high levels of genetic variability (COI π = 0.034, 28S π = 0.0021) and strong spatial structuring (COI ΦST  = 0.230, 28S ΦST  = 0.255) across this transect. Based on the congruence of mitochondrial and nuclear differentiation, as well as differences in shell shape, we identified a primary dispersal barrier in the southern Atlantic subtropical gyre (15-18°S). This barrier is maintained despite the presence of expatriates, a gyral current system, and in the absence of any distinct oceanographic gradients in this region, suggesting that reproductive isolation between these populations must be strong. A secondary dispersal barrier supported only by 28S pairwise ΦST comparisons was identified in the equatorial upwelling region (between 15°N and 4°S), which is concordant with barriers observed in other zooplankton species. Both oceanic dispersal barriers were congruent with regions of low abundance reported for a similar basin-scale transect that was sampled 2 years later. Our finding supports the hypothesis that low abundance indicates areas of suboptimal habitat that result in barriers to gene flow in widely distributed zooplankton species. Such species may in fact consist of several populations or (sub)species that are adapted to local environmental conditions, limiting their potential for adaptive responses to ocean changes. Future analyses of genome-wide diversity in pteropods could provide further insight into the strength, formation and maintenance of oceanic dispersal barriers.